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Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach
Open accessAbstract
BACKGROUND: High throughput sequencing-by-synthesis is an emerging technology that allows the rapid production of millions of bases of data. Although the sequence reads are short, they can readily be used for re-sequencing. By re-sequencing the mRNA products of a cell, one may rapidly discover polymorphisms and splice variants particular to that cell. RESULTS: We present the utility of massively parallel sequencing by synthesis for profiling the transcriptome of a human prostate cancer cell-line, LNCaP, that has been treated with the synthetic androgen, R1881. Through the generation of approximately 20 megabases (MB) of EST data, we detect transcription from over 10,000 gene loci, 25 previously undescribed alternative splicing events involving known exons, and over 1,500 high quality single nucleotide discrepancies with the reference human sequence. Further, we map nearly 10,000 ESTs to positions on the genome where no transcription is currently predicted to occur. We also characterize various obstacles with using sequencing by synthesis for transcriptome analysis and propose solutions to these problems. CONCLUSION: The use of high-throughput sequencing-by-synthesis methods for transcript profiling allows the specific and sensitive detection of many of a cell's transcripts, and also allows the discovery of high quality base discrepancies, and alternative splice variants. Thus, this technology may provide an effective means of understanding various disease states, discovering novel targets for disease treatment, and discovery of novel transcripts.
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“Transcript abundance is directly proportional to the number of sequencing reads that map to a specific transcript, resulting in lower falsenegative and false-positive discovery rates in addition to a greater linear range (Bainbridge et al., 2006;Cloonan et al., 2008;Marioni et al., 2008;Mortazavi et al., 2008;Nagalakshmi et al., 2008;Sultan et al., 2008;Wilhelm et al., 2008;Trapnell et al., 2010;W”
From An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex (2014) · cites this paper as Bainbridge et al., 2006
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Citations
Cites
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
Edgar, R. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.207 · Cited by 13,288
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
Genome sequencing in microfabricated high-density picolitre reactors
Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y.-J., Chen, Z., et al. (2005) · Nature · doi:10.1038/nature03959 · Cited by 7,693
Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy AssessmentPreprint
Ewing, B., Hillier, L., Wendl, M. C., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.175 · Cited by 6,993
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439
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
InterProScan: protein domains identifier
Quévillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., Apweiler, R., & López, R. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki442 · Cited by 2,976
Expression monitoring by hybridization to high-density oligonucleotide arrays
Lockhart, D. J., Dong, H., Byrne, M. C., Follettie, M. T., Gallo, M. V., Chee, M. S., Mittmann, M., Wang, C., Kobayashi, M., Norton, H., et al. (1996) · Nature Biotechnology · doi:10.1038/nbt1296-1675 · Cited by 2,841
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
dbEST — database for “expressed sequence tags”
Boguski, M. S., Lowe, T. M., & Tolstoshev, C. M. (1993) · Nature Genetics · doi:10.1038/ng0893-332 · Cited by 1,340
Research works printed but not linked: 1
- dbEST: [http://www.ncbi.nlm.nih.gov/dbEST/].
Cited by
Sorted by citations
Zhang, Y., Chen, K., Sloan, S. A., Bennett, M. L., Scholze, A. R., O'Keeffe, S., Phatnani, H. P., Guarnieri, P., Caneda, C., Ruderisch, N., et al. (2014) · The Journal of Neuroscience · doi:10.1523/jneurosci.1860-14.2014 · Cited by 4,875
Next-generation DNA sequencing
Shendure, J., & Ji, H. (2008) · Nature Biotechnology · doi:10.1038/nbt1486 · Cited by 4,509
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
Next-Generation DNA Sequencing Methods
Mardis, E. R. (2008) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.9.081307.164359 · Cited by 2,469
Self-citationApplications 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
Self-citationLowe, R. G. T., Shirley, N. J., Bleackley, M. R., Dolan, S., & Shafee, T. M. A. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005457 · Cited by 1,307
A timeline of tumour-associated macrophage biology
Cassetta, L., & Pollard, J. W. (2023) · Nature reviews. Cancer · doi:10.1038/s41568-022-00547-1 · Cited by 615
Applications of New Sequencing Technologies for Transcriptome Analysis
Morozova, O., Hirst, M., & Marra, M. A. (2009) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-082908-145957 · Cited by 590
Self-citationRapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing
VERA, J. C., WHEAT, C. W., FESCEMYER, H. W., FRILANDER, M. J., CRAWFORD, D. L., HANSKI, I., & MARDEN, J. H. (2008) · Molecular Ecology · doi:10.1111/j.1365-294x.2008.03666.x · Cited by 714
The development and impact of 454 sequencing
Rothberg, J. M., & Leamon, J. H. (2008) · Nature Biotechnology · doi:10.1038/nbt1485 · Cited by 561
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
Uncovering the Complexity of Transcriptomes with RNA-Seq
Costa, V., Angelini, C., Feis, I. D., & Ciccodicola, A. (2010) · BioMed Research International · doi:10.1155/2010/853916 · Cited by 460
Sampling the Arabidopsis Transcriptome with Massively Parallel Pyrosequencing
Weber, A. P. M., Weber, K. L., Carr, K. M., Wilkerson, C. G., & Ohlrogge, J. B. (2007) · PLANT PHYSIOLOGY · doi:10.1104/pp.107.096677 · Cited by 369
Transcriptomics in the RNA-seq era
McGettigan, P. (2013) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2012.12.008 · Cited by 383
The epigenetic basis of cellular heterogeneity
Carter, B. C., & Zhao, K. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-00300-0 · Cited by 324
Next-generation tag sequencing for cancer gene expression profilingPreprint
Morrissy, A. S., Morin, R. D., Delaney, A. D., Zeng, T., McDonald, H., Jones, S. J. M., Zhao, Y., Hirst, M., & Marra, M. A. (2009) · Genome Research · doi:10.1101/gr.094482.109 · Cited by 309
Self-citationRNA-Seq and human complex diseases: recent accomplishments and future perspectives
Costa, V., Aprile, M., Esposito, R., & Ciccodicola, A. (2012) · European Journal of Human Genetics · doi:10.1038/ejhg.2012.129 · Cited by 277
Cancer transcriptome profiling at the juncture of clinical translation
Cieslik, M. P., & Chinnaiyan, A. M. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.96 · Cited by 266
Using single-cell genomics to understand developmental processes and cell fate decisions
Griffiths, J. A., Scialdone, A., & Marioni, J. C. (2018) · Molecular Systems Biology · doi:10.15252/msb.20178046 · Cited by 250
Gene expression profiling by massively parallel sequencingPreprint
Torres, T. T., Metta, M., Ottenwälder, B., & Schlötterer, C. (2007) · Genome Research · doi:10.1101/gr.6984908 · Cited by 248
Droege, M., & Hill, B. (2008) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2008.03.021 · Cited by 244
Design and validation issues in RNA-seq experiments
Fang, Z., & Cui, X. (2011) · Briefings in Bioinformatics · doi:10.1093/bib/bbr004 · Cited by 243
Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing
Wang, W., Wang, Y., Zhang, Q., Qi, Y., & Guo, D. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-465 · Cited by 224
Comparison of next generation sequencing technologies for transcriptome characterization
Wall, P. K., Leebens‐Mack, J., Chanderbali, A. S., Barakat, A., Wolcott, E., Liang, H., Landherr, L. L., Tomsho, L. P., Hu, Y., Carlson, J. E., et al. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-347 · Cited by 213
Miniaturizing chemistry and biology in microdroplets
Kelly, B. T., Baret, J., Taly, V., & Griffiths, A. D. (2007) · Chemical Communications · doi:10.1039/b616252e · Cited by 202
Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors
Jones, S. J. M., Laskin, J. J., Li, Y. Y., Griffith, O. L., An, J., Bilenky, M., Butterfield, Y. S. N., Cezard, T., Chuah, E., Corbett, R., et al. (2010) · Genome biology · doi:10.1186/gb-2010-11-8-r82 · Cited by 174
Self-citationFrom human genome to cancer genome: The first decadePreprint
Wheeler, D. A., & Wang, L. (2013) · Genome Research · doi:10.1101/gr.157602.113 · Cited by 183
Hale, M. C., McCormick, C. R., Jackson, J. R., & DeWoody, J. A. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-203 · Cited by 163
Next-generation sequencing: applications beyond genomes
Marguerat, S., Wilhelm, B. T., & Bähler, J. (2008) · Biochemical Society Transactions · doi:10.1042/bst0361091 · Cited by 138
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Kjærulff, O., Brodin, L., & Jung, A. G. (2010) · Cell Biochemistry and Biophysics · doi:10.1007/s12013-010-9137-5 · Cited by 128
Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line
Zhao, Q., Caballero, O. L., Levy, S., Stevenson, B. J., Iseli, C., SOUZA, S. J. D., Galante, P. A. F., Busam, D., Leversha, M. A., Chadalavada, K., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0812945106 · Cited by 120
García‐Cañas, V., Simó, C., León, C., & Cifuentes, A. (2009) · Journal of Pharmaceutical and Biomedical Analysis · doi:10.1016/j.jpba.2009.04.019 · Cited by 122
DeBiasse, M. B., & Kelly, M. W. (2015) · Journal of Heredity · doi:10.1093/jhered/esv073 · Cited by 131
The evolution of gene expression and the transcriptome–phenotype relationship
Harrison, P. W., Wright, A. E., & Mank, J. E. (2011) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2011.12.004 · Cited by 122
O’Neil, S. T., Dzurisin, J. D. K., Carmichael, R., Lobo, N. F., Emrich, S., & Hellmann, J. J. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-310 · Cited by 120
Mudge, J., Miller, N., Khrebtukova, I., Lindquist, I. E., May, G. D., Huntley, J. J., Luo, S. J., Zhang, L., van Velkinburgh, J. C., Farmer, A. D., et al. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003625 · Cited by 120
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Gurdo, N., Volke, D. C., McCloskey, D., & Nikel, P. I. (2023) · New Biotechnology · doi:10.1016/j.nbt.2023.01.002 · Cited by 121
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Bell, D. W. (2009) · The Journal of Pathology · doi:10.1002/path.2645 · Cited by 109
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Coppe, A., Pujolar, J. M., Maes, G. E., Larsen, P. F., Hansen, M. M., Bernatchez, L., Zane, L., & Bortoluzzi, S. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-635 · Cited by 103
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Fox, S. E., Filichkin, S. A., & Mockler, T. C. (2009) · Methods in molecular biology · doi:10.1007/978-1-60327-563-7_5 · Cited by 97
Li, H., Lovci, M., Kwon, Y., Rosenfeld, M. G., Fu, X., & Yeo, G. W.-M. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0807121105 · Cited by 94
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Roeding, F., Borner, J., Kube, M., Klages, S., Reinhardt, R., & Burmester, T. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.08.014 · Cited by 91
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Cheung, E. C. W., & Kraus, W. L. (2010) · Annual Review of Physiology · doi:10.1146/annurev-physiol-021909-135840 · Cited by 86
Mane, S. P., Evans, C., Cooper, K., Crasta, O. R., Folkerts, O., Hutchison, S. K., Harkins, T. T., Thierry‐Mieg, D., Thierry‐Mieg, J., & Jensen, R. V. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-264 · Cited by 84
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Le, P., Romano, G., Nana-Sinkam, P. S., & Acunzo, M. (2021) · Cancers · doi:10.3390/cancers13061372 · Cited by 87
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González‐Roca, E., García‐Albéniz, X., Rodriguez-Mulero, S., Gomis, R. R., Kornacker, K., & Auer, H. (2010) · PLoS ONE · doi:10.1371/journal.pone.0014418 · Cited by 75
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Costa, V., Angelini, C., D’Apice, L., Mutarelli, M., Casamassimi, A., Sommese, L., Gallo, M. A., Aprile, M., Esposito, R., Leone, L., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0018493 · Cited by 70
Zou, Z., Najar, F. Z., Wang, Y., Roe, B. A., & Jiang, H. (2008) · Insect Biochemistry and Molecular Biology · doi:10.1016/j.ibmb.2008.03.009 · Cited by 68
Hardt, O., Wild, S., Oerlecke, I., Hofmann, K., Luo, S., Wiencek, Y., Kantelhardt, E., Vess, C., Smith, G. P., Schroth, G. P., et al. (2012) · Cancer Letters · doi:10.1016/j.canlet.2012.06.010 · Cited by 64
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Strausberg, R. L., Levy, S., & Rogers, Y.-H. (2008) · Drug Discovery Today · doi:10.1016/j.drudis.2008.03.025 · Cited by 62
Moe, K. T., Chung, J., Cho, Y., Moon, J., Ku, J., Jung, J. K., Lee, J., & Park, Y. (2010) · Journal of Integrative Plant Biology · doi:10.1111/j.1744-7909.2010.01012.x · Cited by 63
Wu, J. Q., Du, J., Rozowsky, J. S., Zhang, Z., Urban, A. E., Euskirchen, G. M., Weissman, S. M., Gerstein, M., & Snyder, M. P. (2008) · Genome biology · doi:10.1186/gb-2008-9-1-r3 · Cited by 60
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Bovolenta, M., Erriquez, D., Valli, E., Brioschi, S., Scotton, C., Neri, M., Falzarano, M. S., Gherardi, S., Fabris, M., Rimessi, P., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0045328 · Cited by 57
Fassò, M., Waitz, R., Hou, Y., Rim, T., Greenberg, N. M., Shastri, N., Fong, L. H., & Allison, J. P. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0712269105 · Cited by 58
Souframanien, J., & Reddy, K. S. (2015) · PLoS ONE · doi:10.1371/journal.pone.0128748 · Cited by 56
Valsesia, A., Rimoldi, D., Martinet, D., Ibberson, M. R., Benaglio, P., Quadroni, M., Waridel, P., Gaillard, M., Pidoux, M., Rapin, B., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0018369 · Cited by 54
Transcriptome analysis for Caenorhabditis elegansbased on novel expressed sequence tags
Shin, H., Hirst, M., Bainbridge, M. N., Magrini, V. J., Mardis, E. R., Moerman, D. G., Marra, M. A., Baillie, D. L., & Jones, S. J. M. (2008) · BMC Biology · doi:10.1186/1741-7007-6-30 · Cited by 55
Self-citationMollet, I. G., Ben-Dov, C., Felício‐Silva, D., Grosso, A. R., Eleuterio, P. M. D. S., Alves, R., Staller, R., Silva, T. S., & Carmo‐Fonseca, M. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq197 · Cited by 53
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Exome RNA sequencing reveals rare and novel alternative transcripts
Halvardson, J., Zaghlool, A., & Feuk, L. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks816 · Cited by 50
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Robison, K. E. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbq013 · Cited by 48
Morozova, O., & Marra, M. A. (2008) · Biochemistry and Cell Biology · doi:10.1139/o08-003 · Cited by 46
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Wang, X., Wang, G., Shen, C., Li, L., Wang, X., Mooney, S. D., Edenberg, H. J., Sanford, J. R., & Liu, Y. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-s1-s17 · Cited by 46
Jousheghani, Z. Z., Singh, N., & Patro, R. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf240 · Cited by 48
Silva, J. C., Domingues, D. S., Menotti, D., Hungría, M., & Lopes, F. M. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.11.051 · Cited by 45
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Kornobis, É., Cabellos, L., Aguilar, F., Frías-López, C., Rozas, J., Marco, J., & Zardoya, R. (2015) · Evolutionary Bioinformatics · doi:10.4137/ebo.s23873 · Cited by 43
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Wang, L., & Wheeler, D. A. (2013) · Annual Review of Medicine · doi:10.1146/annurev-med-120811-171056 · Cited by 44
Larson, N. B., McDonnell, S. K., French, A. J., Fogarty, Z. C., Cheville, J. C., Middha, S., Riska, S. M., Baheti, S., Nair, A., Wang, L., et al. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.04.015 · Cited by 44
RNA polymerase II stalling: loading at the start prepares genes for a sprint
Wu, J. Q., & Snyder, M. P. (2008) · Genome biology · doi:10.1186/gb-2008-9-5-220 · Cited by 42
Raizada, A., & Souframanien, J. (2019) · BMC Plant Biology · doi:10.1186/s12870-019-1954-0 · Cited by 40
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Gorringe, K. L., & Campbell, I. (2008) · Molecular Oncology · doi:10.1016/j.molonc.2008.12.005 · Cited by 37
Serfass, J. M., Takahashi, Y., Zhou, Z., Kawasawa, Y. I., Liu, Y., Tsotakos, N., Young, M. M., Tang, Z., Yang, L., Atkinson, J. M., et al. (2017) · Journal of Biological Chemistry · doi:10.1074/jbc.m117.792747 · Cited by 35
Identification of new genes in Sinorhizobium meliloti using the Genome Sequencer FLX system
Mao, C., Evans, C., Jensen, R. V., & Sobral, B. (2008) · BMC Microbiology · doi:10.1186/1471-2180-8-72 · Cited by 36
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Janitz, M. (2008) · Wiley eBooks · doi:10.1002/9783527625130 · Cited by 35
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Wetterbom, A., Ameur, A., Feuk, L., Gyllensten, U. B., & Cavelier, L. B. (2010) · Genome biology · doi:10.1186/gb-2010-11-7-r78 · Cited by 34
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Calarco, J. A., Saltzman, A. L., Ip, J. Y. Y., & Blencowe, B. J. (2007) · Advances in experimental medicine and biology · doi:10.1007/978-0-387-77374-2_5 · Cited by 33
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Bushel, P. R., Ferguson, S., Ramaiahgari, S., Paules, R. S., & Auerbach, S. S. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00594 · Cited by 33
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Edenberg, H. J., & Liu, Y. (2009) · Cold Spring Harbor Protocols · doi:10.1101/pdb.top62 · Cited by 34
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Weber, A. P. M. (2015) · PLANT PHYSIOLOGY · doi:10.1104/pp.15.01081 · Cited by 38
Liu, N., Liu, L., & Pan, X. (2014) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-014-1601-8 · Cited by 33
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Babik, W., Stuglik, M., Qi, W., Künzli-Gontarczyk, M., Kuduk, K., Koteja, P., & Radwan, J. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-390 · Cited by 30
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Metadata
- Authors
- Bainbridge, M. N., Warren, R. L., Hirst, M., Romanuik, T., Zeng, T., Go, A., Delaney, A., Griffith, M., Hickenbotham, M., Magrini, V., Mardis, E. R., Sadar, M. D., Siddiqui, A. S., Marra, M. A., & Jones, S. J.
- Affiliations
- BC Cancer Agency (CA)
- Washington University in St. Louis (US)
- Corresponding author
- Jones, Steven JM
- ORCID
- Venue
- BMC Genomics
- Published
- 2006-09-29
- Volume
- 7
- Issue
- 1
- Pages
- 246-246
- ISSN
- 1471-2164 (ISSN-L)
- PMC
- PMC1592491
- OpenAlex
- W2125013165
- Cited by
- 222
- References
- 33
- Citations by year
- 2026: 6 · 2025: 6 · 2024: 15 · 2023: 15 · 2022: 12 · 2021: 21 · 2020: 8 · 2019: 10 · 2018: 6 · 2017: 6 · 2016: 3 · 2015: 10 · 2014: 5 · 2013: 9 · 2012: 8
- FWCI
- 7.62
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- BMC Genomics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Michael Smith Health Research BC
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- LNCaP cells, prostate cancer, gene expression profiling, sequencing by synthesis, expressed sequence tags, alternative splicing, single nucleotide polymorphisms, R1881, androgen therapy, novel transcripts, genome mapping
- MeSH terms
- Adenocarcinoma, Androgens, Chromosome Mapping, Chromosomes, Human, Exons, Humans, Male, Neoplasms, Hormone-Dependent, Prostatic Neoplasms, RNA, Messenger, RNA, Neoplasm, Sequence Homology, Nucleic Acid, Transcription, Genetic, Metribolone, Gene Expression Regulation, Neoplastic, Sequence Alignment, Alternative Splicing, Sequence Analysis, DNA, DNA, Complementary, Expressed Sequence Tags, Polymorphism, Single Nucleotide, Gene Expression Profiling, Cell Line, Tumor
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