Su, Zhenqiang, Labaj, Pawel P., Li, Sheng, Thierry-Mieg, Jean, Thierry-Mieg, Danielle
ORCID: 0000-0001-9568-4211, Shi, Wei, Wang, Charles, Schroth, Gary P., Setterquist, Robert A., Thompson, John F., Jones, Wendell D., Xiao, Wenzhong, Xu, Weihong
ORCID: 0000-0002-3988-3571, Jensen, Roderick V., Kelly, Reagan, Xu, Joshua, Conesa, Ana, Furlanello, Cesare, Gao, Hanlin, Hong, Huixiao, Jafari, Nadereh, Letovsky, Stan, Liao, Yang, Lu, Fei, Oakeley, Edward J., Peng, Zhiyu
ORCID: 0000-0003-2349-750X, Praul, Craig A., Santoyo-Lopez, Javier
ORCID: 0000-0003-1988-5059, Scherer, Andreas, Shi, Tieliu, Smyth, Gordon K., Staedtler, Frank, Sykacek, Peter, Tan, Xin-Xing, Thompson, E. Aubrey, Vandesompele, Jo
ORCID: 0000-0001-6274-0184, Wang, May D., Wang, Jian, Wolfinger, Russell D., Zavadil, Jiri
ORCID: 0000-0003-0640-5562, Auerbach, Scott S., Bao, Wenjun, Binder, Hans, Blomquist, Thomas, Brilliant, Murray H., Bushel, Pierre R., Cain, Weimin, Catalano, Jennifer G., Chang, Ching-Wei, Chen, Tao, Chen, Geng, Chen, Rong, Chierici, Marco
ORCID: 0000-0001-9791-9301, Chu, Tzu-Ming, Clevert, Djork-Arne
ORCID: 0000-0003-4191-2156, Deng, Youping, Derti, Adnan, Devanarayan, Viswanath, Dong, Zirui, Dopazo, Joaquin, Du, Tingting, Fang, Hong, Fang, Yongxiang, Fasold, Mario, Fernandez, Anita, Fischer, Matthias, Furio-Tari, Pedro, Fuscoe, James C., Caiment, Florian
ORCID: 0000-0002-3325-0466, Gaj, Stan, Gandara, Jorge, Gao, Huan, Ge, Weigong, Gondo, Yoichi
ORCID: 0000-0003-2184-6489, Gong, Binsheng
ORCID: 0000-0002-8724-5435, Gong, Meihua, Gong, Zhuolin, Green, Bridgett, Guo, Chao
ORCID: 0000-0002-6673-0933, Guo, Lei, Guo, Li-Wu, Hadfield, James, Hellemans, Jan, Hochreiter, Sepp
ORCID: 0000-0001-7449-2528, Jia, Meiwen, Jian, Min, Johnson, Charles D., Kay, Suzanne, Kleinjans, Jos, Lababidi, Samir, Levy, Shawn
ORCID: 0000-0002-1369-5740, Li, Quan-Zhen, Li, Li, Li, Li, Li, Peng, Li, Yan, Li, Haiqing, Li, Jianying, Li, Shiyong, Lin, Simon M., Lopez, Francisco J., Lu, Xin, Luo, Heng
ORCID: 0000-0001-5192-8878, Ma, Xiwen, Meehan, Joseph, Megherbi, Dalila B., Mei, Nan
ORCID: 0000-0002-3501-9014, Mu, Bing, Ning, Baitang, Pandey, Akhilesh, Perez-Florido, Javier, Perkins, Roger G., Peters, Ryan, Phan, John H., Pirooznia, Mehdi
ORCID: 0000-0002-4210-6458, Qian, Feng, Qing, Tao, Rainbow, Lucille, Rocca-Serra, Philippe, Sambourg, Laure, Sansone, Susanna-Assunta
ORCID: 0000-0001-5306-5690, Schwartz, Scott, Shah, Ruchir, Shen, Jie, Smith, Todd M., Stegle, Oliver
ORCID: 0000-0002-8818-7193, Stralis-Pavese, Nancy, Stupka, Elia
ORCID: 0000-0003-3154-4011, Suzuki, Yutaka, Szkotnicki, Lee T., Tinning, Matthew, Tu, Bimeng, van Deft, Joost, Vela-Boza, Alicia, Venturini, Elisa, Walker, Stephen J., Wan, Liqing, Wang, Wei, Wang, Jinhui, Wang, Jun
ORCID: 0000-0002-8540-8931, Wieben, Eric D., Willey, James C., Wu, Po-Yen, Xuan, Jiekun, Yang, Yong, Ye, Zhan, Yin, Ye, Yu, Ying, Yuan, Yate-Ching, Zhang, John, Zhang, Ke K., Zhang, Wenqian, Zhang, Wenwei, Zhang, Yanyan
ORCID: 0000-0001-7801-0215, Zhao, Chen, Zheng, Yuanting, Zhou, Yiming, Zumbo, Paul, Tong, Weida, Kreil, David P., Mason, Christopher E. and Shi, Leming
ORCID: 0000-0002-7143-2033
(2014).
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.
Nat. Biotechnol., 32 (9).
S. 903 - 915.
NEW YORK:
NATURE PUBLISHING GROUP.
ISSN 1546-1696
Full text not available from this repository.
Abstract
We present primary results from the Sequencing Quality Control (SEQC) project, coordinated by the US Food and Drug Administration. Examining Illumina HiSeq, Life Technologies SOLiD and Roche 454 platforms at multiple laboratory sites using reference RNA samples with built-in controls, we assess RNA sequencing (RNA-seq) performance for junction discovery and differential expression profiling and compare it to microarray and quantitative PCR (qPCR) data using complementary metrics. At all sequencing depths, we discover unannotated exon-exon junctions, with >80% validated by qPCR. We find that measurements of relative expression are accurate and reproducible across sites and platforms if specific-filters are used. In contrast, RNA-seq and microarrays do not provide accurate absolute measurements, and gene-specific biases are observed for all examined platforms, including qPCR. Measurement performance depends on the platform and data analysis pipeline, and variation is large for transcript-level profiling. The complete SEQC data sets, comprising >100 billion reads (10Tb), provide unique resources for evaluating RNA-seq analyses for clinical and regulatory settings.
Item Type: |
Journal Article
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Creators: |
Creators | Email | ORCID | ORCID Put Code |
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Su, Zhenqiang | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Labaj, Pawel P. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Li, Sheng | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Thierry-Mieg, Jean | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Thierry-Mieg, Danielle | UNSPECIFIED | orcid.org/0000-0001-9568-4211 | UNSPECIFIED | Shi, Wei | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Wang, Charles | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Schroth, Gary P. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Setterquist, Robert A. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Thompson, John F. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Jones, Wendell D. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Xiao, Wenzhong | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Xu, Weihong | UNSPECIFIED | orcid.org/0000-0002-3988-3571 | UNSPECIFIED | Jensen, Roderick V. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Kelly, Reagan | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Xu, Joshua | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Conesa, Ana | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Furlanello, Cesare | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Gao, Hanlin | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Hong, Huixiao | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Jafari, Nadereh | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Letovsky, Stan | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Liao, Yang | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Lu, Fei | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Oakeley, Edward J. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Peng, Zhiyu | UNSPECIFIED | orcid.org/0000-0003-2349-750X | UNSPECIFIED | Praul, Craig A. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Santoyo-Lopez, Javier | UNSPECIFIED | orcid.org/0000-0003-1988-5059 | UNSPECIFIED | Scherer, Andreas | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Shi, Tieliu | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Smyth, Gordon K. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Staedtler, Frank | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Sykacek, Peter | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Tan, Xin-Xing | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Thompson, E. Aubrey | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Vandesompele, Jo | UNSPECIFIED | orcid.org/0000-0001-6274-0184 | UNSPECIFIED | Wang, May D. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Wang, Jian | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Wolfinger, Russell D. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Zavadil, Jiri | UNSPECIFIED | orcid.org/0000-0003-0640-5562 | UNSPECIFIED | Auerbach, Scott S. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Bao, Wenjun | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Binder, Hans | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Blomquist, Thomas | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Brilliant, Murray H. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Bushel, Pierre R. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Cain, Weimin | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Catalano, Jennifer G. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Chang, Ching-Wei | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Chen, Tao | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Chen, Geng | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Chen, Rong | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Chierici, Marco | UNSPECIFIED | orcid.org/0000-0001-9791-9301 | UNSPECIFIED | Chu, Tzu-Ming | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Clevert, Djork-Arne | UNSPECIFIED | orcid.org/0000-0003-4191-2156 | UNSPECIFIED | Deng, Youping | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Derti, Adnan | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Devanarayan, Viswanath | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Dong, Zirui | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Dopazo, Joaquin | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Du, Tingting | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Fang, Hong | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Fang, Yongxiang | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Fasold, Mario | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Fernandez, Anita | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Fischer, Matthias | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Furio-Tari, Pedro | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Fuscoe, James C. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Caiment, Florian | UNSPECIFIED | orcid.org/0000-0002-3325-0466 | UNSPECIFIED | Gaj, Stan | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Gandara, Jorge | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Gao, Huan | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Ge, Weigong | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Gondo, Yoichi | UNSPECIFIED | orcid.org/0000-0003-2184-6489 | UNSPECIFIED | Gong, Binsheng | UNSPECIFIED | orcid.org/0000-0002-8724-5435 | UNSPECIFIED | Gong, Meihua | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Gong, Zhuolin | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Green, Bridgett | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Guo, Chao | UNSPECIFIED | orcid.org/0000-0002-6673-0933 | UNSPECIFIED | Guo, Lei | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Guo, Li-Wu | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Hadfield, James | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Hellemans, Jan | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Hochreiter, Sepp | UNSPECIFIED | orcid.org/0000-0001-7449-2528 | UNSPECIFIED | Jia, Meiwen | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Jian, Min | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Johnson, Charles D. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Kay, Suzanne | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Kleinjans, Jos | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Lababidi, Samir | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Levy, Shawn | UNSPECIFIED | orcid.org/0000-0002-1369-5740 | UNSPECIFIED | Li, Quan-Zhen | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Li, Li | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Li, Li | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Li, Peng | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Li, Yan | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Li, Haiqing | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Li, Jianying | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Li, Shiyong | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Lin, Simon M. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Lopez, Francisco J. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Lu, Xin | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Luo, Heng | UNSPECIFIED | orcid.org/0000-0001-5192-8878 | UNSPECIFIED | Ma, Xiwen | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Meehan, Joseph | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Megherbi, Dalila B. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Mei, Nan | UNSPECIFIED | orcid.org/0000-0002-3501-9014 | UNSPECIFIED | Mu, Bing | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Ning, Baitang | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Pandey, Akhilesh | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Perez-Florido, Javier | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Perkins, Roger G. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Peters, Ryan | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Phan, John H. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Pirooznia, Mehdi | UNSPECIFIED | orcid.org/0000-0002-4210-6458 | UNSPECIFIED | Qian, Feng | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Qing, Tao | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Rainbow, Lucille | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Rocca-Serra, Philippe | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Sambourg, Laure | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Sansone, Susanna-Assunta | UNSPECIFIED | orcid.org/0000-0001-5306-5690 | UNSPECIFIED | Schwartz, Scott | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Shah, Ruchir | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Shen, Jie | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Smith, Todd M. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Stegle, Oliver | UNSPECIFIED | orcid.org/0000-0002-8818-7193 | UNSPECIFIED | Stralis-Pavese, Nancy | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Stupka, Elia | UNSPECIFIED | orcid.org/0000-0003-3154-4011 | UNSPECIFIED | Suzuki, Yutaka | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Szkotnicki, Lee T. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Tinning, Matthew | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Tu, Bimeng | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | van Deft, Joost | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Vela-Boza, Alicia | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Venturini, Elisa | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Walker, Stephen J. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Wan, Liqing | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Wang, Wei | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Wang, Jinhui | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Wang, Jun | UNSPECIFIED | orcid.org/0000-0002-8540-8931 | UNSPECIFIED | Wieben, Eric D. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Willey, James C. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Wu, Po-Yen | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Xuan, Jiekun | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Yang, Yong | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Ye, Zhan | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Yin, Ye | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Yu, Ying | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Yuan, Yate-Ching | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Zhang, John | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Zhang, Ke K. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Zhang, Wenqian | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Zhang, Wenwei | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Zhang, Yanyan | UNSPECIFIED | orcid.org/0000-0001-7801-0215 | UNSPECIFIED | Zhao, Chen | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Zheng, Yuanting | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Zhou, Yiming | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Zumbo, Paul | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Tong, Weida | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Kreil, David P. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Mason, Christopher E. | UNSPECIFIED | UNSPECIFIED | UNSPECIFIED | Shi, Leming | UNSPECIFIED | orcid.org/0000-0002-7143-2033 | UNSPECIFIED |
|
URN: |
urn:nbn:de:hbz:38-431337 |
DOI: |
10.1038/nbt.2957 |
Journal or Publication Title: |
Nat. Biotechnol. |
Volume: |
32 |
Number: |
9 |
Page Range: |
S. 903 - 915 |
Date: |
2014 |
Publisher: |
NATURE PUBLISHING GROUP |
Place of Publication: |
NEW YORK |
ISSN: |
1546-1696 |
Language: |
English |
Faculty: |
Unspecified |
Divisions: |
Unspecified |
Subjects: |
no entry |
Uncontrolled Keywords: |
Keywords | Language |
---|
DIFFERENTIAL GENE-EXPRESSION; GENOME ANNOTATION; TRANSCRIPTOME; ARRAYS; BIAS; PCR | Multiple languages | Biotechnology & Applied Microbiology | Multiple languages |
|
URI: |
http://kups.ub.uni-koeln.de/id/eprint/43133 |
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