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Series GSE130014 Query DataSets for GSE130014
Status Public on Feb 02, 2020
Title Decode-seq: a practical approach to improve differential gene expression analysis
Organisms Oryzias latipes; Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary It is often the case that inadequate numbers of biological replicates are utilized in differential gene expression analysis. We describe an easy and effective RNA-seq approach using molecular barcoding to enable profiling a large number of replicates simultaneously. This approach significantly improved the performance of differential gene expression analysis. Using this approach in medaka fish (Oryzias latipes), we discovered novel genes with sexually dimorphic expression, and genes necessary for germ cell development. We appeal that the common practice of using three replicates in differential gene expression analysis should be abandoned.
 
Overall design Each library contains 20 to 60 barcoded samples, total 12 libraries and 360 barcoded samples.

DE1-1, DE1-2, and DE1-3 contain replicates of mix4.5 (human RNA with 4.5% mouse RNA), mix1.5 (1.5% mouse RNA) and mix0.9 (0.9% mouse RNA), 100ng input RNA per sample;

DE2-2, DE2-3, DE2-4, and DE2-5 contain replicates of F (medaka female gonadal RNA), M (medaka male gonadal RNA) and D (DMY mutant male medaka RNA).

DE3-3 and DE3-4 contain replicates of the same mixes as DE1, 10ng and 1ng input RNA per sample respectively;

DE8-6, DE8-12-1 and DE8-12-2 contain replicates of mix5 (human RNA with 5% mouse RNA) and mix1 (1% mouse RNA), 100ng input RNA per sample;

All libraries were constructed using the Decode-seq protocol we developed except DE8-6, which was constructed using the previous published BRB-seq protocol

 
Contributor(s) Li Y, Tu Q
Citation(s) 32200760
Submission date Apr 18, 2019
Last update date Mar 24, 2020
Contact name Qiang Tu
E-mail(s) qtu@genetics.ac.cn
Organization name Institute of Genetics and Developmental Biology
Street address No.1 West Beichen Road,Chaoyang District
City Beijing
ZIP/Postal code 100101
Country China
 
Platforms (2)
GPL25587 HiSeq X Ten (Oryzias latipes)
GPL26363 HiSeq X Ten (Homo sapiens; Mus musculus)
Samples (12)
GSM3729278 DE1-1
GSM3729279 DE1-2
GSM3729280 DE1-3
Relations
BioProject PRJNA533594
SRA SRP192969

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
GSE130014_DE1_count.tsv.gz 819.7 Kb (ftp)(http) TSV
GSE130014_DE2_count.tsv.gz 748.7 Kb (ftp)(http) TSV
GSE130014_DE3_count.tsv.gz 402.0 Kb (ftp)(http) TSV
GSE130014_DE8-12_count.tsv.gz 1005.8 Kb (ftp)(http) TSV
GSE130014_DE8-6_count.tsv.gz 933.4 Kb (ftp)(http) TSV
GSE130014_USI_table.tsv.gz 1.5 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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