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Series GSE21739 Query DataSets for GSE21739
Status Public on Aug 15, 2010
Title Comprehensive comparative analysis of strand-specific RNA sequencing methods
Organism Saccharomyces cerevisiae
Experiment type Other
Expression profiling by high throughput sequencing
Summary Strand-specific massively-parallel cDNA sequencing (RNA-Seq) is a powerful tool for novel transcript discovery, genome annotation, and expression profiling. Despite multiple published methods for strand-specific RNA-Seq, no consensus exists as to how to choose between them. Here, we developed a comprehensive computational pipeline for the comparison of library quality metrics from any RNA-Seq method. Using the well-annotated Saccharomyces cerevisiae transcriptome as a benchmark, we compared seven library construction protocols, including both published and our own novel methods. We found marked differences in complexity, strand-specificity, evenness and continuity of coverage, agreement with known annotations, and accuracy for expression profiling. Weighing each method’s performance and ease, we identify the dUTP second strand marking and the Illumina RNA ligation methods as the leading protocols, with the former benefitting from the availability of paired-end sequencing. Our analysis provides a comprehensive benchmark, and our computational pipeline is applicable for assessment of future protocols in any organism.
Overall design Examination of 11 different strand-specific RNA-Seq libraries from 7 distinct methods; also 2 control non-strand-specific RNA-Seq libraries. To assess the performance of each strand-specific library in digital expression profiling, we compared them to reference expression measurements estimated from expression profiles using competitive hybridization of a mid-log RNA sample vs. genomic DNA using Agilent arrays.
Contributor(s) Levin JZ, Yassour M, Regev A
Citation(s) 20711195
Submission date May 07, 2010
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)
GPL9294 Agilent-015072 Yeast Oligo Microarray 4x44K G2519F (Probe Name version)
GPL9377 Illumina Genome Analyzer II (Saccharomyces cerevisiae)
Samples (15)
GSM542247 RNA Ligation
GSM542248 Illumina RNA Ligation
GSM542249 Illumina RNA Ligation - SPRI
SRA SRP002790
BioProject PRJNA127357

Download family Format
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE21739_RAW.tar 371.1 Mb (http)(custom) TAR (of BEDGRAPH, TXT)
SRA Run SelectorHelp
Processed data included within Sample table
Processed data provided as supplementary file
Raw data are available in SRA

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