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| Status |
Public on Aug 20, 2014 |
| Title |
Comparison of Poly(A) capture versus Ribosomal RNA depletion methods for RNA-seq |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Expression profiling by array
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| Summary |
Methods: RNA-sequencing was performed on matched samples obtained across several different gene expression measurement methods including: (a) fresh-frozen (FF) RNA samples by mRNA-seq, Ribo-zero and DSN and (b) FFPE samples by Ribo-zero and DSN. We also assayed the matched samples with Agilent microarray. RNA-seq data was compared on the rRNA-removal efficiency, genome profile, library complexity, coverage uniformity and quantitative cosinstency across protocols and with microarray data.
Results: Compared to mRNA-seq, Ribo-zero provides equivalent percentage of rRNA component, genome-based mapped reads, and consistent quantification of transcripts. Moreover, Ribo-zero and DSN protocols achieve concordant transcript profiling in FFPE samples, and provide substantially more information on non-poly(A) RNA, which cannot be captured by mRNA-seq. Therefore, our study provides evidence that RNA-sequencing can generate accurate and reproducible transcript quantification using FFPE tissues.
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| Overall design |
mRNA profile of 11 breast tumors were assayed by Agilent microarray, and by RNA-sequencing on libraries including: (a) fresh-frozen (FF) RNA samples by mRNA-seq, Ribo-zero and DSN and (b) FFPE samples by Ribo-zero and DSN, using Illunia HiSeq2000 2x50bp.
RNA-Seq raw data is to be made available through dbGaP (controlled access) due to patient privacy concerns:
http://www.ncbi.nlm.nih.gov/gap/?term=phs000676
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| |
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| Contributor(s) |
Perou C, Zhao W |
| Citation(s) |
24888378 |
| BioProject |
PRJNA226742 |
| |
| Submission date |
Oct 28, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Charles M. Perou |
| E-mail(s) |
cperou@med.unc.edu
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center
|
| Street address |
12-044 Lineberger Comprehensive Cancer Center CB# 7295
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7264 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL8269 |
UNC PerouLab 244K Custom Human Array version 5 |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (59)
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| Relations |
| SRA |
SRP038753 |
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