The DOI matches its Crossref record; 27 of the 28 references it cites were found in a registry or an index.
RNA-sequence analysis of human B-cells
Open accessAbstract
RNA-sequencing (RNA-seq) allows quantitative measurement of expression levels of genes and their transcripts. In this study, we sequenced complementary DNA fragments of cultured human B-cells and obtained 879 million 50-bp reads comprising 44 Gb of sequence. The results allowed us to study the gene expression profile of B-cells and to determine experimental parameters for sequencing-based expression studies. We identified 20,766 genes and 67,453 of their alternatively spliced transcripts. More than 90% of the genes with multiple exons are alternatively spliced; for most genes, one isoform is predominantly expressed. We found that while chromosomes differ in gene density, the percentage of transcribed genes in each chromosome is less variable. In addition, genes involved in related biological processes are expressed at more similar levels than genes with different functions. Besides characterizing gene expression, we also used the data to investigate the effect of sequencing depth on gene expression measurements. While 100 million reads are sufficient to detect most expressed genes and transcripts, about 500 million reads are needed to measure accurately their expression levels. We provide examples in which deep sequencing is needed to determine the relative abundance of genes and their isoforms. With data from 20 individuals and about 40 million sequence reads per sample, we uncovered only 21 alternatively spliced, multi-exon genes that are not in databases; this result suggests that at this sequence coverage, we can detect most of the known genes. Results from this project are available on the UCSC Genome Browser to allow readers to study the expression and structure of genes in human B-cells.
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Cites
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556
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
TopHat: discovering splice junctions with RNA-Seq
Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,682
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
Accurate whole human genome sequencing using reversible terminator chemistry
Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684
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
Use of a cDNA microarray to analyse gene expression patterns in human cancer
DeRisi, J. L., Penland, L., Brown, P. O., Bittner, M. L., Meltzer, P. S., Ray, M., Chen, Y.-W., Su, Y. A., & Trent, J. M. (1996) · Nature Genetics · doi:10.1038/ng1296-457 · Cited by 1,952
CTLA-4 is a second receptor for the B cell activation antigen B7.
Linsley, P. S., Brady, W., Urnes, M., Grosmaire, L. S., Damle, N. K., & Ledbetter, J. A. (1991) · The Journal of experimental medicine · doi:10.1084/jem.174.3.561 · Cited by 1,685
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
Genetic analysis of genome-wide variation in human gene expression
Morley, M. P., Molony, C. M., Weber, T. M., Devlin, J. L., Ewens, K. G., Spielman, R. S., & Cheung, V. G. (2004) · Nature · doi:10.1038/nature02797 · Cited by 1,212
Self-citationStem 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
A genome-wide association study of global gene expression
Dixon, A. L., Liang, L., Moffatt, M. F., Chen, W., Heath, S. C., Wong, K., Taylor, J. C., Burnett, E. C., Gut, I. G., Farrall, M., et al. (2007) · Nature Genetics · doi:10.1038/ng2109 · Cited by 946
Transcriptome genetics using second generation sequencing in a Caucasian population
Montgomery, S. B., Sammeth, M., Gutierrez-Arcelus, M., Lach, R. P., Ingle, C., Nisbett, J., Guigo, R., & Dermitzakis, E. T. (2010) · Nature · doi:10.1038/nature08903 · Cited by 797
Multiplexed biochemical assays with biological chips
Fodor, S. P. A., Rava, R. P., Huang, X. C., Pease, A. C., Holmes, C. P., & Adams, C. L. (1993) · Nature · doi:10.1038/364555a0 · Cited by 731
STERN, A. S., Podlaski, F., Hulmes, J. D., Pan, Y.-C. E., Quinn, P. M., Wolitzky, A. G., Familletti, P. C., Stremlo, D. L., Truitt, T., & Chizzonite, R. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.17.6808 · Cited by 670
Peters, P. J., Neefjes, J., Oorschot, V. M. J., Ploegh, H. L., & Geuze, H. J. (1991) · Nature · doi:10.1038/349669a0 · Cited by 658
GENCODE: producing a reference annotation for ENCODE
Harrow, J., Denoeud, F., Frankish, A., Reymond, A., Chen, C.-K., Chrast, J., Lagarde, J., Gilbert, J. G., Storey, R., Swarbreck, D., et al. (2006) · Genome Biology · doi:10.1186/gb-2006-7-s1-s4 · Cited by 648
Centre d'Etude du polymorphisme humain (CEPH): Collaborative genetic mapping of the human genome
Dausset, J. B., Cann, H. M., Cohen, D., Lathrop, M. G., Lalouel, J.-M., & White, R. L. (1990) · Genomics · doi:10.1016/0888-7543(90)90491-c · Cited by 575
ENCODE whole-genome data in the UCSC Genome Browser
Rosenbloom, K. R., Dreszer, T. R., Pheasant, M., Barber, G. P., Meyer, L. R., Pohl, A. A., Raney, B. J., Wang, T., Hinrichs, A. S., Zweig, A. S., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp961 · Cited by 353
Noisy Splicing Drives mRNA Isoform Diversity in Human Cells
Pickrell, J. K., Pai, A. A., Gilad, Y., & Pritchard, J. K. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001236 · Cited by 311
Heritability and Linkage Analysis of Sensitivity to Cisplatin-Induced Cytotoxicity
Dolan, M. E., Newbold, K. G., Nagasubramanian, R., Wu, X., Ratain, M. J., Cook, E. H., & Badner, J. A. (2004) · Cancer Research · doi:10.1158/0008-5472.can-04-0340 · Cited by 116
Cited by
Sorted by citations
SEQC/MAQC-III Consortium (2014) · Nature Biotechnology · doi:10.1038/nbt.2957 · Cited by 983
Bueno, R., Stawiski, E. W., Goldstein, L. D., Durinck, S., Rienzo, A. D., Modrusan, Z. D., Gnad, F., Nguyen, T. T., Jaiswal, B. S., Chirieac, L. R., et al. (2016) · Nature Genetics · doi:10.1038/ng.3520 · Cited by 937
Dual RNA-seq of pathogen and host
Westermann, A. J., Gorski, S. A., & Vogel, J. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2852 · Cited by 782
Calculating Sample Size Estimates for RNA Sequencing Data
Hart, S. N., Therneau, T. M., Zhang, Y., Poland, G. A., & Kocher, J.-P. (2013) · Journal of Computational Biology · doi:10.1089/cmb.2012.0283 · Cited by 341
Xu, Z., Dai, X., & Chai, X. (2018) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2018.03.348 · Cited by 327
Metadata
- Authors
- Toung, J. M., Morley, M., Li, M., & Cheung, V. G.
- Affiliations
- University of Pennsylvania (US)
- Children's Hospital of Philadelphia (US)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2011-05-02
- Volume
- 21
- Issue
- 6
- Pages
- 991-998
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC3106332
- OpenAlex
- W2142108845
- Cited by
- 142
- References
- 28
- Citations by year
- 2026: 2 · 2025: 3 · 2024: 3 · 2023: 2 · 2022: 2 · 2021: 7 · 2020: 8 · 2019: 4 · 2018: 9 · 2017: 14 · 2016: 14 · 2015: 8 · 2014: 20 · 2013: 19 · 2012: 20
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institutes of Health
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- human B cells, gene expression profiling, alternative splicing, transcriptome, gene isoforms, sequencing depth, gene density, gene discovery, UCSC Genome Browser
- MeSH terms
- B-Lymphocytes, Humans, Proteins, Sequence Analysis, RNA, DNA, Complementary, Protein Isoforms, Gene Expression Profiling, High-Throughput Nucleotide Sequencing
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