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Series GSE40705 Query DataSets for GSE40705
Status Public on May 15, 2013
Title Comprehensive comparative analysis of RNA sequencing methods for degraded or low input samples
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary RNA-Seq is an effective method to study the transcriptome, but can be difficult to apply to scarce or degraded RNA from fixed clinical samples, rare cell populations, or cadavers. Recent studies have proposed several methods for RNA-Seq of low quality and/or low quantity samples, but their relative merits have not been systematically analyzed. Here, we compare five such methods using a comprehensive set of metrics, relevant to applications such as transcriptome annotation, transcript discovery, and gene expression. Using a single human RNA sample, we constructed and deeply sequenced 10 libraries with these methods and two control libraries. We find that the RNase H method performed best for low quality RNA, and can even effectively replace oligo (dT) based methods for standard RNA-Seq. SMART and NuGEN had distinct strengths for low quantity RNA. Our analysis allows biologists to select the most suitable methods and provides a benchmark for future method development.
Overall design Examination of 9 different RNA-Seq libraries starting from total RNA from 5 distinct methods; also 3 control RNA-Seq libraries
Contributor(s) Levin JZ, Regev A, Adiconis X
Citation(s) 23685885
Submission date Sep 07, 2012
Last update date May 15, 2019
Contact name Joshua Z Levin
Organization name Broad Institute of MIT & Harvard
Street address 320 Charles Street
City Cambridge
State/province MA
ZIP/Postal code 02141
Country USA
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (18)
GSM999527 DSN-lite
GSM999528 DSN-lite PCR
GSM999529 RNase H
BioProject PRJNA174728
SRA SRP015640

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE40705_FFPE_gene.txt.gz 871.6 Kb (ftp)(http) TXT
GSE40705_FFPE_isoform.txt.gz 1.1 Mb (ftp)(http) TXT
GSE40705_K562_Isoform.txt.gz 3.1 Mb (ftp)(http) TXT
GSE40705_K562_gene.txt.gz 1.7 Mb (ftp)(http) TXT
GSE40705_Pancreas_gene.txt.gz 912.7 Kb (ftp)(http) TXT
GSE40705_Pancreas_isoform.txt.gz 1.0 Mb (ftp)(http) TXT
GSE40705_RAW.tar 15.8 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
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Processed data are available on Series record

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