 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 03, 2017 |
| Title |
Cytosine modifications modulate the chromatin architecture of transcriptional enhancers |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
|
| Summary |
The dynamics of cytosine modifications such as 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) have been correlated with activation of transcriptional enhancers. However, their functional relationship with the regulation of enhancer activity by pioneer transcription factors remains elusive. To gain insights into their function, we interrogated chromatin characteristics of enhancers bound by the pioneer factors FOXA1, MEIS1 and PBX1at different ime points during differentiation of mouse embryonal carcinoma cells into neural progenitors.
|
| |
|
| Overall design |
Genomic DNA or chromatin from P19 mouse embryonal carcinoma (EC) cells treated with retinoic acid (RA) and collected at 0 (vehicle, veh), 6, 12, 18, 24 or 48 hrs, were extracted and submitted to immunoprecipitation with 5mC (MeDIP) or 5hmC (hMeDIP) antibodies for genomic DNA or with H3K4me1, H3K27ac, FoxA1, Meis1, Pbx1 and Tet2 antibodies for chromatin. In addition, Formaldehyde Assisted Isolation of Regulatory Elements (FAIRE) was run with chromatin in order to map open chromatin regions. Reads were mapped to the mouse mm8 genome.
|
| |
|
| Contributor(s) |
Salbert G, Mahé E, Avner S |
| Citation(s) |
28396520 |
| |
| Submission date |
Jun 06, 2016 |
| Last update date |
Aug 30, 2019 |
| Contact name |
Gilles Salbert |
| Organization name |
University Rennes 1
|
| Department |
IGDR UMR6290
|
| Street address |
263 Av. Gal. Leclerc
|
| City |
Rennes |
| ZIP/Postal code |
35200 |
| Country |
France |
| |
|
| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL18480 |
Illumina HiSeq 1500 (Mus musculus) |
|
| Samples (46)
|
| GSM2188884 |
H3K4me1 ChIP-seq P19, RA 18hrs |
| GSM2188885 |
H3K4me1 ChIP-seq P19, RA 24hrs |
| GSM2188886 |
H3K4me1 ChIP-seq P19, RA 48hrs |
| GSM2188887 |
FAIRE-seq P19, veh |
| GSM2188888 |
FAIRE-seq P19, RA 6hrs |
| GSM2188889 |
FAIRE-seq P19, RA 12hrs |
| GSM2188890 |
FAIRE-seq P19, RA 18hrs |
| GSM2188891 |
FAIRE-seq P19, RA 24hrs |
| GSM2188892 |
FAIRE-seq P19, RA 48hrs |
| GSM2188893 |
hMeDIP-seq P19, veh |
| GSM2188894 |
hMeDIP-seq P19, RA 6hrs |
| GSM2188895 |
hMeDIP-seq P19, RA 12hrs |
| GSM2188896 |
hMeDIP-seq P19, RA 18hrs |
| GSM2188897 |
hMeDIP-seq P19, RA 24hrs |
| GSM2188898 |
hMeDIP-seq P19, RA 48hrs |
| GSM2188899 |
MeDIP-seq P19, veh |
| GSM2188900 |
MeDIP-seq P19, RA 6hrs |
| GSM2188901 |
MeDIP-seq P19, RA 12hrs |
| GSM2188902 |
MeDIP-seq P19, RA 18hrs |
| GSM2188903 |
MeDIP-seq P19, RA 24hrs |
| GSM2188904 |
MeDIP-seq P19, RA 48hrs |
| GSM2188905 |
FoxA1 ChIP-seq P19, veh |
| GSM2188906 |
FoxA1 ChIP-seq P19, RA 48hrs |
| GSM2188907 |
H3K27ac ChIP-seq P19, veh |
| GSM2188908 |
H3K27ac ChIP-seq P19, RA 6hrs |
| GSM2188909 |
H3K27ac ChIP-seq P19, RA 12hrs |
| GSM2188910 |
H3K27ac ChIP-seq P19, RA 18hrs |
| GSM2188911 |
H3K27ac ChIP-seq P19, RA 24hrs |
| GSM2188912 |
H3K27ac ChIP-seq P19, RA 48hrs |
| GSM2188913 |
Input-seq P19, veh |
| GSM2188914 |
Input-seq P19, RA 6hrs |
| GSM2188915 |
Input-seq P19, RA 12hrs |
| GSM2188916 |
Input-seq P19, RA 18hrs |
| GSM2188917 |
Input-seq P19, RA 24hrs |
| GSM2188918 |
Input-seq P19, RA 48hrs |
| GSM2188919 |
Meis1 ChIP-seq P19, veh |
| GSM2188920 |
Meis1 ChIP-seq P19, RA 6hrs |
| GSM2188921 |
Meis1 ChIP-seq P19, RA 12hrs |
| GSM2188922 |
Meis1 ChIP-seq P19, RA 18hrs |
| GSM2188923 |
Mesi1 ChIP-seq P19, RA 24hrs |
| GSM2188924 |
Meis1 ChIP-seq P19, RA 48hrs |
| GSM2188925 |
Pbx1 ChIP-seq, P19, RA 48 hrs |
| GSM2188926 |
Tet2 ChIP-seq, P19, RA 48 hrs |
|
| Relations |
| BioProject |
PRJNA324606 |
| SRA |
SRP076190 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE82314_RAW.tar |
12.3 Gb |
(http)(custom) |
TAR (of WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...