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Series GSE124198 Query DataSets for GSE124198
Status Public on May 10, 2019
Title Comprehensive analysis of RNA-seq kits for standard, low and ultra-low quantity samples
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary High-throughput RNA-sequencing has now become the gold standard method for whole-transcriptome gene expression analysis. It is widely used in a number of applications studying various transcriptomes of cells and tissues. It is also being increasingly considered for a number of clinical applications, including expression profiling for diagnostics or alternative transcripts detection. However, RNA sequencing can be challenging in some situations, for instance due to low input quantities or degraded RNA samples. Several protocols have been proposed to overcome some of these challenges, and many are available as commercial kits. Here we perform a comprehensive testing of three recent commercial technologies for RNA-seq library preparation (Truseq, Smarter and Smarter Ultra-Low) on human reference tissue preparations, for standard (1ug), low (100 and 10 ng) and ultra-low (< 1 ng) input quantities, and for mRNA and total RNA, stranded or unstranded. We analyze the results using read quality and alignments metrics, gene detection and differential gene expression metrics. Overall, we show that the Truseq kit performs well at 100 ng input quantity, while the Smarter kit shows degraded performances for 100 and 10 ng input quantities, and that the Smarter Ultra-Low kit performs quite well for input quantities < 1 ng. All the results are discussed in details, and we provide guidelines for the selection of a RNA-seq library preparation kits by biologists.
 
Overall design RNA-seq profiles of Human Universal Reference Total RNA (Clontech) and Human Brain reference RNA (Ambion) were generated by deep sequencing, in duplicate, using Illumina HiSeq2000 or 2500 sequencers.
 
Contributor(s) Bonnet E, Palomares M, Dalmasso C
Citation(s) 31101892
Submission date Dec 20, 2018
Last update date Jun 19, 2019
Contact name Eric Bonnet
E-mail(s) [email protected]
Organization name CNRGH
Lab Computational genomics
Street address 2 rue Gaston Crémieux
City Evry
ZIP/Postal code 91000
Country France
 
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (80)
GSM3523752 SmarterUL_NexteraXT_1ng_750pg A2
GSM3523753 mRNATruseq_1ug A1
GSM3523754 SmarterUL_NexteraXT_1ng_750pg A1
Relations
BioProject PRJNA510978
SRA SRP174053

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE124198_RAW.tar 16.1 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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