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Series GSE94585 Query DataSets for GSE94585
Status Public on Jul 09, 2018
Title Systematic assessment of next-generation sequencing for quantitative small RNA profiling: synthetic ratiometric pools
Organism synthetic construct
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Small RNA-seq is increasingly being used for profiling of small RNAs. Quantitative characteristics of long RNA-seq have been extensively described, but small RNA-seq involves fundamentally different methods for library preparation, with distinct protocols and technical variations that have not been fully and systematically studied. Using common sets of reference samples, we evaluated the accuracy, reproducibility and bias of small RNA-seq library preparation for five distinct protocols and across nine different laboratories. As part of this larger study, we assessed reproducibility and accuracy of relative expression measurements using two pools of synthetic small RNA sequences, where subsets of the sRNAs vary in relative amount between pools A and B. The pools each contain 334 small RNAs, varying by 15 different ratios between pools A and B (10:1, 8:1, 5:1, 4:1, 3:1, 2:1, 1.5:1, 1:1, 1:1.5, 1:2, 1:3, 1:4 1:5, 1:8, 1:10). We find that although the sequencing bias varies extensively between protocols, the relative abundance measured between samples A and B is largely reproducible and accurate across labs and protocols. These results suggest that measurements of differential expression should be comparable across institutions and library preparation technologies.
Overall design Two pools of synthetic RNAs were sequenced by 9 different labs, using 1 common library construction protocol (TruSeq), and at least one additional protocol of their choice. The RNA pools contain a common set of synthetic oligos at differing relative concentrations in the SynthA and SynthB pools. A total of 40 sample libraries was produced (20 each for SynthA and SynthB), each in quadruplicate.
Contributor(s) Tewari M
Citation(s) 30010675
Submission date Feb 06, 2017
Last update date May 15, 2019
Contact name Muneesh Tewari
Organization name University of Michigan
Lab 4029 BSRB
Street address 109 Zina Pitcher Pl
City Ann Arbor
State/province MI
ZIP/Postal code 48109-2200
Country USA
Platforms (4)
GPL19424 Illumina NextSeq 500 (synthetic construct)
GPL19604 Illumina HiSeq 2500 (synthetic construct)
GPL21440 Ion Torrent Proton (synthetic construct)
Samples (50)
GSM2478887 4N_A.Lab5.SynthA
GSM2478888 4N_B.Lab2.SynthA
GSM2478889 4N_B.Lab4.SynthA
This SubSeries is part of SuperSeries:
GSE94586 Systematic assessment of next-generation sequencing for quantitative small RNA profiling: a multiple protocol study across multiple laboratories
BioProject PRJNA371517
SRA SRP098949

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
GSE94585_RAW.tar 1.4 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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