|
| 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.
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| |
|
| Overall design |
Examination of PolA+ RNA after heterozygous and homozygous enhancer deletion in F1 ES cells (M. musculus129 x M. castaneus).
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| |
|
| Contributor(s) |
Davidson S, Mitchell JA |
| Citation(s) |
25512558 |
| |
| Submission date |
Jun 09, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jennifer Mitchell |
| E-mail(s) |
ja.mitchell@utoronto.ca
|
| 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)
|
|
| Relations |
| BioProject |
PRJNA252023 |
| SRA |
SRP043053 |
| 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 |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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