A systematic screen for genes expressed in definitive endoderm by Serial Analysis of Gene Expression (SAGE)
Open accessAbstract
Background: The embryonic definitive endoderm (DE) gives rise to organs of the gastrointestinal and respiratory tract including the liver, pancreas and epithelia of the lung and colon. Understanding how DE progenitor cells generate these tissues is critical to understanding the cause of visceral organ disorders and cancers, and will ultimately lead to novel therapies including tissue and organ regeneration. However, investigation into the molecular mechanisms of DE differentiation has been hindered by the lack of early DE-specific markers. Results: We describe the identification of novel as well as known genes that are expressed in DE using Serial Analysis of Gene Expression (SAGE). We generated and analyzed three longSAGE libraries from early DE of murine embryos: early whole definitive endoderm (0–6 somite stage), foregut (8–12 somite stage), and hindgut (8–12 somite stage). A list of candidate genes enriched for expression in endoderm was compiled through comparisons within these three endoderm libraries and against 133 mouse longSAGE libraries generated by the Mouse Atlas of Gene Expression Project encompassing multiple embryonic tissues and stages. Using whole mount in situ hybridization, we confirmed that 22/32 (69%) genes showed previously uncharacterized expression in the DE. Importantly, two genes identified,Pyy and 5730521E12Rik, showed exclusive DE expression at early stages of endoderm patterning. Conclusion: The high efficiency of this endoderm screen indicates that our approach can be successfully used to analyze and validate the vast amount of data obtained by the Mouse Atlas of Gene Expression Project. Importantly, these novel early endoderm-expressing genes will be valuable for further investigation into the molecular mechanisms that regulate endoderm development.
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Written from the paper’s full text.
TL;DR
This study used longSAGE to profile early mouse definitive endoderm (DE) and identify DE-enriched genes, validating candidates by whole-mount in situ hybridization. It reports two genes, Pyy and 5730521E12Rik, with exclusive early DE expression and demonstrates that SAGE plus the Mouse Atlas database can efficiently identify tissue-restricted genes.
Key findings
- Three DE longSAGE libraries were generated from E8.0–E8.5 mouse embryos: early whole DE (0–6 somite), foregut (8–12 somite), and hindgut (8–12 somite), yielding 322,208 total tags and 54,093 distinct tag-sequences.
- From 7,084 tags unambiguously mapped to the most 3′ sense Refseq position, a second candidate list of 60 genes was compiled; 26 were tested by whole-mount in situ hybridization, 21 showed tissue-restricted expression, and including 6 genes from the first list, 27/32 (84%) showed endoderm expression.
- The screen efficiency for DE expression was 69% (22/32, excluding Group 5 yolk-sac-high genes); including yolk sac visceral endoderm expression gave 84% (27/32).
- Pyy and 5730521E12Rik showed exclusive DE expression at early stages: Pyy in foregut and 5730521E12Rik in midgut, with dynamic expression from early somite stages through early organogenesis.
Methods
- DE tissue was enriched by trypsin digestion and manual micro-dissection from E8.0–E8.5 C57BL/6J embryos; somite 0–6 endoderm was pooled for early whole endoderm, and somite 8–12 endoderm was divided into foregut and hindgut for separate libraries.
- longSAGE libraries were constructed with the Invitrogen I-SAGE Long kit; tags were analyzed in DiscoverySpace, mapped to Refseq, MGC, Ensembl, Ensembl gene units, and UCSC mouse genome, and compared with 133 Mouse Atlas longSAGE libraries.
- Candidate genes were selected using T/L criteria (T>4, L<58, T/L ratio ≥0.21) and validated by semi-quantitative RT-PCR, quantitative RT-PCR, whole-mount in situ hybridization, and histological sectioning.
Limitations
- The paper states that SAGE sampling depth (~100,000 tags per library) is sufficient for abundant and moderately abundant transcripts but likely insufficient for rare transcripts; Prox1 was missed due to low/restricted expression, and Hhex was missed because it was expressed in 67 SAGE libraries.
- The paper states that yolk sac endoderm contamination is difficult to avoid when collecting DE, and Group 5 genes may reflect contamination or underestimated DE expression.
- Evident from the text: the notochordal plate/notochord was included in the libraries because it adjoins the DE, and Cxcr4 was expressed in both endoderm and ectoderm, so it is not DE-specific; the study reports expression patterns rather than functional validation.
Model-written summary. Check it against the paper before relying on it.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
27 of 76 cited sources checked · 10 supported · 1 flagged · accuracy not yet measured
- Premisecitation
Prox1 is only expressed by the liver and pancreas progenitors beginning at the 7-8 somite stage.
“For example, Prox1 is only expressed by the liver and pancreas progenitors beginning at the 7–8 somite stage [43].”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [43] Burke Z, Oliver G: Prox1 is an early specific marker for the developing liver and pancreas in the mammalian foregut endoderm. Mech Dev. 2002, 118 (1-2): 147-155. 10.1016/S0925-4773(02)00240-X. source
The Results and discussion section says Prox1 is first detected in hepatic endoderm at the 7–8 somite stage, but section 1.1 places detectable dorsal pancreatic expression later, at 15–18 somites. Figure 1 also reports expression near the node and in the hindgut, contrary to “only” liver and pancreas progenitors. Page numbers are unavailable in our copy. (LLM, conf=0.90)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measured
- Premisecitation
Despite identification of several endoderm enriched genes, no novel DE specific genes were identified.
“Despite the identification of several endoderm enriched genes, no novel DE specific genes were identified.”
Quote in the paperSubstantial claim1 of 5 sources checked- cites [25] Sherwood RI, Jitianu C, Cleaver O, Shaywitz DA, Lamenzo JO, Chen AE, Golub TR, Melton DA: Prospective isolation and global gene expression analysis of definitive and visceral endoderm. Dev Biol. 2007, 304 (2): 541-555. 10.1016/j.ydbio.2007.01.011. source
- cites [26] Sinner D, Kirilenko P, Rankin S, Wei E, Howard L, Kofron M, Heasman J, Woodland HR, Zorn AM: Global analysis of the transcriptional network controlling Xenopus endoderm formation. Development. 2006, 133 (10): 1955-1966. 10.1242/dev.02358. source
- cites [27] Gu G, Wells JM, Dombkowski D, Preffer F, Aronow B, Melton DA: Global expression analysis of gene regulatory pathways during endocrine pancreatic development. Development. 2004, 131 (1): 165-179. 10.1242/dev.00921. source
- cites [28] Gitton Y, Dahmane N, Baik S, Ruiz i Altaba A, Neidhardt L, Scholze M, Herrmann BG, Kahlem P, Benkahla A, Schrinner S, Yildirimman R, Herwig R, Lehrach H, Yaspo ML: A gene expression map of human chromosome 21 orthologues in the mouse. Nature. 2002, 420 (6915): 586-590. 10.1038/nature01270. source
The paper’s expression-mapping passages (indexed as Abstract; page not provided) describe human chromosome 21 orthologues in mouse embryos, but do not address endoderm-enriched genes or whether novel definitive-endoderm-specific genes were identified. Searches for “endoderm” and “DE specific genes” found no passage that settles the claim. (LLM, conf=0.74)
Experimental — accuracy not yet measured - cites [29] Neidhardt L, Gasca S, Wertz K, Obermayr F, Worpenberg S, Lehrach H, Herrmann BG: Large-scale screen for genes controlling mammalian embryogenesis, using high-throughput gene expression analysis in mouse embryos. Mech Dev. 2000, 98 (1-2): 77-94. 10.1016/S0925-4773(00)00453-6. source
- Findingcitation
A total of 322,208 tags were sequenced from the three longSAGE endoderm libraries.
“A total of 322,208 tags were sequenced from these three longSAGE endoderm libraries [33].”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [33] Siddiqui AS, Khattra J, Delaney AD, Zhao Y, Astell C, Asano J, Babakaiff R, Barber S, Beland J, Bohacec S, Brown-John M, Chand S, Charest D, Charters AM, Cullum R, Dhalla N, Featherstone R, Gerhard DS, Hoffman B, Holt RA, Hou J, Kuo BY, Lee LL, Lee S, Leung D, Ma K, Matsuo C, Mayo M, McDonald H, Prabhu AL, Pandoh P, Riggins GJ, de Algara TR, Rupert JL, Smailus D, Stott J, Tsai M, Varhol R, Vrljicak P, Wong D, Wu MK, Xie YY, Yang G, Zhang I, Hirst M, Jones SJ, Helgason CD, Simpson EM, Hoodless PA, Marra MA: A mouse atlas of gene expression: large-scale digital gene-expression profiles from prec source
Materials and Methods reports that the authors sequenced approximately 100,000 LongSAGE tags per library, and the Abstract reports 72 libraries in total (page numbers unavailable). Our copy does not identify three endoderm libraries or give a combined count of 322,208 tags, so the specific figure cannot be verified from it. (LLM, conf=0.77)
Experimental — accuracy not yet measured
- Findingcitation
Sox2 is expressed in both ectoderm and endoderm libraries.
“Similarly, Sox2 is expressed in both ectoderm and endoderm libraries corresponding to published expression patterns [38].”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [38] Wood HB, Episkopou V: Comparative expression of the mouse Sox1, Sox2 and Sox3 genes from pre-gastrulation to early somite stages. Mech Dev. 1999, 86 (1-2): 197-201. 10.1016/S0925-4773(99)00116-1. source
- Premisecitation
5730521E12Rik is identical to nephrocan (Nepn).
“Interestingly, 5730521E12Rik is identical to nephrocan (Nepn), which was recently identified by Mochida et al. as an inhibitor of Transforming Growth Factor-β signaling [52].”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [52] Mochida Y, Parisuthiman D, Kaku M, Hanai J, Sukhatme VP, Yamauchi M: Nephrocan, a novel member of the small leucine-rich repeat protein family, is an inhibitor of transforming growth factor-beta signaling. J Biol Chem. 2006, 281 (47): 36044-36051. 10.1074/jbc.M604787200. source
The Abstract identifies nephrocan (NPN) and describes it as an inhibitor of TGF-β signaling. However, neither that passage nor the passages retrieved by searching for “5730521E12Rik” and its RIKEN-clone variant links that identifier to nephrocan, so our copy cannot verify the claimed identity. (LLM, conf=0.76)
Experimental — accuracy not yet measured
- Findingown data
Of the tag-sequences in the early endoderm library, 51% were unique to the early endoderm library as compared to the later endoderm libraries.
“Of these tag-sequences, 51% were unique to the early endoderm library as compared to the later endoderm libraries.”
Quote in the paperNot a substantial claim - Findingown data
In each of the foregut and hindgut libraries, approximately 50% of the tag-sequences were unique, compared to the other two endoderm libraries.
“In each of these libraries, approximately 50% of the tag-sequences were unique, compared to the other two endoderm libraries (Figure 2A).”
Quote in the paperNot a substantial claim - Findingcitation
Cxcr4 was expressed in both endoderm and ectoderm libraries.
“The exception is Cxcr4, which although used as a DE marker, was expressed in both endoderm and ectoderm, reaffirming it as widely expressed [25].”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [25] Sherwood RI, Jitianu C, Cleaver O, Shaywitz DA, Lamenzo JO, Chen AE, Golub TR, Melton DA: Prospective isolation and global gene expression analysis of definitive and visceral endoderm. Dev Biol. 2007, 304 (2): 541-555. 10.1016/j.ydbio.2007.01.011. source
- Findingown data
There were 26,238 tag-sequences present in the early endoderm library (SM108).
“There were 26,238 tag-sequences present in the early endoderm library (SM108).”
Quote in the paperNot a substantial claim - Findingown data
Analysis of the three libraries revealed the expression of 54,093 different tag-sequences.
“Analysis of the three libraries revealed the expression of 54,093 different tag-sequences (see Methods).”
Quote in the paperSubstantial claim - Findingown data
7,084 tag-sequences (13%) met the criteria of unambiguously mapping to the most 3' position and the sense strand of the Refseq database.
“To simplify the analysis and validation in this study, we focused on tag-sequences that unambiguously mapped to the most 3' position (position number +1) and the sense strand of the Refseq database (refer to Methods); 7,084 tag-sequences (13%) met these criteria.”
Quote in the paperSubstantial claim - Findingown data
The remaining 31% (16,797) of the tag-sequences did not map to any of these databases.
“The remaining 31% (16,797) of the tag-sequences did not map to any of these databases (Figure 2B).”
Quote in the paperNot a substantial claim - Findingcitation
CXCR4 is not an ideal marker for DE as it is widely expressed in the gastrulation stage mouse embryo.
“Although useful, CXCR4 is not an ideal marker for the DE as it is widely expressed in the gastulation stage mouse embryo (Table 1 and [5,25]).”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [5] Yasunaga M, Tada S, Torikai-Nishikawa S, Nakano Y, Okada M, Jakt LM, Nishikawa S, Chiba T, Era T, Nishikawa S: Induction and monitoring of definitive and visceral endoderm differentiation of mouse ES cells. Nat Biotechnol. 2005, 23 (12): 1542-1550. 10.1038/nbt1167. source
- cites [25] Sherwood RI, Jitianu C, Cleaver O, Shaywitz DA, Lamenzo JO, Chen AE, Golub TR, Melton DA: Prospective isolation and global gene expression analysis of definitive and visceral endoderm. Dev Biol. 2007, 304 (2): 541-555. 10.1016/j.ydbio.2007.01.011. source
- Findingown data
Ninety percent of the unmapped tag-sequences were single tags.
“Ninety percent of these unmapped tag-sequences were single tags, implying that many may have been generated by sequencing, PCR, or other errors.”
Quote in the paperNot a substantial claim - Findingown data
All of the other ectoderm genes present in the ectoderm libraries were excluded or present at low level in the endoderm libraries.
“All of the other ectoderm genes present in our ectoderm libraries were excluded or present at low level in the endoderm libraries.”
Quote in the paperSubstantial claim - Findingreasoning
A second list consisting of 60 genes was created by removing tag sequences whose T/L ratio was less than 0.21.
“We removed the tag sequences whose T/L ratio was less than 0.21 to create a second list consisting of 60 genes.”
Quote in the paperSubstantial claim - Findingown data
Including the 6 candidate genes validated from the first list, the efficiency of the new screen for novel genes with tissue-restricted expression patterns was 84% (27/32).
“Including the 6 candidate genes validated from the first list, the efficiency of our new screen for novel genes with tissue-restricted expression patterns was 84% (27/32).”
Quote in the paperSubstantial claim - Findingown data
Most of the genes selected by the criteria for in situ hybridization showed complex tissue-restricted expression patterns in the early embryo, including the DE.
“Thus most of the genes selected by our criteria for in situ hybridization showed complex tissue-restricted expression patterns in the early embryo, including the DE.”
Quote in the paperSubstantial claim - Findingown data
Two genes identified, Pyy and 5730521E12Rik, showed exclusive DE expression at early stages of endoderm patterning.
“Importantly, two genes identified, Pyy and 5730521E12Rik, showed exclusive DE expression at early stages of endoderm patterning.”
- Also stated in: § Background · plain
“Importantly, two genes identified, Pyy and 5730521E12Rik, showed exclusive DE expression at early stages of endoderm patterning.”
Quote in the paperSubstantial claim - Also stated in: § Background · plain
- Findingown data
Eight genes exhibited differential expression levels between the foregut and hindgut.
“However, 8 genes did exhibit differential expression levels between the foregut and hindgut (Figure 3).”
Quote in the paperSubstantial claim - Findingreasoning
Several previously known foregut or hindgut markers were not present in the authors' list likely due to their low expression level and/or their expression being restricted to few cells within the endoderm.
“Several previously known foregut or hindgut markers were not present in our list likely due to their low expression level and/or their expression being restricted to few cells within the endoderm.”
Quote in the paperSubstantial claim - Findingown data
As development proceeds, the bilateral expression domains of 5730521E12Rik extended anteriorly and medially and began to focus in the midgut region at early somite stages.
“As development proceeds, the bilateral expression domains extended anteriorly and medially and began to focus in the midgut region at early somite stages (Figure 8C–F).”
Quote in the paperNot a substantial claim - Findingown data
Pyy was expressed in small lateral regions of the foregut DE as early as the 2 somite stage.
“Interestingly, Pyy was expressed in small lateral regions of the foregut DE as early as the 2 somite stage (Figure 4A, 4B).”
Quote in the paperSubstantial claim - Findingown data
By examining expression patterns of the original list of 45 tag-sequences in 133 longSAGE libraries, 9 genes exhibited high tissue-specificity since they were present in only a few libraries.
“Indeed, by examining the expression patterns of our original list (foregut vs hindgut) of 45 tag-sequences in 133 longSAGE libraries generated by the Mouse Atlas Project, we discovered 9 genes that exhibited high tissue-specificity since they were present in only a few libraries (Figure 5).”
Quote in the paperSubstantial claim - Findingown data
Overall efficiency of the screen for genes with definitive endoderm expression was 69% (22/32, not including Group 5 genes highly expressed in yolk sac).
“Overall, the efficiency of our screen for genes with DE expression was 69% (22/32, not including Group 5 genes which are highly expressed in the yolk sac).”
Quote in the paperSubstantial claim - Findingown data
Pyy was exclusively expressed in the definitive endoderm lineage at early organogenesis stages of development.
“Significantly, two of these genes, Pyy and the Riken gene, 5730521E12Rik, were exclusively expressed in the DE lineage at early organogenesis stages of development.”
- Also stated in: § Discussion · plain
“Pyy and 5730521E12Rik were identified to be exclusively expressed in the DE lineage at gastrulation and early organogenesis stages of development.”
Quote in the paperSubstantial claim - Also stated in: § Discussion · plain
- Findingown data
Hhex was missed in the authors' analysis because it was expressed in 67 of their SAGE libraries and thus did not fit their criteria for validation lists.
“Furthermore, the foregut marker, Hhex, was missed in our analysis since it was expressed in 67 of our SAGE libraries, and thus did not fit our criteria for our validation lists (Table 1 and Additional file 2) [44].”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [44] Thomas PQ, Brown A, Beddington RS: Hex: a homeobox gene revealing peri-implantation asymmetry in the mouse embryo and an early transient marker of endothelial cell precursors. Development. 1998, 125 (1): 85-94. source
- Findingown data
Group 3 contained genes that were expressed in the DE, yolk sac and another germ layer with a tissue-restricted pattern.
“Group 3 contained genes that were expressed in the DE, yolk sac and another germ layer with a tissue-restricted pattern”
Quote in the paperNot a substantial claim - Findingown data
Group 1 includes two genes, 5730521E12Rik and Pyy, which were expressed exclusively in the DE.
“The first group includes two genes, 5730521E12Rik and Pyy, which were expressed exclusively in the DE.”
Quote in the paperNot a substantial claim - Findingown data
Seven of the eight genes, Trh, Otx2, Prrx2, Tbx1, Cyp26a1, Hoxb6, and Cdx1, were expressed in other tissues as well as endoderm at the early somite stage.
“Seven of these genes, Trh, Otx2, Prrx2, Tbx1, Cyp26a1, Hoxb6, and Cdx1 were expressed in other tissues as well as endoderm at the early somite stage.”
Quote in the paperSubstantial claim - Findingown data
At the 6-8 somite stages, strong Pyy expression was observed in the lateral and ventral foregut.
“Subsequently, the lateral expression domains expanded and extended anteriorly to the medial ventral foregut, so that strong expression was observed in the lateral and ventral foregut at the 6–8 somite stages (Figure 4E–J).”
Quote in the paperNot a substantial claim - Findingown data
The majority of genes identified were not only expressed in the definitive endoderm, but also in other tissues such as yolk sac, ectoderm and mesoderm.
“Interestingly, we found the majority of genes identified were not only expressed in the definitive endoderm, but also in other tissues such as yolk sac, ectoderm and mesoderm.”
Quote in the paperNot a substantial claim - Findingown data
Eight of the 9 genes demonstrating a tissue-restricted expression pattern matched the endoderm genes identified in the in situ hybridization analysis.
“Interestingly, 8 of the 9 genes demonstrating a tissue-restricted expression pattern matched the endoderm genes identified in our in situ hybridization analysis (Figure 3).”
Quote in the paperSubstantial claim - Findingown data
By including genes expressed in yolk sac visceral endoderm, 84% (27/32) of genes were identified with endoderm expression.
“By including genes expressed in the yolk sac visceral endoderm, we observed 84% (27/32) of genes identified with endoderm expression.”
Quote in the paperSubstantial claim - Findingown data
At E9.5, 5730521E12Rik expression was still maintained in the midgut region with decreased expression level.
“At E9.5, 5730521E12Rik expression was still maintained in the midgut region with the expression level decreased (Figure 8H).”
Quote in the paperNot a substantial claim - Findingown data
By E9.0, strong 5730521E12Rik expression was observed in the midgut.
“By E9.0 strong expression was observed in the midgut (Figure 8G).”
Quote in the paperNot a substantial claim - Findingnone given
Pyy is initially expressed at the early somite stage in the bilateral and medial regions of the foregut.
“Initially, Pyy is expressed at the early somite stage in the bilateral and medial regions of the foregut.”
Quote in the paperNot a substantial claim - Findingown data
At the late head-fold stage, 5730521E12Rik expression expanded in the lateral region of the endoderm on the posterior side.
“At the late head-fold stage, 5730521E12Rik expression has expanded in the lateral region of the endoderm on the posterior side (Figure 8B).”
Quote in the paperNot a substantial claim - Findingown data
Six out of the 60 genes were present in and validated by the first list.
“Confirming the effectiveness of these criteria, 6 out of the 60 genes were present in and validated by our first list, and 24 out of the 60 genes were previously shown to be expressed in endoderm, either with or without expression in other germ layer tissues, including Sox17, Foxa1-3, Ihh and Shh [see Additional file 2].”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [see Additional file 2]
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Findingown data
Group 5 genes were expressed in yolk sac endoderm at high levels, without obvious expression within the DE.
“The genes in Group 5 were expressed in yolk sac endoderm at high levels, without obvious expression within the DE.”
Quote in the paperNot a substantial claim - Findingown data
By screening with both semi-quantitative RT-PCR and quantitative RT-PCR, 14 of the 45 genes were shown to exhibit differential expression between the foregut and hindgut.
“By screening with both semi-quantitative RT-PCR and quantitative RT-PCR, 14 of the 45 genes were shown to exhibit differential expression between the foregut and hindgut.”
Quote in the paperSubstantial claim - Findingcitation
Twenty-four out of the 60 genes were previously shown to be expressed in endoderm, either with or without expression in other germ layer tissues, including Sox17, Foxa1-3, Ihh and Shh.
“Confirming the effectiveness of these criteria, 6 out of the 60 genes were present in and validated by our first list, and 24 out of the 60 genes were previously shown to be expressed in endoderm, either with or without expression in other germ layer tissues, including Sox17, Foxa1-3, Ihh and Shh [see Additional file 2].”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [see Additional file 2]
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Findingown data
At early organogenesis stage, Pyy expression remained in the posterior foregut extending to the midgut junction.
“At early organogenesis stage, Pyy expression remained in the posterior foregut extending to the midgut junction (Figure 4K–N).”
Quote in the paperNot a substantial claim - Findingown data
Pre-selection of candidate genes by comparisons with 133 SAGE libraries from various tissues allowed elimination of approximately 95% of widely expressing genes from the endoderm libraries.
“In addition, pre-selection of candidate genes by comparisons with 133 SAGE libraries from various tissues allowed us to eliminate ~95% of the widely expressing genes from our endoderm libraries.”
Quote in the paperSubstantial claim - Findingown data
Pyy was exclusively expressed in the foregut endoderm.
“Significantly, one of the genes, Pyy, was exclusively expressed in the foregut endoderm.”
Quote in the paperSubstantial claim - Findingown data
22/32 (69%) genes showed previously uncharacterized expression in the DE.
“Using whole mount in situ hybridization, we confirmed that 22/32 (69%) genes showed previously uncharacterized expression in the DE.”
- Also stated in: § Background · plain
“Sixty nine percent of these candidate genes showed previously uncharacterized expression in restricted tissues, including DE, after further whole mount in situ hybridization validation.”
Quote in the paperSubstantial claim - Also stated in: § Background · plain
- Findingown data
5730521E12Rik was first expressed in a few cells at E7.25 in the endoderm at the posterior region adjacent to the embryonic-extraembryonic junction.
“Interestingly, 5730521E12Rik was first expressed in a few cells at E7.25 in the endoderm at the posterior region adjacent to the embryonic-extraembryonic junction (Figure 8A).”
Quote in the paperNot a substantial claim - Findingown data
Of the remaining 30 genes, 26 genes were successfully examined using whole mount in situ hybridization.
“Of the remaining 30 genes, we successfully examined the expression of 26 genes using whole mount in situ hybridization.”
Quote in the paperSubstantial claim - Findingown data
5730521E12Rik exhibited exclusive expression in the definitive endoderm at early somite stages in the authors' analysis.
“In addition to Pyy, 5730521E12Rik exhibited exclusive expression in the DE at early somite stages in our analysis.”
- Also stated in: § Discussion · plain
“Significantly, two of these genes, Pyy and the Riken gene, 5730521E12Rik, were exclusively expressed in the DE lineage at early organogenesis stages of development.”
Quote in the paperSubstantial claim - Also stated in: § Discussion · plain
- Findingown data
The authors identified novel as well as known genes that are expressed in definitive endoderm progenitors by analyzing and validating definitive endoderm longSAGE libraries.
“We identified novel as well as known genes that are expressed in DE progenitors by analyzing and validating DE longSAGE libraries.”
Quote in the paperSubstantial claim - Premisenone given
One major hurdle in analysis of early DE development in both the embryo and ES cells is the lack of both pan-endodermal and endodermal region-specific genetic markers, since the majority of DE markers are also expressed in the visceral endoderm and/or other germ layers.
“In summary, one major hurdle in the analysis of early DE development in both the embryo and ES cells is the lack of both pan-endodermal and endodermal region-specific genetic markers, since the majority of DE markers are also expressed in the visceral endoderm and/or other germ layers.”
Quote in the paperSubstantial claim - Interpretationreasoning
Many of the unmapped tag-sequences may have been generated by sequencing, PCR, or other errors.
“Ninety percent of these unmapped tag-sequences were single tags, implying that many may have been generated by sequencing, PCR, or other errors.”
Quote in the paperNot a substantial claim - Interpretationown data
Some of the unmapped tag-sequences likely represent valid, novel transcripts, since 44 unmapped tag-sequences expressed in the endoderm were found at a level of at least 4 tags.
“However, some of these tag-sequences likely represent valid, novel transcripts, since 44 unmapped tag-sequences expressed in the endoderm were found at a level of at least 4 tags.”
Quote in the paperNot a substantial claim - Premisecitation
By the 8-12 somite stage, endoderm patterning has initiated.
“By this stage endoderm patterning has initiated [14,35].”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [14] Wells JM, Melton DA: Early mouse endoderm is patterned by soluble factors from adjacent germ layers. Development. 2000, 127 (8): 1563-1572. source
- cites [35] Ang SL, Wierda A, Wong D, Stevens KA, Cascio S, Rossant J, Zaret KS: The formation and maintenance of the definitive endoderm lineage in the mouse: involvement of HNF3/forkhead proteins. Development. 1993, 119 (4): 1301-1315. source
- Premisereasoning
At present there is no DE-specific marker that can unequivocally identify this cell type.
“At present there is no DE-specific marker that can unequivocally identify this cell type.”
Quote in the paperSubstantial claim - Premisecitation
At the 0-6 somite stage, the newly formed endoderm has not yet been patterned.
“At this stage the newly formed endoderm has not yet been patterned, based on endoderm explant experiments [14,34].”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [14] Wells JM, Melton DA: Early mouse endoderm is patterned by soluble factors from adjacent germ layers. Development. 2000, 127 (8): 1563-1572. source
- cites [34] Deutsch G, Jung J, Zheng M, Lora J, Zaret KS: A bipotential precursor population for pancreas and liver within the embryonic endoderm. Development. 2001, 128 (6): 871-881. source
- Interpretationown data
The endoderm libraries and the SAGE library database are powerful resources to identify tissue specific genes.
“The high efficiency of this screen suggests that our endoderm libraries and the SAGE library database are powerful resources to identify tissue specific genes.”
Quote in the paperSubstantial claim - Interpretationown data
In the context of looking for specificity of gene expression, the SAGE data is an excellent tool for identifying genes with tissue restricted expression.
“This suggests that in the context of looking for specificity of gene expression, the SAGE data is an excellent tool for identifying genes with tissue restricted expression.”
Quote in the paperSubstantial claim - Interpretationcitation
Pyy's early regionalized expression within definitive endoderm reflects an early specification of cell fate along both the anterior-posterior and lateral-medial axis of the embryonic gut.
“Its early regionalized expression within DE reflects an early specification of cell fate along both the anterior-posterior and lateral-medial axis of the embryonic gut [6,45].”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [6] Lewis SL, Tam PP: Definitive endoderm of the mouse embryo: formation, cell fates, and morphogenetic function. Dev Dyn. 2006, 235 (9): 2315-2329. 10.1002/dvdy.20846. source
- cites [45] Tam PP, Khoo PL, Lewis SL, Bildsoe H, Wong N, Tsang TE, Gad JM, Robb L: Sequential allocation and global pattern of movement of the definitive endoderm in the mouse embryo during gastrulation. Development. 2007, 134 (2): 251-260. 10.1242/dev.02724. source
- Study design and conductown data
The endoderm longSAGE libraries were generated from enriched definitive endoderm tissues at early stages of definitive endoderm formation (E8.0-E8.5) obtained by proteolytic and manual micro-dissection.
“We were able to enhance our screening efficiency since the endoderm longSAGE libraries were generated from enriched DE tissues at early stages of DE formation (E8.0–E8.5) that were obtained by a combination of proteolytic and manual micro-dissection methods.”
Quote in the paperSubstantial claim - Interpretationreasoning
It is likely that some endoderm-specific or enriched genes were excluded from the gene list determined by the authors' selection criteria.
“It is likely that some endoderm-specific or enriched genes were excluded from the gene list determined by our selection criteria.”
Quote in the paperSubstantial claim - Interpretationown data
5730521E12Rik expression was specific to the midgut during gastrulation and early organogenesis stages in the mouse embryo.
“Thus 5730521E12Rik expression was specific to the midgut during the gastrulation and early organogenesis stages in the mouse embryo.”
Quote in the paperNot a substantial claim - Interpretationown data
The results indicate the approach was successful in the identification of novel markers of endoderm expression.
“Overall, these results indicate our approach was successful in the identification of novel markers of endoderm expression.”
Quote in the paperSubstantial claim - Interpretationown data
The high efficiency of this endoderm screen indicates that the approach can be successfully used to analyze and validate the vast amount of data obtained by the Mouse Atlas of Gene Expression Project.
“The high efficiency of this endoderm screen indicates that our approach can be successfully used to analyze and validate the vast amount of data obtained by the Mouse Atlas of Gene Expression Project.”
Quote in the paperSubstantial claim - Premisecitation
The high functional similarity between visceral and definitive endoderm suggests that these tissues have highly related transcriptomes.
“Furthermore, the high functional similarity between visceral and definitive endoderm suggests that these tissues have highly related transcriptomes [25].”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [25] Sherwood RI, Jitianu C, Cleaver O, Shaywitz DA, Lamenzo JO, Chen AE, Golub TR, Melton DA: Prospective isolation and global gene expression analysis of definitive and visceral endoderm. Dev Biol. 2007, 304 (2): 541-555. 10.1016/j.ydbio.2007.01.011. source
- Interpretationreasoning
The tags for Group 5 genes may be included in the libraries due to yolk sac endoderm contamination, which is difficult to avoid when collecting the DE tissue.
“The tags for these genes may be included in our libraries due to yolk sac endoderm contamination, which is difficult to avoid when collecting the DE tissue.”
Quote in the paperNot a substantial claim- Rests on an assumption: Yolk sac endoderm contamination is difficult to avoid when collecting DE tissue.
- Interpretationreasoning
Prox1 transcripts could be diluted by the total number of transcripts present in the foregut endoderm tissues, and thus not detected at the authors' sequencing depth.
“Therefore, the Prox1 transcripts could be diluted by the total number of transcripts present in the foregut endoderm tissues, and thus not detected at our sequencing depth.”
Quote in the paperSubstantial claim - Premisenone given
Pyy's early embryonic expression pattern has not been described.
“Pyy is known to be highly expressed in pancreatic islets and endocrine L cells of the lower gastrointestinal tract [39], but its early embryonic expression pattern has not been described.”
Quote in the paperSubstantial claim - Premisecitation
SAGE sampling depth of approximately 100,000 tags per library yields gene-detection sensitivity approximately equivalent to that of fluorescence-based microarray approaches.
“Our SAGE sampling depth (~100,000 tags per library) yields gene-detection sensitivity approximately equivalent to that of fluorescence-based microarray approaches [42]”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [42] Lu J, Lal A, Merriman B, Nelson S, Riggins G: A comparison of gene expression profiles produced by SAGE, long SAGE, and oligonucleotide chips. Genomics. 2004, 84 (4): 631-636. 10.1016/j.ygeno.2004.06.014. source
- Interpretationreasoning
5730521E12Rik is the earliest definitive endoderm specific and regional marker reported to date.
“Furthermore, 5730521E12Rik is the earliest DE specific and regional marker reported to date.”
Quote in the paperSubstantial claim - Interpretationreasoning
5730521E12Rik's early regionalized expression in the few cells in the posterior definitive endoderm at as early as E7.25 embryo may reflect the early specification of the definitive endoderm.
“Its early regionalized expression in the few cells in the posterior DE at as early as E7.25 embryo may reflect the early specification of the DE.”
Quote in the paperSubstantial claim - Interpretationreasoning
The expression of Pyy follows a similar pattern as that observed by the lineage tracing of the liver bud progenitors.
“Intriguingly, the expression of Pyy follows a similar pattern as that observed by the lineage tracing of the liver bud progenitors.”
Quote in the paperNot a substantial claim - Interpretationown data
5730521E12Rik is the first known gene that marks exclusively the entire midgut region at early organogenesis stages.
“The RIKEN gene, 5730521E12Rik, expressed in the mid-gut region, is the first known gene that marks exclusively the entire midgut region at early organogenesis stages.”
Quote in the paperSubstantial claim
- Classified as probably not a substantial claim. 27
- May combine two claims. 28
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationMany key genes involved in the initial formation of DE are evolutionarily conserved.
“Many of the key genes involved in the initial formation of DE are evolutionarily conserved.”
Quote in the paperNot a substantial claim2 of 5 sources checked- cites [7] Fukuda K, Kikuchi Y: Endoderm development in vertebrates: fate mapping, induction and regional specification. Dev Growth Differ. 2005, 47 (6): 343-355. 10.1111/j.1440-169X.2005.00815.x. source
- cites [8] Hart AH, Hartley L, Sourris K, Stadler ES, Li R, Stanley EG, Tam PP, Elefanty AG, Robb L: Mixl1 is required for axial mesendoderm morphogenesis and patterning in the murine embryo. Development. 2002, 129 (15): 3597-3608. source
- cites [9] Kanai-Azuma M, Kanai Y, Gad JM, Tajima Y, Taya C, Kurohmaru M, Sanai Y, Yonekawa H, Yazaki K, Tam PP, Hayashi Y: Depletion of definitive gut endoderm in Sox17-null mutant mice. Development. 2002, 129 (10): 2367-2379. source
- cites [10] Hoodless PA, Pye M, Chazaud C, Labbe E, Attisano L, Rossant J, Wrana JL: FoxH1 (Fast) functions to specify the anterior primitive streak in the mouse. Genes Dev. 2001, 15 (10): 1257-1271. 10.1101/gad.881501. source
The discussion section “FoxH1 is required for formation of the definitive endoderm” states that FoxH1 is required for definitive endoderm formation. The paper also identifies FoxH1 homologs in several vertebrates, but it does not establish that many genes involved in the initial formation of definitive endoderm are evolutionarily conserved. Page numbers are unavailable in our copy. (LLM, conf=0.82)
Experimental — accuracy not yet measured - cites [11] Tremblay KD, Hoodless PA, Bikoff EK, Robertson EJ: Formation of the definitive endoderm in mouse is a Smad2-dependent process. Development. 2000, 127 (14): 3079-3090. source
May combine two claims.
PremisecitationSeveral methods of differentiation of ES cells to hepatic and insulin-producing cells have been described, but determining the precise identity of these cells is problematic due to a lack of suitable markers.
“While several methods of differentiation of ES cells to hepatic and insulin-producing cells have been described, determining the precise identity of these cells is problematic due to a lack of suitable markers [20-23].”
Quote in the paperSubstantial claim2 of 4 sources checked- cites [20] Lavon N, Benvenisty N: Study of hepatocyte differentiation using embryonic stem cells. J Cell Biochem. 2005, 96 (6): 1193-1202. 10.1002/jcb.20590. source
- cites [21] Hansson M, Tonning A, Frandsen U, Petri A, Rajagopal J, Englund MC, Heller RS, Hakansson J, Fleckner J, Skold HN, Melton D, Semb H, Serup P: Artifactual insulin release from differentiated embryonic stem cells. Diabetes. 2004, 53 (10): 2603-2609. 10.2337/diabetes.53.10.2603. source
The introduction describes several approaches to deriving insulin-containing cells from ES cells. The discussion explains that overlapping pancreatic and neural gene markers can make the identity of purported β-like cells difficult to establish. The paper does not address hepatic-cell differentiation, and it identifies a problem with marker specificity rather than a general lack of suitable markers (page numbers unavailable in our copy). (LLM, conf=0.87)
Experimental — accuracy not yet measured - cites [22] Blyszczuk P, Asbrand C, Rozzo A, Kania G, St-Onge L, Rupnik M, Wobus AM: Embryonic stem cells differentiate into insulin-producing cells without selection of nestin-expressing cells. Int J Dev Biol. 2004, 48 (10): 1095-1104. 10.1387/ijdb.041904pb. source
The Discussion (page unavailable) describes several methods for producing insulin-positive cells from ES cells and cautions that some cells may absorb insulin from the medium rather than produce it, supporting a difficulty in identifying them. It does not discuss ES-cell differentiation into hepatic cells or attribute the identification difficulty to a lack of suitable markers. (LLM, conf=0.84)
Experimental — accuracy not yet measured - cites [23] Blyszczuk P, Wobus AM: Stem cells and pancreatic differentiation in vitro. J Biotechnol. 2004, 113 (1-3): 3-13. 10.1016/j.jbiotec.2004.03.023. source
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationThe longSAGE protocol generates tags that are 21 bp long and provides enhanced efficiency and accuracy of tag-to-gene mapping.
“SAGE has been improved by the development of a longSAGE protocol, which generates tags that are 21 bp long and provides enhanced efficiency and accuracy of tag-to-gene mapping [30-32].”
Quote in the paperNot a substantial claim1 of 3 sources checked- cites [30] Wahl MB, Heinzmann U, Imai K: LongSAGE analysis significantly improves genome annotation: identifications of novel genes and alternative transcripts in the mouse. Bioinformatics. 2005, 21 (8): 1393-1400. 10.1093/bioinformatics/bti207. source
- cites [31] Saha S, Sparks AB, Rago C, Akmaev V, Wang CJ, Vogelstein B, Kinzler KW, Velculescu VE: Using the transcriptome to annotate the genome. Nat Biotechnol. 2002, 20 (5): 508-512. 10.1038/nbt0502-508. source
- cites [32] Khattra J, Delaney AD, Zhao Y, Siddiqui A, Asano J, McDonald H, Pandoh P, Dhalla N, Prabhu AL, Ma K, Lee S, Ally A, Tam A, Sa D, Rogers S, Charest D, Stott J, Zuyderduyn S, Varhol R, Eaves C, Jones S, Holt R, Hirst M, Hoodless PA, Marra MA: Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines. Genome Res. 2007, 17 (1): 108-116. 10.1101/gr.5488207. source
The Results and Discussion identify LongSAGE tags as 21 bp, and the introduction says longer tags improve the specificity of tag-to-gene mapping. The paper reports improved cloning and sequencing efficiency, but the cited passages do not establish improved efficiency of tag-to-gene mapping itself. Page numbers were not available in our copy. (LLM, conf=0.84)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationFGF4, expressed in the neighboring cardiac mesoderm, can induce differentiation of ventral foregut endoderm in a concentration-dependent manner.
“FGF4, which is expressed in the neighboring cardiac mesoderm, can induce the differentiation of ventral foregut endoderm in a concentration-dependent manner [13,14].”
Quote in the paperNot a substantial claim1 of 2 sources checked- cites [13] Tremblay KD, Zaret KS: Distinct populations of endoderm cells converge to generate the embryonic liver bud and ventral foregut tissues. Dev Biol. 2005, 280 (1): 87-99. 10.1016/j.ydbio.2005.01.003. source
The Discussion mentions inductive signaling between mesoderm and endoderm but does not identify FGF4 or describe a concentration-dependent effect. Searches for FGF4 and cardiac-mesoderm FGF signaling found only a References entry for a study of FGF thresholds, not a passage in this paper addressing the attributed claim. No page number is available in our copy. (LLM, conf=0.75)
Experimental — accuracy not yet measured - cites [14] Wells JM, Melton DA: Early mouse endoderm is patterned by soluble factors from adjacent germ layers. Development. 2000, 127 (8): 1563-1572. source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationFGF2 and Activin, secreted by the notochord, lead to expression of pancreatic markers by repressing Shh in pancreatic endoderm.
“FGF2 and Activin, secreted by the notochord, lead to the expression of pancreatic markers by repressing expression of Shh in pancreatic endoderm [15-19].”
Quote in the paperNot a substantial claim3 of 5 sources checked- cites [15] Hebrok M, Kim SK, Melton DA: Notochord repression of endodermal Sonic hedgehog permits pancreas development. Genes Dev. 1998, 12 (11): 1705-1713. source
The “Notochord factors activin and FGF initiate pancreatic differentiation” section reports that activin-βB reduces endodermal Shh and induces the pancreatic markers Pdx1 and insulin. Figure 4 reports notochord expression of activin-βB and FGF2, but the “possible role” section says FGF2’s effects are concentration-dependent and that further work is needed to determine whether it is an endogenous notochord signal. Thus the paper does not establish that notochord-secreted FGF2 drives pancreatic-marker expression in the way the sentence states. (LLM, conf=0.88)
Experimental — accuracy not yet measured - cites [16] Hebrok M, Kim SK, St Jacques B, McMahon AP, Melton DA: Regulation of pancreas development by hedgehog signaling. Development. 2000, 127 (22): 4905-4913. source
- cites [17] Kim SK, Hebrok M, Li E, Oh SP, Schrewe H, Harmon EB, Lee JS, Melton DA: Activin receptor patterning of foregut organogenesis. Genes Dev. 2000, 14 (15): 1866-1871. source
The Results and Discussion say that notochord-derived activin signals may repress Shh in chick pancreatic endoderm, and report that activin receptor signaling restricts Shh in mouse foregut endoderm and regulates pancreatic Isl1 expression. They do not establish the claimed pathway from Shh repression to pancreatic-marker expression or address a role for FGF2. Page numbers are unavailable in our copy. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites [18] Kim SK, Hebrok M, Melton DA: Notochord to endoderm signaling is required for pancreas development. Development. 1997, 124 (21): 4243-4252. source
- cites [19] Cleaver O, Krieg PA: Notochord patterning of the endoderm. Dev Biol. 2001, 234 (1): 1-12. 10.1006/dbio.2001.0214. source
In “Notochord Signals Are Required for Pancreas Development,” the paper says activin-βB and FGF2 mimicked notochord signaling in vitro by inhibiting SHH expression and allowing pancreatic marker expression. “Possible Nature of Notochord Signals” describes them as implicated signals, but the copy does not establish that both are secreted by the notochord. The claim states that point more definitively than the source does. (LLM, conf=0.86)
Experimental — accuracy not yet measured
Classified as probably not a substantial claim.
PremisecitationSeveral groups have carried out screens for novel genes expressed in the endoderm of Xenopus and mouse embryos using microarray or cDNA hybridization.
“Several groups have carried out screens for novel genes expressed in the endoderm of Xenopus and mouse embryos using microarray or cDNA hybridization [25-29].”
Quote in the paperSubstantial claim1 of 5 sources checked- cites [25] Sherwood RI, Jitianu C, Cleaver O, Shaywitz DA, Lamenzo JO, Chen AE, Golub TR, Melton DA: Prospective isolation and global gene expression analysis of definitive and visceral endoderm. Dev Biol. 2007, 304 (2): 541-555. 10.1016/j.ydbio.2007.01.011. source
- cites [26] Sinner D, Kirilenko P, Rankin S, Wei E, Howard L, Kofron M, Heasman J, Woodland HR, Zorn AM: Global analysis of the transcriptional network controlling Xenopus endoderm formation. Development. 2006, 133 (10): 1955-1966. 10.1242/dev.02358. source
- cites [27] Gu G, Wells JM, Dombkowski D, Preffer F, Aronow B, Melton DA: Global expression analysis of gene regulatory pathways during endocrine pancreatic development. Development. 2004, 131 (1): 165-179. 10.1242/dev.00921. source
- cites [28] Gitton Y, Dahmane N, Baik S, Ruiz i Altaba A, Neidhardt L, Scholze M, Herrmann BG, Kahlem P, Benkahla A, Schrinner S, Yildirimman R, Herwig R, Lehrach H, Yaspo ML: A gene expression map of human chromosome 21 orthologues in the mouse. Nature. 2002, 420 (6915): 586-590. 10.1038/nature01270. source
The paper’s expression-mapping passage (labelled Abstract in our copy; no page given) describes a systematic screen of genes in mouse embryos using whole-mount in situ hybridization. It does not describe a screen specifically for endoderm-expressed genes or say that this screen used a microarray or cDNA hybridization. The Xenopus portion may relate to other citations in the group, not this mouse study. (LLM, conf=0.85)
Experimental — accuracy not yet measured - cites [29] Neidhardt L, Gasca S, Wertz K, Obermayr F, Worpenberg S, Lehrach H, Herrmann BG: Large-scale screen for genes controlling mammalian embryogenesis, using high-throughput gene expression analysis in mouse embryos. Mech Dev. 2000, 98 (1-2): 77-94. 10.1016/S0925-4773(00)00453-6. source
Probably not a substantial claim: may not pass S3 (load-bearing).
InterpretationcitationThe 44 unmapped tag-sequences may span an unknown splice junction.
“For example, these 44 tag-sequences may span an unknown splice junction [37].”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [37] Kuo BY, Chen Y, Bohacec S, Johansson O, Wasserman WW, Simpson EM: SAGE2Splice: unmapped SAGE tags reveal novel splice junctions. PLoS Comput Biol. 2006, 2 (4): e34-10.1371/journal.pcbi.0020034. source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationMany of the tag-sequences can be mapped by allowing a one-basepair mismatch, insertion or deletion.
“We have previously shown that many of these tag-sequences can be mapped by allowing a one-basepair mismatch, insertion or deletion [33].”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [33] Siddiqui AS, Khattra J, Delaney AD, Zhao Y, Astell C, Asano J, Babakaiff R, Barber S, Beland J, Bohacec S, Brown-John M, Chand S, Charest D, Charters AM, Cullum R, Dhalla N, Featherstone R, Gerhard DS, Hoffman B, Holt RA, Hou J, Kuo BY, Lee LL, Lee S, Leung D, Ma K, Matsuo C, Mayo M, McDonald H, Prabhu AL, Pandoh P, Riggins GJ, de Algara TR, Rupert JL, Smailus D, Stott J, Tsai M, Varhol R, Vrljicak P, Wong D, Wu MK, Xie YY, Yang G, Zhang I, Hirst M, Jones SJ, Helgason CD, Simpson EM, Hoodless PA, Marra MA: A mouse atlas of gene expression: large-scale digital gene-expression profiles from prec source
The Results and Discussion (Data Overview and Quality Filtering; page unavailable) report that many tag sequences mapped to mouse sequence resources. The Tag-Sequence Mapping section (Materials and Methods; page unavailable) describes the resources used, but neither passage says that mapping allowed a one-base-pair mismatch, insertion, or deletion. (LLM, conf=0.84)
Experimental — accuracy not yet measured
Classified as probably not a substantial claim.
PremisecitationPrevious studies have used cDNA cloning or microarray analysis to screen for novel endoderm genes.
“Previous studies focusing on screening for novel endoderm genes have used cDNA cloning or microarray analysis [25-29,40].”
Quote in the paperSubstantial claim2 of 6 sources checked- cites [25] Sherwood RI, Jitianu C, Cleaver O, Shaywitz DA, Lamenzo JO, Chen AE, Golub TR, Melton DA: Prospective isolation and global gene expression analysis of definitive and visceral endoderm. Dev Biol. 2007, 304 (2): 541-555. 10.1016/j.ydbio.2007.01.011. source
- cites [26] Sinner D, Kirilenko P, Rankin S, Wei E, Howard L, Kofron M, Heasman J, Woodland HR, Zorn AM: Global analysis of the transcriptional network controlling Xenopus endoderm formation. Development. 2006, 133 (10): 1955-1966. 10.1242/dev.02358. source
- cites [27] Gu G, Wells JM, Dombkowski D, Preffer F, Aronow B, Melton DA: Global expression analysis of gene regulatory pathways during endocrine pancreatic development. Development. 2004, 131 (1): 165-179. 10.1242/dev.00921. source
- cites [28] Gitton Y, Dahmane N, Baik S, Ruiz i Altaba A, Neidhardt L, Scholze M, Herrmann BG, Kahlem P, Benkahla A, Schrinner S, Yildirimman R, Herwig R, Lehrach H, Yaspo ML: A gene expression map of human chromosome 21 orthologues in the mouse. Nature. 2002, 420 (6915): 586-590. 10.1038/nature01270. source
The paper’s expression-mapping passage (labelled Abstract in our copy; page unavailable) describes screening human chromosome 21 orthologues in mouse embryos using whole-mount in situ hybridization and EST mining. Searches for endoderm, cDNA cloning, and microarray screening found no passage showing that this study screened for novel endoderm genes by either method. (LLM, conf=0.77)
Experimental — accuracy not yet measured - cites [29] Neidhardt L, Gasca S, Wertz K, Obermayr F, Worpenberg S, Lehrach H, Herrmann BG: Large-scale screen for genes controlling mammalian embryogenesis, using high-throughput gene expression analysis in mouse embryos. Mech Dev. 2000, 98 (1-2): 77-94. 10.1016/S0925-4773(00)00453-6. source
- cites [40] Sousa-Nunes R, Rana AA, Kettleborough R, Brickman JM, Clements M, Forrest A, Grimmond S, Avner P, Smith JC, Dunwoodie SL, Beddington RS: Characterizing embryonic gene expression patterns in the mouse using nonredundant sequence-based selection. Genome Res. 2003, 13 (12): 2609-2620. 10.1101/gr.1362303. source
May combine two claims.
PremisecitationSousa-Nunes et al. identified 29/160 (18%) genes with restricted expression patterns from E7.5 mouse endoderm cDNA libraries using non-redundant sequence-based selection and in situ hybridization, but not all were endoderm enriched.
“Sousa-Nunes et al. identified 29/160 (18%) genes with restricted expression patterns from E7.5 mouse endoderm cDNA libraries using non-redundant sequence-based selection and in situ hybridization, but not all of these genes were endoderm enriched in their expression [40,41].”
Quote in the paperNot a substantial claim1 of 2 sources checked- cites [40] Sousa-Nunes R, Rana AA, Kettleborough R, Brickman JM, Clements M, Forrest A, Grimmond S, Avner P, Smith JC, Dunwoodie SL, Beddington RS: Characterizing embryonic gene expression patterns in the mouse using nonredundant sequence-based selection. Genome Res. 2003, 13 (12): 2609-2620. 10.1101/gr.1362303. source
- cites [41] Harrison SM, Dunwoodie SL, Arkell RM, Lehrach H, Beddington RS: Isolation of novel tissue-specific genes from cDNA libraries representing the individual tissue constituents of the gastrulating mouse embryo. Development. 1995, 121 (8): 2479-2489. source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationNephrocan (Nepn) was identified by Mochida et al. as an inhibitor of Transforming Growth Factor-β signaling.
“Interestingly, 5730521E12Rik is identical to nephrocan (Nepn), which was recently identified by Mochida et al. as an inhibitor of Transforming Growth Factor-β signaling [52].”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [52] Mochida Y, Parisuthiman D, Kaku M, Hanai J, Sukhatme VP, Yamauchi M: Nephrocan, a novel member of the small leucine-rich repeat protein family, is an inhibitor of transforming growth factor-beta signaling. J Biol Chem. 2006, 281 (47): 36044-36051. 10.1074/jbc.M604787200. source
May combine two claims.
InterpretationcitationPancreatic progenitors were rarely labeled by this lineage tracing, suggesting that Pyy may not mark the identical domain.
“However, pancreatic progenitors were rarely labeled by this lineage tracing [13] suggesting that Pyy may not mark the identical domain.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [13] Tremblay KD, Zaret KS: Distinct populations of endoderm cells converge to generate the embryonic liver bud and ventral foregut tissues. Dev Biol. 2005, 280 (1): 87-99. 10.1016/j.ydbio.2005.01.003. source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationGenetic lineage tracing using Pyy-Cre and a ROSA26 reporter mouse strain demonstrated that in the adult, descendants of Pyy-expressing cells can contribute to the periphery of pancreatic islets and the L-type cells of the distal intestine.
“However, genetic lineage tracing using Pyy-Cre and a ROSA26 reporter mouse strain demonstrated that in the adult, descendants of Pyy-expressing cells can contribute to the periphery of pancreatic islets and the L-type cells of the distal intestine [46].”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [46] Schonhoff S, Baggio L, Ratineau C, Ray SK, Lindner J, Magnuson MA, Drucker DJ, Leiter AB: Energy homeostasis and gastrointestinal endocrine differentiation do not require the anorectic hormone peptide YY. Mol Cell Biol. 2005, 25 (10): 4189-4199. 10.1128/MCB.25.10.4189-4199.2005. source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationThese domains converge to generate the epithelial cells of the liver bud.
“These domains converge to generate the epithelial cells of the liver bud [13].”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [13] Tremblay KD, Zaret KS: Distinct populations of endoderm cells converge to generate the embryonic liver bud and ventral foregut tissues. Dev Biol. 2005, 280 (1): 87-99. 10.1016/j.ydbio.2005.01.003. source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationDeletion of Pyy in mice does not reveal any obvious defects in endoderm patterning.
“Deletion of Pyy in mice does not reveal any obvious defects in endoderm patterning [46,47].”
Quote in the paperNot a substantial claim2 of 2 sources checked- cites [46] Schonhoff S, Baggio L, Ratineau C, Ray SK, Lindner J, Magnuson MA, Drucker DJ, Leiter AB: Energy homeostasis and gastrointestinal endocrine differentiation do not require the anorectic hormone peptide YY. Mol Cell Biol. 2005, 25 (10): 4189-4199. 10.1128/MCB.25.10.4189-4199.2005. source
The Discussion reports that Pyy-null mice largely retain endocrine differentiation in the colon and pancreas, supporting a narrower finding about these endoderm-derived tissues. It also notes an exception for pancreatic PP cells. The paper does not establish that endoderm patterning overall is unaffected. (LLM, conf=0.84)
Experimental — accuracy not yet measured - cites [47] Boey D, Lin S, Karl T, Baldock P, Lee N, Enriquez R, Couzens M, Slack K, Dallmann R, Sainsbury A, Herzog H: Peptide YY ablation in mice leads to the development of hyperinsulinaemia and obesity. Diabetologia. 2006, 49 (6): 1360-1370. 10.1007/s00125-006-0237-0. source
The 'Generation of Pyy knock-out mice' section reports no obvious morphological changes in the pancreas or colon of Pyy-deficient mice. That supports the absence of visible defects in those tissues, but the paper does not assess endoderm patterning more broadly. (LLM, conf=0.84)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationTremblay et al. identified two distinct types of definitive endoderm progenitor cells, lateral and medial, arising from three spatially separated embryonic domains.
“They identified two distinct types of DE progenitor cells, lateral and medial, arising from three spatially separated embryonic domains.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [13] Tremblay KD, Zaret KS: Distinct populations of endoderm cells converge to generate the embryonic liver bud and ventral foregut tissues. Dev Biol. 2005, 280 (1): 87-99. 10.1016/j.ydbio.2005.01.003. source
May combine two claims.
Findingown dataAll of the known endoderm genes (Cxcr4, Ecad, Foxa1-3, Gata4, Gata6, Hhex, Ihh, Shh, and Sox17) were present in the endoderm libraries and excluded or present at low levels in the ectoderm libraries.
“Significantly, all of these endoderm genes were present in our endoderm libraries and excluded or present at low levels in the ectoderm libraries.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataOf the combined 54,093 tag-sequences, 37% mapped to known transcripts, 12% mapped to known genes using Ensembl genes, and 20% mapped to the mouse genome.
“Of the combined 54,093 tag-sequences, 37% (19,782) mapped to known transcripts using the Refseq, MGC and Ensembl transcript databases, 12% (6,560) mapped to known genes using the Ensembl genes, implicating alternative splicing and alternative 3' UTRs of known genes, and 20% (10,954) mapped to the mouse genome.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown data25,097 and 25,509 tag-sequences were present in the foregut (SM107) and hindgut (SM112) libraries, respectively.
“Similarly, 25,097 and 25,509 tag-sequences were present in the foregut (SM107) and hindgut (SM112) libraries, respectively.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataSeveral genes in the authors' study were found to be expressed in both visceral and definitive endoderm, supporting the similarity of the two tissues.
“Several genes in our study were found to be expressed in both visceral and definitive endoderm, supporting the similarity of the two tissues.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataPyy expression was restricted to the posterior half of the foregut and never observed in the anterior half of the foregut pocket.
“Interestingly, the expression was restricted to the posterior half of the foregut and never observed in the anterior half of the foregut pocket.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataGroup 4 contained genes that were not expressed in yolk sac and heart, but expressed in all 3 germ layers.
“Group 4 contained genes that were not expressed in yolk sac and heart, but expressed in all 3 germ layers.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataTwenty-one of the 26 genes showed tissue-restricted expression patterns, while the remaining 5 genes showed ubiquitous expression at E8.5.
“21 of the 26 genes showed tissue-restricted expression patterns (Figure 6, 7 and Table 2), while the remaining 5 genes showed ubiquitous expression at E8.5.”
Quote in the paperSubstantial claimMay combine two claims.
FindingcitationGroup 2 included genes that were expressed in the definitive endoderm and yolk sac endoderm, which support the functional similarity between these two lineages.
“Group 2 included genes that were expressed in the definitive endoderm and yolk sac endoderm, which support the functional similarity between these two lineages [6].”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [6] Lewis SL, Tam PP: Definitive endoderm of the mouse embryo: formation, cell fates, and morphogenetic function. Dev Dyn. 2006, 235 (9): 2315-2329. 10.1002/dvdy.20846. source
May combine two claims.
Findingown dataAt the 4 somite stage, the expression domains in the lateral region were expanded and a second expression domain in the medial ventral foregut was observed.
“At the 4 somite stage, the expression domains in the lateral region were expanded and a second expression domain in the medial ventral foregut was observed (Figure 4C, 4D).”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataSix of the 14 genes showed a ubiquitous expression pattern, making it difficult to determine whether there was differential expression within the DE.
“Six of these genes showed a ubiquitous expression pattern, making it difficult to determine whether there was differential expression within the DE.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataSubsequently, Pyy is expressed in the posterior foregut extending to the midgut junction, and at later stages (E14.5-adult) expression becomes restricted to the pancreas, stomach and intestine.
“Subsequently, Pyy is expressed in the posterior foregut extending to the midgut junction, and at later stages (E14.5-adult) expression becomes restricted to the pancreas, stomach and intestine (data not shown).”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Findingown dataCpn1 and 1700011H14Rik showed strikingly similar expression patterns suggesting they may be co-regulated.
“In addition, Cpn1 and 1700011H14Rik showed strikingly similar expression patterns suggesting they may be co-regulated.”
Quote in the paperNot a substantial claimClassified as probably not a substantial claim.
PremisecitationProcesses that govern early development of DE-derived tissues may be recapitulated during stem cell differentiation.
“Interest in the endoderm has intensified recently because processes that govern early development of DE-derived tissues may be recapitulated during stem cell differentiation [4,5]”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [4] D'Amour KA, Agulnick AD, Eliazer S, Kelly OG, Kroon E, Baetge EE: Efficient differentiation of human embryonic stem cells to definitive endoderm. Nat Biotechnol. 2005, 23 (12): 1534-1541. 10.1038/nbt1163. source
- cites [5] Yasunaga M, Tada S, Torikai-Nishikawa S, Nakano Y, Okada M, Jakt LM, Nishikawa S, Chiba T, Era T, Nishikawa S: Induction and monitoring of definitive and visceral endoderm differentiation of mouse ES cells. Nat Biotechnol. 2005, 23 (12): 1542-1550. 10.1038/nbt1167. source
Classified as probably not a substantial claim.
PremisecitationTwo groups achieved efficient differentiation of human and murine ES cells into DE by combining directive culture conditions and FACS sorting using CXCR4.
“More recently, two groups achieved efficient differentiation of human and murine ES cells into DE by combining directive culture conditions (serum concentration reduction and Activin supplements) and FACS sorting using the cell surface marker, CXCR4 [4,5,24].”
Quote in the paperSubstantial claim0 of 3 sources checked- cites [4] D'Amour KA, Agulnick AD, Eliazer S, Kelly OG, Kroon E, Baetge EE: Efficient differentiation of human embryonic stem cells to definitive endoderm. Nat Biotechnol. 2005, 23 (12): 1534-1541. 10.1038/nbt1163. source
- cites [5] Yasunaga M, Tada S, Torikai-Nishikawa S, Nakano Y, Okada M, Jakt LM, Nishikawa S, Chiba T, Era T, Nishikawa S: Induction and monitoring of definitive and visceral endoderm differentiation of mouse ES cells. Nat Biotechnol. 2005, 23 (12): 1542-1550. 10.1038/nbt1167. source
- cites [24] Loebel DA, Tam PP: A gut feeling. Nat Biotechnol. 2005, 23 (12): 1491-1492. 10.1038/nbt1205-1491. source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationEndoderm patterning is controlled by soluble factors provided by an adjacent germ layer.
“Studies of ventral foregut patterning suggest that endoderm patterning is controlled by soluble factors provided by an adjacent germ layer [12].”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [12] Jung J, Zheng M, Goldfarb M, Zaret KS: Initiation of mammalian liver development from endoderm by fibroblast growth factors. Science. 1999, 284 (5422): 1998-2003. 10.1126/science.284.5422.1998. source
Classified as probably not a substantial claim. May combine two claims.
Premisenone givenThe precise hierarchical relationships between these factors and their downstream targets are still largely unknown, and complete molecular hierarchies have not been obtained.
“However, the precise hierarchical relationships between these factors and their downstream targets are still largely unknown, and complete molecular hierarchies have not been obtained.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing), S4 (based).
Premisenone givenMidgut and hindgut development is largely unexplored.
“In addition, midgut and hindgut development is largely unexplored.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationThe notochordal plate at 0-6 somite stage and the notochord at 8-12 somite stage adjoin the DE.
“The notochordal plate at 0–6 somite stage and the notochord at 8–12 somite stage adjoin the DE and thus were included in the library [36].”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [36] Sulik K, Dehart DB, Iangaki T, Carson JL, Vrablic T, Gesteland K, Schoenwolf GC: Morphogenesis of the murine node and notochordal plate. Dev Dyn. 1994, 201 (3): 260-278. source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationSherwood et al. used fluorescent activated cell sorting to isolate definitive and visceral endoderm cell populations for microarray analysis.
“Sherwood et al. recently used fluorescent activated cell sorting to isolate definitive and visceral endoderm cell populations for microarray analysis [25].”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [25] Sherwood RI, Jitianu C, Cleaver O, Shaywitz DA, Lamenzo JO, Chen AE, Golub TR, Melton DA: Prospective isolation and global gene expression analysis of definitive and visceral endoderm. Dev Biol. 2007, 304 (2): 541-555. 10.1016/j.ydbio.2007.01.011. source
May combine two claims.
Interpretationown dataPyy is expressed earlier than previously reported and demonstrates a dynamic expression pattern in the early DE.
“Thus, Pyy is expressed earlier than previously reported and demonstrates a dynamic expression pattern in the early DE.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationSherwood et al. identified 18 out of 27 (67%) novel genes whose expression was enriched in endoderm.
“They identified 18 out of 27 (67%) novel genes whose expression was enriched in endoderm.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [25] Sherwood RI, Jitianu C, Cleaver O, Shaywitz DA, Lamenzo JO, Chen AE, Golub TR, Melton DA: Prospective isolation and global gene expression analysis of definitive and visceral endoderm. Dev Biol. 2007, 304 (2): 541-555. 10.1016/j.ydbio.2007.01.011. source
May combine two claims.
InterpretationreasoningSAGE sampling depth is sufficient for detection of abundant and moderately abundant transcripts but likely insufficient for reliable detection of rare transcripts.
“and is thus sufficient for detection of abundant and moderately abundant transcripts but is likely insufficient for reliable detection of rare transcripts.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationSherwood et al. defined a pan-endodermal signature composed of 22 novel and known genes preferentially expressed in definitive and visceral endoderm.
“They defined a pan-endodermal signature composed of 22 novel and known genes that is preferentially expressed in definitive and visceral endoderm.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [25] Sherwood RI, Jitianu C, Cleaver O, Shaywitz DA, Lamenzo JO, Chen AE, Golub TR, Melton DA: Prospective isolation and global gene expression analysis of definitive and visceral endoderm. Dev Biol. 2007, 304 (2): 541-555. 10.1016/j.ydbio.2007.01.011. source
May combine two claims.
InterpretationreasoningNeither the Sousa-Nunes nor the Sherwood study was able to identify novel genes expressed specifically in the definitive endoderm.
“Interestingly, neither study was able to identify novel genes that are expressed specifically in the DE.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationPyy is known to be highly expressed in pancreatic islets and endocrine L cells of the lower gastrointestinal tract.
“Pyy is known to be highly expressed in pancreatic islets and endocrine L cells of the lower gastrointestinal tract [39], but its early embryonic expression pattern has not been described.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [39] Pieribone VA, Brodin L, Friberg K, Dahlstrand J, Soderberg C, Larhammar D, Hokfelt T: Differential expression of mRNAs for neuropeptide Y-related peptides in rat nervous tissues: possible evolutionary conservation. J Neurosci. 1992, 12 (9): 3361-3371. source
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
InterpretationreasoningAlternatively, Group 5 genes may be expressed in the DE at low levels but their expression in DE could be under-estimated by in situ hybridization due to very high levels in yolk sac endoderm.
“Alternatively, these genes may be expressed in the DE at low levels but their expression in DE could be under-estimated by in situ hybridization due to very high levels in yolk sac endoderm.”
Quote in the paperNot a substantial claimMay combine two claims.
Study design and conductown dataThe expression patterns observed in the libraries support known expression data for these genes, indicating that the libraries are representative of endoderm and ectoderm transcription.
“Overall, the expression patterns observed in our libraries supports known expression data for these genes, indicating that the libraries are representative of endoderm and ectoderm transcription.”
Quote in the paperSubstantial claimMay combine two claims.
Study design and conductown dataThe relatively high purity of the tissue source used for the construction of the definitive endoderm longSAGE libraries and the comparison with a large number of longSAGE libraries from a variety of tissues and embryonic stages are the two critical factors for achieving an efficient screen.
“The relatively high purity of the tissue source used for the construction of our DE longSAGE libraries and the comparison with a large number of longSAGE libraries from a variety of tissues and embryonic stages are the two critical factors for achieving an efficient screen.”
Quote in the paperSubstantial claimMay combine two claims.
InterpretationreasoningThe dynamic expression pattern of 5730521E12Rik suggests that it may mark the last population of the definitive endoderm precursors recruited, and is possibly a midgut lineage marker.
“Fascinatingly, the dynamic expression pattern of 5730521E12Rik suggests that it may mark the last population of the DE precursors recruited, thus is possibly a midgut lineage marker.”
Quote in the paperNot a substantial claimClassified as probably not a substantial claim. May combine two claims.
Study design and conductnone givenAt least three embryos at each stage were examined for each probe, and restricted expression patterns were confirmed by independent sets of hybridizations.
“At least three embryos at each stage were examined for each probe, and restricted expression patterns were confirmed by independent sets of hybridizations.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
InterpretationreasoningThe dynamic expression pattern of Pyy appears to reiterate the morphogenetic movement of foregut progenitors along anterior-posterior and medial-lateral axes prior to tissue specification.
“Regardless, the dynamic expression pattern of Pyy appears to reiterate the morphogenetic movement of foregut progenitors along anterior-posterior and medial-lateral axes prior to tissue specification.”
Quote in the paperNot a substantial claim
The paper relies on this without support.
Directing differentiation efficiently into specific lineages at high purities from ES cells requires both optimal selective culture conditions and markers to guide and monitor the differentiation process.
“Directing differentiation efficiently into specific lineages at high purities from ES cells requires both optimal selective culture conditions and markers to guide and monitor the differentiation process.”
The paper relies on this without support.
Compared with microarrays, SAGE has the additional advantage that it permits the identification of novel transcripts.
“Compared with microarrays, SAGE has the additional advantage that it permits the identification of novel transcripts.”
The paper relies on this without support.
SAGE data are digital and thus can be easily shared among investigators and compared across different experiments and tissues.
“SAGE also has the added benefit that the data are digital and thus can be easily shared among investigators and compared across different experiments and tissues.”
The paper relies on this without support.
Higher T values and lower L values (higher T/L ratio) correspond to the degree of endoderm-enrichment.
“We rationalized that higher T values and lower L values and thus higher T/L ratio would correspond to the degree of the endoderm-enrichment.”
The paper relies on this without support.
Including the adjoining notochordal plate/notochord in the endoderm libraries does not significantly contaminate the DE expression profile.
“The notochordal plate at 0–6 somite stage and the notochord at 8–12 somite stage adjoin the DE and thus were included in the library [36].”
The paper relies on this without support.
Yolk sac endoderm contamination is difficult to avoid when collecting DE tissue.
“The tags for these genes may be included in our libraries due to yolk sac endoderm contamination, which is difficult to avoid when collecting the DE tissue.”
The paper relies on this without support.
Formation, specification and patterning of the definitive endoderm are poorly understood in the embryo compared to other germ layers.
“Formation, specification and patterning of the definitive endoderm are poorly understood in the embryo compared to other germ layers.”
The paper relies on this without support.
There is a lack of exploratory tools to aid studies of definitive endoderm formation, specification and patterning.
“Due to a lack of exploratory tools to aid these studies, interest in the identification of novel endoderm genes is growing.”
The paper relies on this without support.
In situ hybridization is the ultimate and proven method to validate tissue-specific genes.
“while in situ hybridization is considered to be the ultimate and proven method to validate tissue-specific genes”
The paper relies on this without support.
Obtaining embryos for in situ hybridization at appropriate stages is more costly and time-consuming in mouse than in chicken, frog or fish.
“obtaining embryos for in situ hybridization at appropriate stages is more costly and time-consuming in mouse than in chicken, frog or fish.”
The paper relies on this without support.
Many developmentally important genes are transcribed repeatedly and presumably function during multiple developmental processes.
“Since many developmentally important genes are transcribed repeatedly and presumably function during multiple developmental processes, further refining of library and tissue choices for comparisons would be required to identify genes that are expressed in many stages of development and many tissues.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Pyy is specifically expressed within the posterior foregut endoderm.
“with Pyy being specifically expressed within the posterior foregut endoderm”
From Single-Cell Transcriptomics Reveals Early Emergence of Liver Parenchymal and Non-parenchymal Cell Lineages (2020) · cites this paper as Hou et al., 2007
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Cubn total does not equal its three library counts
MinorThe Cubn counts in the foregut, whole endoderm, and hindgut libraries sum to 34, but the table reports a total (T) of 23.
Reported 23 · recomputed 34
“| Cubn | Cubilin (intrisic factor-cobalamin receptor) | 23 | 1 | 16 | 17 | 23 | yolk sac endoderm |”
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Background[22] Detection of messenger RNA by in Situ hybridization to tissue sections and whole mounts
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“Whole mount in situ hybridization was performed as described previously [54].”
MethodInitiation of Mammalian Liver Development from Endoderm by Fibroblast Growth Factors
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BackgroundDepletion of definitive gut endoderm in <i>Sox17</i> -null mutant mice
Kanai-Azuma, M., Kanai, Y., Gad, J. M., Tajima, Y., Taya, C., Kurohmaru, M., Sanai, Y., Yonekawa, H., Yazaki, K., Tam, P. P. L., et al. (2002) · Development · doi:10.1242/dev.129.10.2367 · Cited by 704 · see citing works
Using the transcriptome to annotate the genome
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MethodNotochord repression of endodermal Sonic hedgehog permits pancreas development
Hebrok, M., Kim, S. K., & Melton, D. A. (1998) · Genes & Development · doi:10.1101/gad.12.11.1705 · Cited by 628 · cited 1× · see citing works
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“By this stage endoderm patterning has initiated [14,35].”
BackgroundA bipotential precursor population for pancreas and liver within the embryonic endoderm
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“Similarly, Sox2 is expressed in both ectoderm and endoderm libraries corresponding to published expression patterns [38].”
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Vertebrate Endoderm Development
Wells, J. M., & Melton, D. A. (1999) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev.cellbio.15.1.393 · Cited by 522 · cited 1× · see citing works
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BackgroundInduction and monitoring of definitive and visceral endoderm differentiation of mouse ES cells
Yasunaga, M., Tada, S., Torikai-Nishikawa, S., Nakano, Y., Okada, M., Jakt, L. M., Nishikawa, S., Chiba, T., Era, T., & Nishikawa, S.-I. (2005) · Nature Biotechnology · doi:10.1038/nbt1167 · Cited by 471 · cited 4× · see citing works
“Although useful, CXCR4 is not an ideal marker for the DE as it is widely expressed in the gastulation stage mouse embryo (Table 1 and [5,25]).”
BackgroundMethodInfluentialRegulation of pancreas development by hedgehog signaling
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Notochord to endoderm signaling is required for pancreas development
Kim, S. K., Hebrok, M., & Melton, D. A. (1997) · Development · doi:10.1242/dev.124.21.4243 · Cited by 405 · see citing works
Early mouse endoderm is patterned by soluble factors from adjacent germ layers
Wells, J. M., & Melton, D. A. (2000) · Development · doi:10.1242/dev.127.8.1563 · Cited by 366 · see citing works
Morphogenesis of the murine node and notochordal plate
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“The notochordal plate at 0–6 somite stage and the notochord at 8–12 somite stage adjoin the DE and thus were included in the library [36].”
BackgroundTremblay, K. D., & Zaret, K. S. (2005) · Developmental Biology · doi:10.1016/j.ydbio.2005.01.003 · Cited by 299 · cited 3× · see citing works
“FGF4, which is expressed in the neighboring cardiac mesoderm, can induce the differentiation of ventral foregut endoderm in a concentration-dependent manner [13,14].”
BackgroundLawson, K. A., Pedersen, R. A., & van de Geer, S. (1987) · Development · doi:10.1242/dev.101.3.627 · Cited by 279 · see citing works
Endoderm development: from patterning to organogenesis
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“into a tube that runs along the anterior-posterior axis of the embryo [1-3].”
BackgroundGlobal expression analysis of gene regulatory pathways during endocrine pancreatic development
Gu, G., Wells, J. M., Dombkowski, D., Preffer, F., Aronow, B., & Melton, D. A. (2004) · Development · doi:10.1242/dev.00921 · Cited by 229 · cited 1× · see citing works
“Previous studies focusing on screening for novel endoderm genes have used cDNA cloning or microarray analysis [25-29,40].”
Background<i>Mixl1</i>is required for axial mesendoderm morphogenesis and patterning in the murine embryo
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“... endoderm and the dorsal endoderm of the rostral segment of the foregut at early-streak stage; (b) the ventral endoderm of the rostral foregut and additional posterior endoderm at the mid-streak stage; (c) the dorsal and then the ventral endoderm of the posterior segment of the foregut at the late-streak to late-bu…”
BackgroundArtifactual Insulin Release From Differentiated Embryonic Stem Cells
Hansson, M., Tonning, A., Frandsen, U., Petri, A., Rajagopal, J., Englund, M. C. O., Heller, R. S., Håkansson, J., Fleckner, J., Sköld, H. N., et al. (2004) · Diabetes · doi:10.2337/diabetes.53.10.2603 · Cited by 225 · cited 1× · see citing works
“While several methods of differentiation of ES cells to hepatic and insulin-producing cells have been described, determining the precise identity of these cells is problematic due to a lack of suitable markers [20-23].”
BackgroundActivin receptor patterning of foregut organogenesis
Kim, S. K., Hebrok, M., Li, E., Oh, S. P., Schrewe, H., Harmon, E. B., Lee, J. S., & Melton, D. A. (2000) · Genes & Development · doi:10.1101/gad.14.15.1866 · Cited by 212 · cited 1× · see citing works
“FGF2 and Activin, secreted by the notochord, lead to the expression of pancreatic markers by repressing expression of Shh in pancreatic endoderm [15-19].”
Background<i>FoxH1</i>(<i>Fast</i>) functions to specify the anterior primitive streak in the mouse
Hoodless, P. A., Pye, M., Chazaud, C., Labbé, E., Attisano, L., Rossant, J., & Wrana, J. L. (2001) · Genes & Development · doi:10.1101/gad.881501 · Cited by 203 · cited 1× · see citing works
“They include Nodal and components of its signaling pathway, transcription factors of the mix-like paired homeodomain class, Forkhead domain factors, and Sox17 HMG domain proteins [7-11].”
BackgroundSelf-citationPeptide YY ablation in mice leads to the development of hyperinsulinaemia and obesity
Boey, D., Lin, S., Karl, T., Baldock, P., Lee, N., Enriquez, R., Couzens, M., Slack, K., Dallmann, R., Sainsbury, A., et al. (2006) · Diabetologia · doi:10.1007/s00125-006-0237-0 · Cited by 186 · cited 1× · see citing works
“Deletion of Pyy in mice does not reveal any obvious defects in endoderm patterning [46,47].”
BackgroundEarly endoderm development in vertebrates: lineage differentiation and morphogenetic function
Tam, P. (2003) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(03)00085-6 · Cited by 181 · see citing works
Formation of the definitive endoderm in mouse is a Smad2-dependent process
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Self-citationClonal Analysis of Cell Fate During Gastrulation and Early Neurulation in the Mouse
Lawson, K. A., & Pedersen, R. A. (2007) · Novartis Foundation symposium · doi:10.1002/9780470514221.ch2 · Cited by 177 · see citing works
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“For example, Prox1 is only expressed by the liver and pancreas progenitors beginning at the 7–8 somite stage [43].”
BackgroundDefinitive endoderm of the mouse embryo: Formation, cell fates, and morphogenetic function
Lewis, S. L., & Tam, P. P. L. (2006) · Developmental Dynamics · doi:10.1002/dvdy.20846 · Cited by 164 · cited 3× · see citing works
“Its early regionalized expression within DE reflects an early specification of cell fate along both the anterior-posterior and lateral-medial axis of the embryonic gut [6,45].”
BackgroundStudy of hepatocyte differentiation using embryonic stem cells
Lavon, N., & Benvenisty, N. (2005) · Journal of Cellular Biochemistry · doi:10.1002/jcb.20590 · Cited by 134 · cited 1× · see citing works
“While several methods of differentiation of ES cells to hepatic and insulin-producing cells have been described, determining the precise identity of these cells is problematic due to a lack of suitable markers [20-23].”
BackgroundA gene expression map of human chromosome 21 orthologues in the mouse
initiative, T. H. E. M., *Group 1:, Gitton, Y., Dahmane, N., Baik, S., Ruiz i Altaba, A., *Group 2:, Neidhardt, L., Scholze, M., Herrmann, B. G., et al. (2002) · Nature · doi:10.1038/nature01270 · Cited by 127 · cited 1× · see citing works
“Previous studies focusing on screening for novel endoderm genes have used cDNA cloning or microarray analysis [25-29,40].”
BackgroundProspective isolation and global gene expression analysis of definitive and visceral endoderm
Sherwood, R. I., Jitianu, C., Cleaver, O., Shaywitz, D. A., Lamenzo, J. O., Chen, A. E., Golub, T. R., & Melton, D. A. (2007) · Developmental Biology · doi:10.1016/j.ydbio.2007.01.011 · Cited by 122 · cited 5× · see citing works
“Furthermore, the high functional similarity between visceral and definitive endoderm suggests that these tissues have highly related transcriptomes [25].”
BackgroundMethodInfluentialSiddiqui, A. S., Khattra, J., Delaney, A. D., Zhao, Y., Astell, C., Asano, J., Babakaiff, R., Barber, S., Beland, J., Bohacec, S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0509455102 · Cited by 116 · cited 9× · see citing works
“Conclusion: The high efficiency of this endoderm screen indicates that our approach can be successfully used to analyze and validate the vast amount of data obtained by the Mouse Atlas of Gene Expression Project.”
BackgroundMethodInfluentialSelf-citationNotochord Patterning of the Endoderm
Cleaver, O., & Krieg, P. A. (2001) · Developmental Biology · doi:10.1006/dbio.2001.0214 · Cited by 114 · cited 1× · see citing works
“FGF2 and Activin, secreted by the notochord, lead to the expression of pancreatic markers by repressing expression of Shh in pancreatic endoderm [15-19].”
BackgroundBlyszczuk, P., Asbrand, C., Rozzo, A., Kania, G., St-onge, L., Rupnik, M., & Wobus, A. M. (2004) · The International Journal of Developmental Biology · doi:10.1387/ijdb.041904pb · Cited by 110 · see citing works
Pieribone, V., Brodin, L., Friberg, K., Dahlstrand, J., Soderberg, C., Larhammar, D., & Hokfelt, T. (1992) · The Journal of Neuroscience · doi:10.1523/jneurosci.12-09-03361.1992 · Cited by 96 · cited 1× · see citing works
“Pyy is known to be highly expressed in pancreatic islets and endocrine L cells of the lower gastrointestinal tract [39], but its early embryonic expression pattern has not been described.”
BackgroundTam, P. P. L., Khoo, P.-L., Lewis, S. L., Bildsoe, H., Wong, N., Tsang, T. E., Gad, J. M., & Robb, L. (2007) · Development · doi:10.1242/dev.02724 · Cited by 94 · cited 3× · see citing works
“recently depicted the sequential allocation and global pattern of movement of the DE in the mouse embryo during gastrulation, by tracing cells electroporated with Gfp or painted with carbocyanine dyes [45].”
BackgroundEndoderm development in vertebrates: fate mapping, induction and regional specification
Fukuda, K., & Kikuchi, Y. (2005) · Development, Growth & Differentiation · doi:10.1111/j.1440-169x.2005.00815.x · Cited by 82 · cited 1× · see citing works
“They include Nodal and components of its signaling pathway, transcription factors of the mix-like paired homeodomain class, Forkhead domain factors, and Sox17 HMG domain proteins [7-11].”
BackgroundNeidhardt, L., Gasca, S., Wertz, K., Obermayr, F., Worpenberg, S., Lehrach, H., & Herrmann, B. G. (2000) · Mechanisms of Development · doi:10.1016/s0925-4773(00)00453-6 · Cited by 79 · cited 1× · see citing works
“Previous studies focusing on screening for novel endoderm genes have used cDNA cloning or microarray analysis [25-29,40].”
BackgroundHarrison, S. M., Dunwoodie, S. L., Arkell, R. M., Lehrach, H., & Beddington, R. S. P. (1995) · Development · doi:10.1242/dev.121.8.2479 · Cited by 71 · see citing works
Global analysis of the transcriptional network controlling <i>Xenopus</i> endoderm formation
Sinner, D., Kirilenko, P., Rankin, S., Wei, E., Howard, L., Kofron, M., Heasman, J., Woodland, H. R., & Zorn, A. M. (2006) · Development · doi:10.1242/dev.02358 · Cited by 71 · cited 1× · see citing works
“Previous studies focusing on screening for novel endoderm genes have used cDNA cloning or microarray analysis [25-29,40].”
BackgroundA comparison of gene expression profiles produced by SAGE, long SAGE, and oligonucleotide chips
Lu, J., Lal, A., Merriman, B., Nelson, S., & Riggins, G. (2004) · Genomics · doi:10.1016/j.ygeno.2004.06.014 · Cited by 55 · cited 1× · see citing works
“Our SAGE sampling depth (~100,000 tags per library) yields genedetection sensitivity approximately equivalent to that of fluorescence-based microarray approaches [42], and is thus sufficient for detection of abundant and moderately abundant transcripts but is likely insufficient for reliable detection of rare transcri…”
BackgroundSchonhoff, S., Baggio, L., Ratineau, C., Ray, S. K., Lindner, J., Magnuson, M. A., Drucker, D. J., & Leiter, A. B. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.10.4189-4199.2005 · Cited by 53 · cited 2× · see citing works
“Deletion of Pyy in mice does not reveal any obvious defects in endoderm patterning [46,47].”
BackgroundDiscoverySpace: an interactive data analysis application
Robertson, N., Oveisi-Fordorei, M., Zuyderduyn, S., et al. (2007) · Genome biology · doi:10.1186/gb-2007-8-1-r6 · Cited by 41 · cited 1× · see citing works
“SAGE data was analyzed using DiscoverySpace software [53].”
MethodSelf-citationKhattra, J., Delaney, A. D., Zhao, Y., Siddiqui, A., Asano, J., McDonald, H., Pandoh, P., Dhalla, N., Prabhu, A.-L., Ma, K., et al. (2007) · Genome Research · doi:10.1101/gr.5488207 · Cited by 40 · cited 7× · see citing works
“Conclusion: The high efficiency of this endoderm screen indicates that our approach can be successfully used to analyze and validate the vast amount of data obtained by the Mouse Atlas of Gene Expression Project.”
BackgroundMethodInfluentialSelf-citationMochida, Y., Parisuthiman, D., Kaku, M., Hanai, J.-I., Sukhatme, V. P., & Yamauchi, M. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m604787200 · Cited by 34 · cited 1× · see citing works
“as an inhibitor of Transforming Growth Factor-β signaling [52].”
BackgroundStem cells and pancreatic differentiation in vitro
Blyszczuk, P., & Wobus, A. M. (2004) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2004.03.023 · Cited by 31 · cited 1× · see citing works
“While several methods of differentiation of ES cells to hepatic and insulin-producing cells have been described, determining the precise identity of these cells is problematic due to a lack of suitable markers [20-23].”
BackgroundSousa-Nunes, R. (2003) · Genome Research · doi:10.1101/gr.1362303 · Cited by 31 · see citing works
Wahl, M. B., Heinzmann, U., & Imai, K. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti207 · Cited by 29 · cited 1× · see citing works
“SAGE has been improved by the development of a longSAGE protocol, which generates tags that are 21 bp long and provides enhanced efficiency and accuracy of tag-to-gene mapping [30-32].”
MethodLoebel, D. A. F., & Tam, P. P. L. (2005) · Nature Biotechnology · doi:10.1038/nbt1205-1491 · Cited by 18 · see citing works
SAGE2Splice: Unmapped SAGE Tags Reveal Novel Splice Junctions
Kuo, B. Y.-L., Chen, Y., Bohacec, S., Johansson, Ö., Wasserman, W. W., & Simpson, E. M. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020034 · Cited by 12 · cited 1× · see citing works
“For example, these 44 tag-sequences may span an unknown splice junction [37].”
Background
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The emergent landscape of the mouse gut endoderm at single-cell resolution
Nowotschin, S., Setty, M., Kuo, Y.-Y., Liu, V., Garg, V., Sharma, R., Simon, C. S., Saiz, N., Gardner, R., Boutet, S. C., et al. (2019) · Nature · doi:10.1038/s41586-019-1127-1 · Cited by 383 · see citing works
Self-citationMolecular recording of mammalian embryogenesis
Chan, M. M., Smith, Z. D., Grosswendt, S., Kretzmer, H., Norman, T. M., Adamson, B., Jost, M., Quinn, J. J., Yang, D., Jones, M. G., et al. (2019) · Nature · doi:10.1038/s41586-019-1184-5 · Cited by 364 · see citing works
Foxa2 regulates polarity and epithelialization in the endoderm germ layer of the mouse embryo
Burtscher, I., & Lickert, H. (2009) · Development · doi:10.1242/dev.028415 · Cited by 213 · see citing works
“(Sousa-Nunes et al., 2003; Hou et al., 2007) might explain the ectopic localization of ZO-1 at the apical membrane of Foxa2 mutant endoderm-like cells.”
BackgroundVisualizing the structure of RNA-seq expression data using grade of membership models
Dey, K. K., Hsiao, C. J., & Stephens, M. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006599 · Cited by 161 · see citing works
“…, Krt8 , Id2 [59]), while the purple cluster is enriched with genes responsible for the formation of inner cell mass (ICM) (e.g., Pdgfra , Pyy [61]). pre-implantation stage; however only PCA and MDS seem to capture the developmental trajectory from zygote to blastocyst, exhibiting a…”
Kurek, D., Neagu, A., Tastemel, M., Tüysüz, N., Lehmann, J., van de Werken, H. J. G., Philipsen, S., van der Linden, R., Maas, A., van IJcken, W. F. J., et al. (2014) · Stem Cell Reports · doi:10.1016/j.stemcr.2014.11.007 · Cited by 157 · see citing works
“A set of 98 genes expressed in committed human- and mouse-definitive endoderm and endoderm precursors (Hou et al., 2007; McLean et al., 2007; Ogaki et al., 2011;Tadaet al., 2005)washighlyenriched inconventional EpiSCs (Figure 2F; Table S3).”
BackgroundWang, P.-R., Rodriguez, R. T., Wang, J., Ghodasara, A., & Kim, S. K. (2011) · Cell Stem Cell · doi:10.1016/j.stem.2011.01.017 · Cited by 154 · see citing works
Ibarra-Soria, X., Jawaid, W., Pijuan-Sala, B., Ladopoulos, V., Scialdone, A., Jörg, D. J., Tyser, R. C. V., Calero‐Nieto, F. J., Mulas, C., Nichols, J., et al. (2017) · Nature Cell Biology · doi:10.1038/s41556-017-0013-z · Cited by 121 · see citing works
Lotto, J., Drissler, S., Cullum, R., Wei, W., Setty, M., Bell, E. M., Boutet, S. C., Nowotschin, S., Kuo, Y.-Y., Garg, V., et al. (2020) · Cell · doi:10.1016/j.cell.2020.09.012 · Cited by 86 · see citing works
Self-citationTamplin, O. J., Kinzel, D., Cox, B., Bell, C., Rossant, J., & Lickert, H. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-511 · Cited by 85 · see citing works
Artus, J., Douvaras, P., Piliszek, A., Isern, J., Baron, M. H., & Hadjantonakis, A.-K. (2012) · Developmental Biology · doi:10.1016/j.ydbio.2011.10.015 · Cited by 83 · see citing works
Efficient Derivation of Alveolar Type II Cells from Embryonic Stem Cells for In Vivo Application
Roszell, B. R., Mondrinos, M., Seaton, A., Simons, D. M., Koutzaki, S. H., Fong, G., Lelkes, P., & Finck, C. (2009) · Tissue Engineering. Part A · doi:10.1089/ten.tea.2008.0664 · Cited by 89 · see citing works
Gata4 directs development of cardiac-inducing endoderm from ES cells
Holtzinger, A., Rosenfeld, G. E., & Evans, T. (2009) · Developmental Biology · doi:10.1016/j.ydbio.2009.10.003 · Cited by 80 · see citing works
“N IH -PA Author M anuscript N IH -PA Author M anuscript N IH -PA Author M anuscript characterize genes that distinguish the endoderm sub-types, through expression profiling of isolated embryonic endoderm tissues (Hou et al., 2007; Sherwood et al., 2007).”
BackgroundChal, J., Tanoury, Z. A., Oginuma, M., Moncuquet, P., Gobert, B., Miyanari, A., Tassy, O., Guevara, G., Hubaud, A., Bera, A. N., et al. (2018) · Development · doi:10.1242/dev.157339 · Cited by 76 · see citing works
“…protein vitronectin (Vtn), the epithelial remodelling factor Shroom3 (Sousa-Nunes et al., 2003), and a number of genes with unknown function in the PSM including Abca1, Fam101a (Cfm2) (Hirano et al., 2005), Arg1 (Hou et al., 2007), Pgm5 and Ism1 (Tamplin et al., 2008) (Figure 1A, data not shown).”
BackgroundHansson, M. D., Olesen, D. R., Peterslund, J. M. L., Engberg, N., Kahn, M., Winzi, M., Klein, T., Maddox‐Hyttel, P., & Serup, P. (2009) · Developmental Biology · doi:10.1016/j.ydbio.2009.03.026 · Cited by 75 · see citing works
“Additional marker analyses revealed that such cells were also Pyy+, Foxa2+ and CXCR4+ but Sox7− and Tdh−, suggesting embryonic rather than extraembryonic endoderm had formed (Kanai-Azuma et al., 2002; Tada et al., 2005; Yasunaga et al., 2005).”
BackgroundInfluentialRodríguez-Seguel, E. D. P., Mah, N., Naumann, H., Pongrac, I. M., Cerdá‐Esteban, N., Fontaine, J., Wang, Y., Chen, W., Andrade-Navarro, M. A., & Spagnoli, F. M. (2013) · Genes & Development · doi:10.1101/gad.220244.113 · Cited by 71 · see citing works
Lionetti, V., Bianchi, G., Recchia, F. A., & Ventura, C. (2010) · Heart Failure Reviews · doi:10.1007/s10741-010-9165-7 · Cited by 55 · see citing works
“The molecular patterning triggered by candidate synthetic molecules may be further uncovered at both transcriptional and signaling level by the aid of wideranging transcriptional profiling, using DNA microarrays or the ‘‘Serial Analysis of Gene Expression (SAGE)’’ [50], and proteomic profiling [51].”
BackgroundWoolnough, J. L., Atwood, B. L., Liu, Z., Zhao, R., & Giles, K. E. (2016) · PLoS ONE · doi:10.1371/journal.pone.0157276 · Cited by 52 · see citing works
“This expected result was confirmed with the changes in morphology, loss of TRA-1-60, increase in CXCR4 staining, and general induction of differentiation transcription patterns (Fig 1A–1D).”
MethodInfluentialTrowe, M., Shah, S., Petry, M., Airik, R., Schuster-Gossler, K., Kist, R., & Kispert, A. (2010) · Developmental Biology · doi:10.1016/j.ydbio.2010.03.014 · Cited by 51 · see citing works
Wang, P.-R., McKnight, K. D., Wong, D. J., Rodriguez, R. T., Sugiyama, T., Gu, X.-Y., Ghodasara, A., Qu, K., Chang, H. Y., & Kim, S. K. (2012) · Stem Cells and Development · doi:10.1089/scd.2011.0416 · Cited by 45 · see citing works
“We also identified additional DE markers not described in Hou et al. (2007), including Eppk1 , Gfpt2, Sorcs2, Nedd9 , and Krt19.”
Rhou maintains the epithelial architecture and facilitates differentiation of the foregut endoderm
Loebel, D. A. F., Studdert, J. B., Power, M., Radziewic, T., Jones, V. J., Coultas, L., Jackson, Y., Rao, R. S., Steiner, K. A., Fossat, N., et al. (2011) · Development · doi:10.1242/dev.063867 · Cited by 47 · see citing works
Gadue, P. J., Gouon–Evans, V., Cheng, X., Wandzioch, E., Zaret, K. S., Grompe, M., Streeter, P. R., & Keller, G. M. (2009) · Stem Cells · doi:10.1002/stem.147 · Cited by 40 · see citing works
“25 mouse embryos by cell sorting and analyzed for the expression of genes found either in visceral endoderm (Apoc2, Tdh, Cubn, and Amn [24,25]) or definitive endoderm as well as in other embryonic tissue (Cdx1, Tbx1, Pyy, and Otx2 [24]) and pan-endodermal genes (Foxa2, Foxa3, Sox17).”
Expression of two novel transcripts in the mouse definitive endoderm
Hassan, A. S., Hou, J., Wei, W., & Hoodless, P. A. (2010) · Gene Expression Patterns · doi:10.1016/j.gep.2010.02.001 · Cited by 31 · see citing works
“Three mouse definitive endoderm LongSAGE libraries were compared against more than 200 mouse LongSAGE libraries from various embryonic stages and tissues, successfully identifying several genes as new markers for the definitive endoderm, including Nephrocan (Nepn) and Peptide YY (Pyy) (Hou et al., 2007).”
BackgroundMethodInfluentialSelf-citationSingle-cell patterning and axis characterization in the murine and human definitive endoderm
Li, L., Wang, X., Xu, Z., Wang, Y., Ye, F., Yang, L., Qiu, W., Li, Y., Yu, X., Gu, J., et al. (2020) · Cell Research · doi:10.1038/s41422-020-00426-0 · Cited by 32 · see citing works
Sox17-dependent gene expression and early heart and gut development in Sox17-deficient mouse embryos
Pfister, S., Jones, V. J., Power, M., Truisi, G. L., Khoo, P., Steiner, K. A., Kanai‐Azuma, M., Kanai, Y., Tam, P., & Loebel, D. A. F. (2011) · The International Journal of Developmental Biology · doi:10.1387/ijdb.103158sp · Cited by 30 · see citing works
“Also of note is the reduced expression of Nepn (Table 3, Supplementary Table S1), which is normally expressed in the lateral midgut endoderm at this stage (Hou et al., 2007).”
BackgroundEdwards, D., Stajich, J., & Hansen, D. T. (2009) · Springer eBooks · doi:10.1007/978-0-387-92738-1 · Cited by 28 · see citing works
G-protein Coupled Receptors in Stem Cell Self-Renewal and Differentiation
Kobayashi, N. R., Hawes, S., Crook, J., & Pébay, A. (2010) · Stem Cell Reviews and Reports · doi:10.1007/s12015-010-9167-9 · Cited by 28 · see citing works
“CXCR4 is also present in definitive endoderm cells in mouse gastrulation [67, 68] and has been used to isolate definitive endoderm cells from differentiated hESC [69] although its localisation in the early embryo is not exclusive to endoderm [70].”
BackgroundSmith, R. J., Zhang, H., Hu, S. S., Yung, T. M., Francis, R., Lee, L., Onaitis, M. W., Dirks, P. B., Zang, C., & Kim, T.-H. (2022) · Nature Communications · doi:10.1038/s41467-022-30624-w · Cited by 24 · see citing works
A gastruloid model of the interaction between embryonic and extra-embryonic cell types
Bérenger-Currias, N. M. L. P., Mircea, M., Adegeest, E., van den Berg, P. R., Feliksik, M., Hochane, M., Idema, T., Tans, S. J., & Semrau, S. (2022) · Journal of Tissue Engineering · doi:10.1177/20417314221103042 · Cited by 25 · see citing works
Kahan, B. W., Magliocca, J., Merriam, F., Treff, N., Budde, M. L., Nelson, J., Browning, V., Ziehr, B., & Odorico, J. (2010) · Stem Cell Research · doi:10.1016/j.scr.2010.10.003 · Cited by 27 · see citing works
“…that all nodules expressed high transcript levels (low ΔCt values) of YY, a marker specific for definitive foregut endoderm in the early embryo (Hou et al., 2007), and Pdx1, the first pancreas transcription factor, that were significantly enriched over levels present in the fresh-sorted…”
Single-cell transcriptional landscapes of bovine peri-implantation development
Scatolin, G. N., Ming, H., Wang, Y., et al. (2024) · iScience · doi:10.1016/j.isci.2024.109605 · Cited by 22 · see citing works
Dynamic expression of Thyrotropin‐releasing hormone in the mouse definitive endoderm
McKnight, K. D., Hou, J., & Hoodless, P. A. (2007) · Developmental Dynamics · doi:10.1002/dvdy.21313 · Cited by 22 · see citing works
“A description of the Trh in situ probe can be found in Hou et al. (2007).”
BackgroundMethodInfluentialSelf-citationFormation of the Murine Endoderm
Tremblay, K. D. (2010) · Progress in Molecular Biology and Translational Science · doi:10.1016/b978-0-12-381280-3.00001-4 · Cited by 21 · see citing works
Extraembryonic endoderm cells induce neuroepithelial tissue in gastruloidsPreprint
Bérenger-Currias, N. M. L. P., Mircea, M., Adegeest, E., van den Berg, P. R., Feliksik, M., Hochane, M., Idema, T., Tans, S. J., & Semrau, S. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.02.13.947655 · Cited by 21 · see citing works
Wei, W., Hou, J., Alder, O., Ye, X., Lee, S., Cullum, R., Chu, A., Zhao, Y., Warner, S. M., Knight, D. A., et al. (2013) · Hepatology · doi:10.1002/hep.26252 · Cited by 19 · see citing works
“Foregut endoderm was isolated by mechanical dissociation from embryos at somite stage 8-12.(12) Since nearly 70% cells of E14.”
Self-citationSmad1 signaling restricts hematopoietic potential after promoting hemangioblast commitment
Cook, B. D., Liu, S. X., & Evans, T. (2011) · Blood · doi:10.1182/blood-2010-10-312389 · Cited by 19 · see citing works
Foxh1 and Foxa2 are not required for formation of the midgut and hindgut definitive endoderm
McKnight, K. D., Hou, J., & Hoodless, P. A. (2009) · Developmental Biology · doi:10.1016/j.ydbio.2009.10.040 · Cited by 18 · see citing works
“RNA extraction, cDNA synthesis, and RT–PCR were performed as described (Hou et al., 2007).”
BackgroundMethodInfluentialSelf-citationChuykin, I. A., Schulz, H., Guan, K., & Bäder, M. (2012) · Journal of Cell Science · doi:10.1242/jcs.110239 · Cited by 17 · see citing works
“…2.7 22.2 21.5 Sherwood et al., 2007 13 Krt19, keratin 19 1.4 21.5 21.2 Brown et al., 2010 13 Lgals2, lectin, galactose binding, soluble 2 2.1 21.9 1 Hou et al., 2007 13 Llgl2, lethal giant larvae homolog 2 1.4 21.6 21.5 Tight junctions; Chalmers et al., 2005 13 Npas2, neuronal PAS domain protein 2…”
BackgroundInfluentialMafB is required for development of the hindbrain choroid plexus
Koshida, R., Oishi, H., Hamada, M., Takei, Y., & Takahashi, S. (2016) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2016.12.150 · Cited by 14 · see citing works
Grapin-Botton, A. (2008) · StemBook · doi:10.3824/stembook.1.30.1 · Cited by 16 · see citing works
Visualizing the Structure of RNA-seq Expression Data using Grade of Membership ModelsPreprint
Dey, K. K., Hsiao, C. J., & Stephens, M. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/051631 · Cited by 12 · see citing works
Trinh, L. T., Osipovich, A. B., Liu, B., Shrestha, S., Cartailler, J., Wright, C. V. E., & Magnuson, M. A. (2023) · Stem Cells · doi:10.1093/stmcls/sxad030 · Cited by 8 · see citing works
Kearns, N. A., Lobo, M., Genga, R. M. J., Abramowitz, R. G., Parsi, K. M., Min, J., Kernfeld, E. M., Huey, J. D., Kady, J., Hennessy, E., et al. (2023) · Developmental Cell · doi:10.1016/j.devcel.2023.08.024 · Cited by 8 · see citing works
A Transcriptome Landscape of Mouse Embryogenesis
Fossat, N., Pfister, S., & Tam, P. (2007) · Developmental Cell · doi:10.1016/j.devcel.2007.11.011 · Cited by 7 · see citing works
“More value may be added to this resource if the whole-embryo transcriptomes were complemented by germ layer- and tissue lineage-specific transcriptomes of embryos at comparable developmental stages (Harrison et al., 1995; Gu et al., 2004; Sherwood et al., 2007; Hou et al., 2007).”
BackgroundA regulatory network controls nephrocan expression and midgut patterning
Hou, J., Wei, W., Saund, R. S., Xiang, P., Cunningham, T. J., Yi, Y., Alder, O., Lu, D. Y. D., Savory, J. G. A., Krentz, N. A. J., et al. (2014) · Development · doi:10.1242/dev.108274 · Cited by 7 · see citing works
“5, Nepn is expressed caudally from the stomach throughout dorsal pancreas and intestine (Hou et al., 2007), encompassing the Pdx1 expression domain (supplementary material Fig.”
BackgroundMethodInfluentialSelf-citationCharting the emergent organotypic landscape of the mammalian gut endoderm at single-cell resolutionPreprint
Nowotschin, S., Setty, M. N., Kuo, Y.-Y., Lui, V. C. H., Garg, V., Sharma, R., Simon, C. S., Saiz, N., Gardner, R., Boutet, S. C., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/471078 · Cited by 7 · see citing works
Self-citationImprinted expression in cystic embryoid bodies shows an embryonic and not an extra-embryonic pattern
Kuliński, T. M., Casari, M. R. T., Guenzl, P. M., Wenzel, D., Andergassen, D., Hladik, A., Datlinger, P., Farlik, M., Theussl, H., Penninger, J. M., et al. (2015) · Developmental Biology · doi:10.1016/j.ydbio.2015.04.010 · Cited by 6 · see citing works
Sequence Based Gene Expression Analysis
Matukumalli, L. K., & Schroeder, S. (2009) · Springer eBooks · doi:10.1007/978-0-387-92738-1_9 · Cited by 4 · see citing works
Wlizla, M., & Zorn, A. M. (2014) · Elsevier eBooks · doi:10.1016/b978-0-12-405945-0.00013-2 · Cited by 5 · see citing works
Joseph, D. B., Chandrashekar, A. S., Abler, L. L., Chu, L., Thomson, J. A., & Vezina, C. M. (2019) · Developmental Biology · doi:10.1016/j.ydbio.2019.01.011 · Cited by 2 · see citing works
“In contrast, glandular epithelia in cDnmt1KO grafts are devoid of FOXA1+ cells and instead harbor PAX2+ cells, consistent with seminal vesicle identity (Fig.”
BackgroundInfluentialThe Assessment of CDX1, IHH, SHH, GATA4, FOXA2, FOXF1 in Congenital Intra-Abdominal Adhesions
Pope, H., Pilmane, M., Junga, A., et al. (2024) · Acta medica Lituanica · doi:10.15388/amed.2024.31.1.15 · Cited by 1 · see citing works
“Additionally, the FOXA families of transcription factors could collaborate to control gene expression across the whole genome in the intestinal epithelium [18].”
BackgroundJohannesson, M., Semb, H., Serup, P., & Hansson, M. (2012) · Journal of Stem Cell Research & Therapy · doi:10.4172/2157-7633.1000128 · Cited by 1 · see citing works
“Furthermore, PYY, a novel endoderm marker [39], is upregulated in mDE, whereas it is downregulated in hDE as well as in control cells (Figure 3C).”
BackgroundDigital Graphical Resources and Developmental Anatomy in the Mouse
Richardson, L., & Armit, C. J. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-800043-4.00024-5 · Cited by 1 · see citing works
Transcriptional Profiling of Pancreatic Progenitor Cells
Potter, L. A. (2011)
Garside, V. C. (2015) · cIRcle (University of British Columbia) · doi:10.14288/1.0220645
“ISH was performed as described previously(107).”
Faculty Opinions recommendation of Molecular recording of mammalian embryogenesis.
Papaioannou, V. E. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.735751521.793561896
SOX9 modulates the expression of key transcription factors required for heart valve development
Garside, V. C., Cullum, R., Alder, O., Lu, D. Y., Vander Werff, R., Bilenky, M., Zhao, Y., Jones, S. J. M., Marra, M. A., Underhill, T. M., et al. (2015) · Development · doi:10.1242/dev.125252 · Cited by 65 · see citing works
“In situ hybridization was performed as described (Hou et al., 2007).”
MethodSelf-citation
- Authors
- Hou, J., Charters, A. M., Lee, S. C., Zhao, Y., Wu, M. K., Jones, S. J., Marra, M. A., & Hoodless, P. A.
- Affiliations
- BC Cancer Agency (CA)
- Corresponding author
- Hoodless, Pamela A
- Venue
- BMC Developmental Biology
- Published
- 2007-08-02
- Volume
- 7
- Issue
- 1
- Pages
- 92-92
- ISSN
- 1471-213X (ISSN-L)
- PMC
- PMC1950885
- OpenAlex
- W2110806916
- Cited by
- 56
- References
- 55
- Citations by year
- 2024: 2 · 2023: 2 · 2022: 2 · 2020: 3 · 2019: 4 · 2018: 2 · 2017: 2 · 2016: 3 · 2015: 4 · 2014: 3 · 2013: 2 · 2012: 3
- FWCI
- 2.15
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by
- Locations
- BMC Developmental Biology (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (submittedVersion, cc-by)
- PubMed Central (submittedVersion, cc-by)
- Funders
- Genome Canada
- Canada's Michael Smith Genome Sciences Centre
- Michael Smith Health Research BC
- Terry Fox Foundation
- National Cancer Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Renal and related cancers
- Keywords
- definitive endoderm, endoderm differentiation, foregut, hindgut, peptide YY, endoderm patterning, mouse embryo, gene expression profiling, organ regeneration
- MeSH terms
- Animals, Endoderm, Female, Mice, Inbred C57BL, Time Factors, In Situ Hybridization, Gene Expression Regulation, Developmental, Reverse Transcriptase Polymerase Chain Reaction, Gene Expression Profiling, Mice
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-23.
Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-23.
Cited sources are checked by gpt-6-sol.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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