The DOI matches its Crossref record; 57 of the 58 references it cites were found in a registry or an index.
Deep sequencing of the zebrafish transcriptome response to mycobacterium infection
Open accessAbstract
Novel high-throughput deep sequencing technology has dramatically changed the way that the functional complexity of transcriptomes can be studied. Here we report on the first use of this technology to gain insight into the wide range of transcriptional responses that are associated with an infectious disease process. Using Solexa/Illumina's digital gene expression (DGE) system, a tag-based transcriptome sequencing method, we investigated mycobacterium-induced transcriptome changes in a model vertebrate species, the zebrafish. We obtained a sequencing depth of over 5 million tags per sample with strong correlation between replicates. Tag mapping indicated that healthy and infected adult zebrafish express over 70% of all genes represented in transcript databases. Comparison of the data with a previous multi-platform microarray analysis showed that both types of technologies identified regulation of similar functional groups of genes. However, the unbiased nature of DGE analysis provided insights that microarray analysis could not have achieved. In particular, we show that DGE data sets are instrumental for verification of predicted gene models and allowed us to detect mycobacterium-regulated switching between different transcript isoforms. Moreover, genomic mapping of infection-induced DGE tags revealed novel transcript forms for which any previous EST-based evidence of expression was lacking. In conclusion, our deep sequencing analysis revealed in depth the high degree of transcriptional complexity of the host response to mycobacterial infection and resulted in the discovery and validation of new gene products with induced expression in infected individuals.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
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?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Over the last two years, with the further confirmation that the relatively short reads can be effectively assembled [15], especially with the great advantage of paired-end sequencing [54], the Illumina transcriptome or whole genome de novo sequencing and assembly have been successfully used for model [12,16,55-58]and non-model organisms [25-27,59].”
From De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas) (2010) · cites this paper as [55]
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696
RNA-Seq: a revolutionary tool for transcriptomics
Wang, Z., Gerstein, M., & Snyder, M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2484 · Cited by 13,174
Alternative isoform regulation in human tissue transcriptomes
Wang, E. T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S. F., Schroth, G. P., & Burge, C. B. (2008) · Nature · doi:10.1038/nature07509 · Cited by 5,181
Pan, Q., Shai, O., Lee, L. J., Frey, B. J., & Blencowe, B. J. (2008) · Nature Genetics · doi:10.1038/ng.259 · Cited by 3,951
Serial Analysis of Gene Expression
Velculescu, V. E., Zhang, L., Vogelstein, B., & Kinzler, K. W. (1995) · Science · doi:10.1126/science.270.5235.484 · Cited by 3,713
The Transcriptional Landscape of the Mammalian Genome
Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C. A., et al. (2005) · Science · doi:10.1126/science.1112014 · Cited by 3,492
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
Marioni, J. C., Mason, C. E., Mane, S. M., Stephens, M., & Gilad, Y. (2008) · Genome Research · doi:10.1101/gr.079558.108 · Cited by 2,771
The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing
Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M., & Snyder, M. (2008) · Science · doi:10.1126/science.1158441 · Cited by 2,479
Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis
Lister, R., O’Malley, R. C., Tonti‐Filippini, J., Gregory, B. D., Berry, C. C., Millar, A. H., & Ecker, J. R. (2008) · Cell · doi:10.1016/j.cell.2008.03.029 · Cited by 2,424
Antisense Transcription in the Mammalian Transcriptome
Katayama, S., Tomaru, Y., Kasukawa, T., Waki, K., Nakanishi, M., Nakamura, M., Nishida, H., Yap, C.-S., Suzuki, M., Kawai, J., et al. (2005) · Science · doi:10.1126/science.1112009 · Cited by 1,699
Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays.
Brenner, S., Johnson, M., Bridgham, J., Golda, G., Lloyd, D. H., Johnson, D., Luo, S., McCurdy, S., Foy, M., Ewan, M., et al. (2000) · Nature Biotechnology · doi:10.1038/76469 · Cited by 1,360
Sultan, M., Schulz, M. H., Richard, H., Magen, A., Klingenhoff, A., Scherf, M., Seifert, M., Borodina, T., Soldatov, A., Parkhomchuk, D., et al. (2008) · Science · doi:10.1126/science.1160342 · Cited by 1,293
Applications of next-generation sequencing technologies in functional genomics
Morozova, O., & Marra, M. A. (2008) · Genomics · doi:10.1016/j.ygeno.2008.07.001 · Cited by 1,222
Stem cell transcriptome profiling via massive-scale mRNA sequencing
Cloonan, N., Forrest, A. R. R., Kolle, G., Gardiner, B. B. A., Faulkner, G. J., Brown, M. K., Taylor, D. F., Steptoe, A. L., Wani, S., Bethel, G., et al. (2008) · Nature Methods · doi:10.1038/nmeth.1223 · Cited by 1,035
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution
Wilhelm, B. T., Marguerat, S., Watt, S. B., Schubert, F., Wood, V., Goodhead, I., Penkett, C. J., Rogers, J., & Bähler, J. (2008) · Nature · doi:10.1038/nature07002 · Cited by 974
Multiple-laboratory comparison of microarray platforms
Irizarry, R. A., Warren, D., Spencer, F., Kim, I. F., Biswal, S., Frank, B. C., Gabrielson, E., Garcia, J. G. N., Geoghegan, J., Germino, G., et al. (2005) · Nature Methods · doi:10.1038/nmeth756 · Cited by 862
't Hoen, P. A. C., Ariyurek, Y., Thygesen, H. H., Vreugdenhil, E., Vossen, R. H. A. M., de Menezes, R. X., Boer, J. M., van Ommen, G.-J. B., & den Dunnen, J. T. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn705 · Cited by 742
Widespread occurrence of antisense transcription in the human genome
Yelin, R., Dahary, D., Sorek, R., Levanon, E. Y., Goldstein, O., Shoshan, A., Diber, A., Biton, S., Tamir, Y., Khosravi, R., et al. (2003) · Nature Biotechnology · doi:10.1038/nbt808 · Cited by 646
Mycobacterium tuberculosis and the Macrophage: Maintaining a Balance
Pieters, J. (2008) · Cell Host & Microbe · doi:10.1016/j.chom.2008.05.006 · Cited by 516
RNA-Seq—quantitative measurement of expression through massively parallel RNA-sequencing
Wilhelm, B. T., & Landry, J. (2009) · Methods · doi:10.1016/j.ymeth.2009.03.016 · Cited by 500
He, Z., & Bateman, A. (2003) · Journal of Molecular Medicine · doi:10.1007/s00109-003-0474-3 · Cited by 477
Morin, R. D., Bainbridge, M. N., Fejes, A. P., Hirst, M., Krzywinski, M. I., Pugh, T. J., McDonald, H., Varhol, R., Jones, S. J. M., & Marra, M. A. (2008) · BioTechniques · doi:10.2144/000112900 · Cited by 433
SAGEmap: A Public Gene Expression ResourcePreprint
Lash, A., Tolstoshev, C. M., Wagner, L., Schuler, G. D., Strausberg, R. L., Riggins, G. J., & Altschul, S. F. (2000) · Genome Research · doi:10.1101/gr.10.7.1051 · Cited by 418
Swaim, L. E., Connolly, L. E., Volkman, H. E., Humbert, O., Born, D. E., & Ramakrishnan, L. (2006) · Infection and Immunity · doi:10.1128/iai.00887-06 · Cited by 339
The beginning of the end for microarrays?
Shendure, J. (2008) · Nature Methods · doi:10.1038/nmeth0708-585 · Cited by 331
Molecular basis for Rac2 regulation of phagocyte NADPH oxidase
Diebold, B. A., & Bokoch, G. M. (2001) · Nature Immunology · doi:10.1038/85259 · Cited by 318
Survival of Mycobacteria in Macrophages Is Mediated by Coronin 1-Dependent Activation of Calcineurin
Jayachandran, R., Sundaramurthy, V., Combaluzier, B., Mueller, P., Korf, H., Huygen, K., Miyazaki, T., Albrecht, I., Massner, J., & Pieters, J. (2007) · Cell · doi:10.1016/j.cell.2007.04.043 · Cited by 310
New functions for an iron storage protein: The role of ferritin in immunity and autoimmunity
Recalcati, S., Invernizzi, P., Arosio, P., & Cairo, G. (2008) · Journal of Autoimmunity · doi:10.1016/j.jaut.2007.11.003 · Cited by 259
Wellen, K. E., Fucho, R., Gregor, M. F., Furuhashi, M., Morgan, C., Lindstad, T., Vaillancourt, E., Gorgun, C. Z., Saatcioglu, F., & Hotamisligil, G. S. (2007) · Cell · doi:10.1016/j.cell.2007.02.049 · Cited by 222
Stockhammer, O. W., Zakrzewska, A., Hegedüs, Z., Spaink, H. P., & Meijer, A. H. (2009) · The Journal of Immunology · doi:10.4049/jimmunol.0900082 · Cited by 220
Self-citationPolony Multiplex Analysis of Gene Expression (PMAGE) in Mouse Hypertrophic Cardiomyopathy
Kim, J. B., Porreca, G. J., Song, L., Greenway, S. C., Gorham, J., Church, G. M., Seidman, C. E., & Seidman, J. G. (2007) · Science · doi:10.1126/science.1137325 · Cited by 202
Tag-based approaches for transcriptome research and genome annotation
Harbers, M., & Carninci, P. (2005) · Nature Methods · doi:10.1038/nmeth768 · Cited by 193
Ebralidze, A. K., Guibal, F. C., Steidl, U. G., Zhang, P., Lee, S., Bartholdy, B., Alberich-Jordà, M., Petkova, V., Rosenbauer, F., Huang, G., et al. (2008) · Genes & Development · doi:10.1101/gad.1654808 · Cited by 183
The Prevalence and Evolution of Anemia Associated with Tuberculosis
Lee, S. W., Kang, Y. A., Yoon, Y.-S., Um, S., Lee, S., Yoo, C., Kim, Y. W., Han, S. K., Shim, Y., & Yim, J. (2006) · Journal of Korean Medical Science · doi:10.3346/jkms.2006.21.6.1028 · Cited by 180
Meijer, A. H., Verbeek, F. J., Vidal, E. S., Corredor-Adámez, M., Bussman, J., van der Sar, A. M., Otto, G., Geisler, R., & Spaink, H. P. (2005) · Molecular Immunology · doi:10.1016/j.molimm.2004.11.014 · Cited by 142
Self-citationKorkmaz, C. G., Korkmaz, K., Kurys, P., Elbi, C., Wang, L., Klokk, T. I., Hammarström, C. L., Trøen, G., Svindland, A., Hager, G. L., et al. (2005) · Oncogene · doi:10.1038/sj.onc.1208677 · Cited by 139
Transcriptome content and dynamics at single-nucleotide resolution
Cloonan, N., & Grimmond, S. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-234 · Cited by 134
van der Sar, A. M., Abdallah, A. M., Sparrius, M., Reinders, E., Vandenbroucke‐Grauls, C. M. J. E., & Bitter, W. (2004) · Infection and Immunity · doi:10.1128/iai.72.11.6306-6312.2004 · Cited by 127
Pore-forming toxins and cellular non-immune defenses (CNIDs)
Aroian, R., & van der Goot, F. (2007) · Current Opinion in Microbiology · doi:10.1016/j.mib.2006.12.008 · Cited by 119
van der Sar, A. M., Spaink, H. P., Zakrzewska, A., Bitter, W., & Meijer, A. H. (2009) · Molecular Immunology · doi:10.1016/j.molimm.2009.03.024 · Cited by 116
Self-citationAntisense transcription: A critical look in both directions
Beiter, T., Reich, E., Williams, R. W., & Simon, P. D. (2008) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-008-8381-y · Cited by 116
Characterizing the mouse ES cell transcriptome with Illumina sequencing
Rosenkranz, R., Borodina, T., Lehrach, H., & Himmelbauer, H. (2008) · Genomics · doi:10.1016/j.ygeno.2008.05.011 · Cited by 106
Moldes, M., Lasnier, F., Gauthereau, X., Klein, C., Pairault, J., Fève, B., & Chambaut‐Guérin, A. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m105726200 · Cited by 102
Insights into early mycobacterial pathogenesis from the zebrafish
Lesley, R., & Ramakrishnan, L. (2008) · Current Opinion in Microbiology · doi:10.1016/j.mib.2008.05.013 · Cited by 88
Stanniocalcin-1, an inhibitor of macrophage chemotaxis and chemokinesis
Kanellis, J., Bick, R. J., García, G., Truong, L. D., Tsao, C. C., Etemadmoghadam, D., Poindexter, B. J., Feng, L., Johnson, R. J., & Sheikh‐Hamad, D. (2004) · American Journal of Physiology-Renal Physiology · doi:10.1152/ajprenal.00138.2003 · Cited by 81
Reduced hGC-1 Protein Expression Is Associated with Malignant Progression of Colon Carcinoma
Liu, W., Liu, Y., Zhu, J., Wright, E., Ding, I., & Rodgers, G. P. (2008) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-07-4125 · Cited by 77
Chakraborty, A. R., Brooks, H. L., Zhang, P., Smith, W. C., McReynolds, M. R., Hoying, J. B., Bick, R. J., Truong, L. D., Poindexter, B. J., Lan, H. Y., et al. (2006) · American Journal of Physiology-Renal Physiology · doi:10.1152/ajprenal.00219.2006 · Cited by 60
Can subtle changes in gene expression be consistently detected with different microarray platforms?
Pedotti, P., Hoen, P. A. C. ’., Vreugdenhil, E., Schenk, G. J., Vossen, R. H. A. M., Ariyürek, Y., de Hollander, M., Kuiper, R., van Ommen, G. B., den Dunnen, J. T., et al. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-124 · Cited by 56
The regulation of OLFM4 expression in myeloid precursor cells relies on NF‐κB transcription factor
Chin, K., Aerbajinai, W., Zhu, J., Drew, L. R., Chen, L., Liu, W., & Rodgers, G. P. (2008) · British Journal of Haematology · doi:10.1111/j.1365-2141.2008.07368.x · Cited by 51
Martı́n, M., del Valle-Mendoza, J., Saborit-Villarroya, I., & Engel, P. (2005) · The Journal of Immunology · doi:10.4049/jimmunol.174.10.5977 · Cited by 47
High-Resolution Analysis of the 5′-End Transcriptome Using a Next Generation DNA Sequencer
Hashimoto, S., Qü, W., Ahsan, B., Ogoshi, K., Sasaki, A., Nakatani, Y., Lee, Y., Ogawa, M., Ametani, A., Suzuki, Y., et al. (2008) · PLoS ONE · doi:10.1371/journal.pone.0004108 · Cited by 46
Pettersson, M., Bessonova, M., Gu, H. F., Groop, L. C., & Jönsson, J. (2000) · Genomics · doi:10.1006/geno.2000.6278 · Cited by 34
Nucleobindin Co-Localizes and Associates with Cyclooxygenase (COX)-2 in Human Neutrophils
Leclerc, P., Biarc, J., St‐Onge, M., Gilbert, C., Dussault, A., Laflamme, C., & Pouliot, M. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002229 · Cited by 27
Post-transcriptional Regulation of the Stanniocalcin Gene by Calcium
Ellis, T. J., & Wagner, G. F. (1995) · Journal of Biological Chemistry · doi:10.1074/jbc.270.4.1960 · Cited by 24
Modeling Transcriptome Based on Transcript-Sampling Data
Zhu, J., He, F., Wang, J., & Yu, J. M. (2008) · PLoS ONE · doi:10.1371/journal.pone.0001659 · Cited by 21
Coronin-1A epigenomics governs mycobacterial persistence in tuberculosis
Kaul, D. (2007) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2007.00976.x · Cited by 10
Vos, J. B., Datson, N. A., Rabe, K. F., & Hiemstra, P. S. (2006) · American Journal of Physiology-Lung Cellular and Molecular Physiology · doi:10.1152/ajplung.00242.2006 · Cited by 10
Flagged first, then by citations
1 of the 58 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Zhou, L., Chen, J., Li, Z., Li, X., Hu, X., Huang, Y., Zhao, X., Liang, C. Y., Wang, Y., Sun, L., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015224 · Cited by 647
Wang, Z., Fang, B., Chen, J., Zhang, X., Luo, Z., Huang, L., Chen, X., & Li, Y. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-726 · Cited by 433
Wei, W., Qi, X., Wang, L., Zhang, Y., Hua, W., Li, D., Lv, H., & Zhang, X. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-451 · Cited by 426
Wang, X.-W., Luan, J.-B., Li, J.-M., Bao, Y.-Y., Zhang, C.-X., & Liu, S.-S. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-400 · Cited by 390
Optimization of de novo transcriptome assembly from next-generation sequencing data
Surget-Groba, Y., & Montoya-Burgos, J. I. (2010) · Genome Research · doi:10.1101/gr.103846.109 · Cited by 339
Metadata
- Authors
- Hegedűs, Z., Zakrzewska, A., Ágoston, V. C., Ordas, A., Rácz, P., Mink, M., Spaink, H. P., & Meijer, A. H.
- Affiliations
- Leiden University (NL)
- University of Szeged (HU)
- Corresponding author
- Meijer, Annemarie H.
- Venue
- Molecular Immunology
- Publisher
- Elsevier BV
- Published
- 2009-09
- Volume
- 46
- Issue
- 15
- Pages
- 2918-2930
- ISSN
- 0161-5890 (ISSN-L)
- OpenAlex
- W1966486838
- Cited by
- 216
- References
- 58
- Citations by year
- 2025: 2 · 2024: 1 · 2023: 4 · 2022: 1 · 2021: 6 · 2020: 13 · 2019: 16 · 2018: 5 · 2017: 6 · 2016: 15 · 2015: 19 · 2014: 26 · 2013: 25 · 2012: 30
- FWCI
- 10.29
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Molecular Immunology (publishedVersion)
- PubMed (publishedVersion)
- Leiden Repository (Leiden University) (submittedVersion)
- Funders
- European Commission
- Universiteit Leiden
- Leids Universitair Medisch Centrum
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Health Sciences › Medicine › Infectious Diseases › Tuberculosis Research and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Keywords
- zebrafish, mycobacterial infection, transcriptome, digital gene expression, gene expression profiling, alternative splicing, isoform switching, novel transcripts, microarray comparison
- MeSH terms
- Animals, Disease Models, Animal, Humans, Male, Mycobacterium Infections, Zebrafish, Transcriptional Activation, Sequence Analysis, RNA, Mycobacterium marinum, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Host-Pathogen Interactions
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.
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 ›
Are you an author, or do you see a problem with this page? Request a review
