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E-GEOD-51783 - Comparison of Poly(A) capture versus Ribosomal RNA depletion methods for RNA-seq

Released on 20 August 2014, last updated on 22 August 2014
Homo sapiens
Samples (70)
Array (1)
Protocols (16)
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:
Experiment types
transcription profiling by array, RNA-seq of coding RNA 
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-51783.idf.txt
Sample and data relationshipE-GEOD-51783.hyb.sdrf.txt, E-GEOD-51783.seq.sdrf.txt
Processed data (1)
Additional data (1)
Array designA-GEOD-8269.adf.txt