Toward the human cellular microRNAome

In the paper

“In this role, they control essential cell processes in health and disease (Ambros 2004; Mendell and Olson 2012).”

What the sources say

• ?Not checked — no full text of the sourcecites Ambros 2004 source
• Supported

  The Introduction describes miRNA functions in normal mammalian physiology and disease, including their influence on how developed tissues respond to stress. The MicroRNAs in Cancer section identifies cell proliferation and apoptosis as processes they regulate. Together, these passages support the broad paraphrase. (LLM, conf=0.88)

  cites Mendell and Olson 2012 source

In the paper

“Superenhancers are dense genomic regions of transcription factor binding sites that have a multiplicative effect on increasing adjacent gene expression (Whyte et al. 2013; Suzuki et al. 2017).”

What the sources say

• Partly supported

  The Results sections on large genomic domains and functional attributes describe super-enhancers as clusters of transcription-factor-bound enhancers associated with higher expression of target genes. They report 3.8-fold higher luciferase activity for constituent segments than for typical enhancer segments, but do not establish a multiplicative effect on adjacent gene expression. The section on key ESC identity genes also notes that enhancer targets can be distant, not necessarily adjacent. (LLM, conf=0.86)

  cites Whyte et al. 2013 sourceExperimental — accuracy not yet measured
• Partly supported

  The Introduction describes super-enhancers as regions with high densities of transcription factors that are closely associated with genes. The Results (CRISPR/Cas9 functional genomics of miRNA super-enhancers) find cooperative, rather than additive, effects of their constituents on specific miRNAs. The paper does not establish a general multiplicative effect on the expression of adjacent genes. (LLM, conf=0.85)

  cites Suzuki et al. 2017 sourceExperimental — accuracy not yet measured

In the paper

“This included miR-199b-3p (+1 shift), miR-181c-3p (+1 shift), and miR-302a-5p (+3 shift), all of which had highly abundant reads containing a completely different seed sequence than the one currently assigned, with strong implications for the targeting of genes (Tan et al. 2014).”

What the sources say

• Partly supported

  The Results section (‘MiRNAs from the same precursor have different 5′ and 3′ lengths’; page unavailable) reports a common 5′ isomiR of miR-302a and substantial differences in its predicted targets, supporting the general targeting implication. Our copy does not identify it as miR-302a-5p with a +3 shift, or report the claimed abundant reads and seed changes for miR-199b-3p and miR-181c-3p (searched by those names and shift terms). (LLM, conf=0.84)

  cites Tan et al. 2014 sourceExperimental — accuracy not yet measured

In the paper

“DICER1 knockouts are known to significantly repress 3p driver microRNA levels while allowing for longer 5p microRNAs that are loaded into Ago and trimmed back from the 3p end (Hill et al. 2009).”

What the sources say

• ?Could not verify

  The section “Germline DICER1 Mutations in Familial Pleuropulmonary Blastoma” identifies DICER1 as involved in generating small RNAs and describes loss-of-function mutations, but does not address 3p versus 5p microRNA levels, Ago loading, or trimming. Searches for those strand-specific processing details found no passage supporting the attributed claim; page numbers are unavailable in our copy. (LLM, conf=0.76)

  cites Hill et al. 2009 sourceExperimental — accuracy not yet measured

In the paper

“This number of new microRNAs seems impossibly high and likely mostly false positives and/or nonfunctional transcripts (Mullokandov et al. 2012).”

What the sources say

• Partly supported

  The Discussion (page unavailable in our copy) reports that almost 60% of miRNAs detected in the cells studied had no discernible suppressive activity, supporting concern that many detected miRNAs may have little biological activity. It does not assess the number of *new* miRNAs or conclude that most are false-positive identifications. The Results’ reference to possible false positives concerns a small set of sensor results, not the miRNA transcripts themselves. (LLM, conf=0.87)

  cites Mullokandov et al. 2012 sourceExperimental — accuracy not yet measured

In the paper

“Our data matched certain “ground truths” about specific microRNA expression in certain cell types, including miR-192 in epithelial cells, miR-126 in endothelial cells and platelets, and miR-9 in brain (McCall et al. 2011a; Haider et al. 2014; Kent et al. 2014).”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites McCall et al. 2011a
• Partly supported

  The Results section, “MicroRNA biomarker plausibility across studies” (page unavailable), states that miR-126 is highly expressed in endothelial cells. Our copy does not establish the other listed pairings—miR-126 in platelets, miR-192 in epithelial cells, or miR-9 in brain—so it supports only part of what this citation is offered for. The citing authors’ statement that their own data matched these patterns is their conclusion, not a finding attributed to Haider et al. (LLM, conf=0.86)

  cites Haider et al. 2014 sourceExperimental — accuracy not yet measured
• Partly supported

  The Introduction section “miR-126—an endothelial miRNA” identifies miR-126 as highly expressed in endothelial cells. The passages from our copy do not establish the other cited associations: miR-126 in platelets, miR-192 in epithelial cells, or miR-9 in brain. Page numbers were not available in our copy. (LLM, conf=0.87)

  cites Kent et al. 2014 sourceExperimental — accuracy not yet measured

In the paper

“The PhyloP conservation data (Fig. 3B) show that, beyond the most ideal microRNAs identified in miRGeneDB, there is a lack of genetic conservation, with overlap in a large segment of miRBase microRNAs and the novel microRNAs reported here and in a prior large study (Londin et al. 2015).”

What the sources say

• Supported

  Split into 2 atoms — 2 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

  cites Londin et al. 2015 source

In the paper

“As an example of potentially interesting novel microRNAs, JHU_ID_23828-3p was validated by PCR and is located in intron 8 of the EGFL7 gene, approximately 900 bp from mir-126 and within the same pri-miRNA transcript (Fig. 3D,E; Chang et al. 2015).”

What the sources say

• ?Could not verify

  The Results passages describe PCR validation of other pri-miRNA transcripts, but do not identify JHU_ID_23828-3p. Searches for that identifier, EGFL7, miR-126, and the approximately 900-bp distance found no passage addressing the claimed location or shared transcript (page numbers unavailable). (LLM, conf=0.76)

  cites Chang et al. 2015 sourceExperimental — accuracy not yet measured

In the paper

“As well, another recent paper investigating microRNA RNA-seq across multiple laboratories found relative quantification to be “remarkably accurate and reproducible” (Giraldez et al. 2017), consistent with our work.”

What the sources say

• Supported

  The Accuracy and cross-protocol concordance section reports that all evaluated protocols were remarkably accurate at relative quantification of synthetic miRNAs. The Discussion reports that relative-quantification results were strongly correlated across institutions, even when they used different protocols. Together, these passages support the citing sentence’s characterization. (LLM, conf=0.94)

  cites Giraldez et al. 2017 source

In the paper

“The remaining miRBase microRNAs had modest conservation and were similarly distributed to both the putative novel microRNAs reported here and the 3707 novel microRNAs reported as TJU microRNAs (Fig. 3B; Londin et al. 2015).”

What the sources say

• Supported

  The citation identifies the comparison set as Londin et al.’s 3,707 novel TJU microRNAs. Table 1 lists 3,707 novel miRNAs, and Fig. 6 uses TJU identifiers for examples. The statement about their similar conservation distribution is presented as the citing paper’s Fig. 3B finding, not as a finding attributed to Londin et al. (LLM, conf=0.91)

  cites Londin et al. 2015 source

In the paper

“miR-451a was abundantly present in 20 of 26 tissues but is from only one cell class (red blood cells).”

In the paper

“Strong clustering by biological group was observed for all samples, overcoming most technical concerns.”

In the paper

“and miR-150-5p, abundant in lymphocytes, was present in 11 tissues.”

In the paper

“We found the average z-score was right-shifted to 1.07 (indicating less similarity) for a subset of the 21,338 loci, while for the 495 highest confidence loci it was 0.90, indicating more consistency with miRBase microRNAs (Supplemental Fig. S8A,B; Backes et al. 2016).”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites Backes et al. 2016

In the paper

“Eight primary T lymphocyte samples and 14 T lymphocyte malignancy samples also revealed moderate to strong correlation but with separate primary and cancer-derived cell clustering (Supplemental Fig. S6C).”

In the paper

“Thirty-four were also adjacent to a known microRNA.”

In the paper

“but could vary widely between both primary and cancer/immortalized cells as a reflection of either biological differences or technical factors (Fig. 4C,D).”

In the paper

“Certain aspects of the data also helped with normalization, including 98% of sequencing runs being performed on an Illumina Genome Analyzer or HiSeq system and >74% of libraries being generated using an Illumina sequencing kit.”

In the paper

“and 15 were orthologous to a different species’ microRNA (primarily primate) (Supplemental Tables S8, S9).”

In the paper

“Additionally, while miR-126 is highly conserved throughout chordates, JHU_ID_ 23828 is only conserved among primates (Fig. 3G).”

In the paper

“A test for the difference in proportions between wild-type and DICER1 knockout samples revealed the proportion in wild-type dropped from 0.151 to 0.047 in the DICER1 samples, representing a significant decrease (P < 2.2−16).”

In the paper

“The most abundant isomiR was widely variable between cells and often incongruent with the expected sequence.”

In the paper

“This was quite variable and rarely >90%, suggesting methods that fail to acquire isomiRs significantly underestimate the presence of microRNAs in a variable fashion (Mestdagh et al. 2014).”

What the sources say

• ?Not checked — no full text of the sourcecites Mestdagh et al. 2014 source

In the paper

“An analysis of 12 primary and three immortalized fibroblast cell line microRNA signatures identified overall strong correlation (RUV-corrected, log2-normalized, pairwise R > 0.80–0.99), with the immortalized lines being slightly less correlated (Supplemental Fig. S6A).”

In the paper

“There were more microRNAs that differed between primary and cancer-derived cells (Supplemental Fig. S6D), including miR-150-5p which was 64-fold higher in the primary T cells, as has been reported (He et al. 2014).”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites He et al. 2014

In the paper

“Using a number of validation steps, we reduced this number down to 495 highest confidence miRNAs, which is roughly one new microRNA per sample evaluated.”

In the paper

“Our data also demonstrate general consistencies, but not without some concerning differences, between primary cells and immortalized/cancer cell lines.”

In the paper

“MicroRNAs are an established class of small regulatory RNAs that, within the RISC complex, bind mRNAs and repress protein production (Valencia-Sanchez et al. 2006).”

What the sources say

• ?Not checked — no full text of the sourcecites Valencia-Sanchez et al. 2006 source

In the paper

“Because all tissues are composed of multiple, unique cell types, it is essential to understand from which cell the microRNA signal is obtained.”

In the paper

“The most thorough of these microRNA localization projects performed small RNA library sequencing (RNA-seq) on over 250 libraries from 26 organ systems. However, this nascent effort sequenced only ∼1200 reads per library (Landgraf et al. 2007).”

What the sources say

• ?Not checked — no full text of the sourcecites Landgraf et al. 2007 source

In the paper

“IsomiRs are related sequences with mostly 5′ and 3′ nucleotide modifications that collectively make up the totality of a given microRNA (Neilsen et al. 2012).”

What the sources say

• ?Not checked — no full text of the sourcecites Neilsen et al. 2012 source

In the paper

“MicroRNA expression has been predominantly characterized in tissues, with no comprehensive cellular studies.”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites Lagos-Quintana et al. 2002
• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites Barad et al. 2004
• ?Not checked — no full text of the sourcecites Liu et al. 2004 source

In the paper

“Due to the inexact cutting of DICER1 and DROSHA and nucleotide additions/modifications, a collection of mostly similar sequences (with most diversity on the 3′ end) make up the isomiR family of a microRNA (Morin et al. 2008; Neilsen et al. 2012).”

What the sources say

• ?Not checked — no full text of the sourcecites Morin et al. 2008 source
• ?Not checked — no full text of the sourcecites Neilsen et al. 2012 source

In the paper

“This technical driver of isomiR type will challenge those groups working toward a standard isomiR nomenclature.”

In the paper

“Either this suggests that much of miRBase is inaccurate or that, while conservation provides evidence for a microRNA to be authentic, it is not a requirement.”

In the paper

“Altogether, these data demonstrate the importance and feasibility of solving for the cellular content of tissues to better understand the composition of the analyzed tissue.”

In the paper

“The cell line H1264, which is a lung carcinoma cell line, has been reported as being cross-contaminated with H157, which is a separate human lung carcinoma cell line (ICLAC.org).”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites ICLAC.org

In the paper

“A consensus adapter sequence could not be determined for 45 samples, and the sequences were trimmed to 21 bp using the CutAdapt –u command (e.g., $ cutadapt <FILE>.fastq -u -14 -o <FILE>_cut.fastq for a 35-bp read length). These samples were excluded from isomiR analyses.”

In the paper

“The microRNAs designated as .5p/.3p were named as such, as each of these microRNA loci was identified in more than one sample, with two different pre-miRNA structures designating the sequence to the 5p or 3p arm. There were no “passenger” reads to distinguish the correct structure, so either location remains plausible.”

In the paper

“We verified the ability of the five estimated latent factors to capture and adjust for batch effects by examining biological clusters comprised of multiple experiments. The RUV-normalized data clustered by biological cluster and not experimental batch.”

In the paper

“These microRNA expression patterns from 42 cell types are the first step toward a complete understanding of microRNA expression across all cells and establishing a human cell atlas.”

In the paper

“Finally, we are only moving toward a complete cellular microRNAome, as many cell types (hepatocytes, neutrophils, pneumocytes) were not available for this study.”

In the paper

“Of note, distinguishing linker sequences in this data set was not necessarily feasible, and 54% of reads were adjusted by CutAdapt to only 21- or 22-bp lengths using the command described above, likely resulting in an overidentification of Ago-bound microRNAs.”

In the paper

“We caution that the activity of these superenhancers on adjacent genes and microRNAs is generally unknown, and these reported correlations are not proof of activity of the superenhancer on the microRNA.”

In the paper

“The 159 samples that had less than 1 million microRNA reads were excluded and are not represented in the data.”

In the paper

“This type of expression discretization has been shown to greatly reduce batch effects when combining data across studies and technologies (McCall et al. 2011b, 2014).”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites McCall et al. 2011b, 2014

In the paper

“We also removed five tissue samples (SRR1635903-8) with extreme technical skewing of microRNA reads (>60% of all reads were microRNA let-7b-5p).”