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Series GSE58339 Query DataSets for GSE58339
Status Public on Nov 19, 2014
Title A Sox2 distal enhancer cluster regulates embryonic stem cell differentiation potential
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary We report the effect on genome-wide gene expression after deletion of an enhancer region downstream of Sox2 in F1 ES cells. The Sox2 transcription factor must be robustly transcribed in embryonic stem (ES) cells to maintain pluripotency.  Reporter assays reveal novel enhancers, including two enhancers over 100 kb downstream (SRR107 and SRR111) which, through the formation of chromatin loops, localise to the Sox2 promoter in ES cells.  Using CRISPR/Cas9 we deleted a region containing these two enhancers, which we term the Sox2 control region (SCR). This deletion revealed that the SCR is required for Sox2 transcription in ES cells.  Furthermore, homozygous deletion of this distal Sox2 control region (SCR) caused significant reduction in Sox2 mRNA and protein levels, loss of ES cell colony morphology, genome-wide changes in gene expression and impaired neuroectodermal formation upon spontaneous differentiation to embryoid bodies. Together these data identify a distal control region essential for Sox2 transcription in ES cells.
Overall design Examination of PolA+ RNA after heterozygous and homozygous enhancer deletion in F1 ES cells (M. musculus129 x M. castaneus).
Contributor(s) Davidson S, Mitchell JA
Citation(s) 25512558
Submission date Jun 09, 2014
Last update date May 15, 2019
Contact name Jennifer Mitchell
Phone 4169786711
Organization name University of Toronto
Department Cell and Systems Biology
Street address 25 Harbord Street
City Toronto
State/province Ontario
ZIP/Postal code M5S 3G5
Country Canada
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (12)
GSM1407412 F1 ES [Illumina MiSeq]
GSM1407413 Del_SCR_129_15 [Illumina MiSeq]
GSM1407414 Del_SCR_129_37 [Illumina MiSeq]
BioProject PRJNA252023
SRA SRP043053

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Supplementary file Size Download File type/resource
GSE58339_Del_SCR_129Cast_1_p5.bedgraph.gz 83.2 Mb (ftp)(http) BEDGRAPH
GSE58339_Del_SCR_129Cast_1_p5_129.bedgraph.gz 17.3 Mb (ftp)(http) BEDGRAPH
GSE58339_Del_SCR_129Cast_1_p5_Cast.bedgraph.gz 16.2 Mb (ftp)(http) BEDGRAPH
GSE58339_Del_SCR_129Cast_1_p9.bedgraph.gz 67.9 Mb (ftp)(http) BEDGRAPH
GSE58339_Del_SCR_129Cast_1_p9_129.bedgraph.gz 13.9 Mb (ftp)(http) BEDGRAPH
GSE58339_Del_SCR_129Cast_1_p9_Cast.bedgraph.gz 13.3 Mb (ftp)(http) BEDGRAPH
GSE58339_Del_SCR_129_15.bedgraph.gz 109.7 Mb (ftp)(http) BEDGRAPH
GSE58339_Del_SCR_129_15_129.bedgraph.gz 25.6 Mb (ftp)(http) BEDGRAPH
GSE58339_Del_SCR_129_15_Cast.bedgraph.gz 24.2 Mb (ftp)(http) BEDGRAPH
GSE58339_Del_SCR_129_37.bedgraph.gz 69.0 Mb (ftp)(http) BEDGRAPH
GSE58339_Del_SCR_129_37_129.bedgraph.gz 13.4 Mb (ftp)(http) BEDGRAPH
GSE58339_Del_SCR_129_37_Cast.bedgraph.gz 12.9 Mb (ftp)(http) BEDGRAPH
GSE58339_Del_SCR_Cast_11.bedgraph.gz 89.0 Mb (ftp)(http) BEDGRAPH
GSE58339_Del_SCR_Cast_11_129.bedgraph.gz 20.1 Mb (ftp)(http) BEDGRAPH
GSE58339_Del_SCR_Cast_11_Cast.bedgraph.gz 19.1 Mb (ftp)(http) BEDGRAPH
GSE58339_F1_ES.bedgraph.gz 78.3 Mb (ftp)(http) BEDGRAPH
GSE58339_F1_ES_129.bedgraph.gz 15.8 Mb (ftp)(http) BEDGRAPH
GSE58339_F1_ES_Cast.bedgraph.gz 15.0 Mb (ftp)(http) BEDGRAPH
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