Dataset Information


Comparison of Poly(A) capture versus Ribosomal RNA depletion methods for RNA-seq

ABSTRACT: 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. 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:

ORGANISM(S): Homo sapiens  

SUBMITTER: Charles Perou   Wei Zhao 

PROVIDER: E-GEOD-51783 | ArrayExpress | 2014-08-20



altmetric image


Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling.

Zhao Wei W   He Xiaping X   Hoadley Katherine A KA   Parker Joel S JS   Hayes David Neil DN   Perou Charles M CM  

BMC genomics 20140602

RNA sequencing (RNA-Seq) is often used for transcriptome profiling as well as the identification of novel transcripts and alternative splicing events. Typically, RNA-Seq libraries are prepared from total RNA using poly(A) enrichment of the mRNA (mRNA-Seq) to remove ribosomal RNA (rRNA), however, this method fails to capture non-poly(A) transcripts or partially degraded mRNAs. Hence, a mRNA-Seq protocol will not be compatible for use with RNAs coming from Formalin-Fixed and Paraffin-Embedded (FFP  ...[more]

Similar Datasets

| GSE74270 | GEO
2014-09-04 | E-MTAB-2523 | ArrayExpress
2015-06-22 | E-GEOD-19249 | ExpressionAtlas
2011-03-16 | E-GEOD-18377 | ArrayExpress
2011-09-14 | E-GEOD-31735 | ArrayExpress
2012-06-30 | E-GEOD-30472 | ArrayExpress
2010-11-25 | E-GEOD-19249 | ArrayExpress
2011-03-16 | GSE18377 | GEO
2012-07-01 | GSE30472 | GEO
2010-11-25 | GSE19249 | GEO