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Series GSE54932 Query DataSets for GSE54932
Status Public on Oct 14, 2014
Title Quantitative Analysis of Wild Type(wt) and Setd2 knockout(ko) mESCs Transcriptomes [RNA-Seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: This study aimed at exploring the deregulated genes in setd2 knockout mESCs compared with wt, more particularly to find the mechanism controlled by setd2,which was required for endoderm differentiation.
Methods: Setd2 wt and ko mESCs were generated by deep sequencing, using Illumina GAIIx. Using Avadis NGS (version:1.3) software to analyze the sequence reads that passed quality filter to acquire the expression level of all genes. qRT–PCR validation was performed usingSYBR Green assays.
Results: Using an optimized data analysis workflow, we mapped about 80 million sequence reads per sample to the mouse genome (build mm9) and identified 17,827 transcripts in the sted2 wt and ko mESCs. About 2,516 genes were deregulated in setd2 ko mESCs, more than 10 genes were validated using qRT-PCR.
Conclusions: Through RNA-seq,we noticed that a subset of genes that related to MAPK signaling pathways were down-regulated in ko mESCs. This provided a bridge to connect setd2 and mESCs endoderm differentiation.
Overall design One wt and one ko mESCs were generated by deep sequencing, using Illumina GAIIx.
Contributor(s) Zhang Y, Chen Z, Huang Q, Chen S
Citation(s) 25242323
Submission date Feb 12, 2014
Last update date May 15, 2019
Contact name Qiuhua Huang
Phone 0086-21-34187717
Organization name Shanghai Institute of Hematology
Street address 197 ruijin road II
City Shanghai
ZIP/Postal code 200025
Country China
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (2)
GSM1326666 Sted2 wt.1
GSM1326667 Setd2 ko.1
This SubSeries is part of SuperSeries:
GSE54933 Gene expression pattern between Wild-type and Setd2 knockout mESCs
BioProject PRJNA238051
SRA SRP037727

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE54932_ALL_gene_expression.txt.gz 467.5 Kb (ftp)(http) TXT
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Processed data are available on Series record
Raw data are available in SRA

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