|
| Status |
Public on Aug 08, 2019 |
| Title |
repB ESRRB 8h |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic stem cells stably expressing a cRAF-ErT2 expression cassette
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic stem cells stably expressing a cRAF-ErT2 expression cassette
treatment: 8h 4OHT
antibody: anti-ESRRB
strain: E14tg2a
background strain: 129SV
Stage: embryonic
|
| Treatment protocol |
Cells were left untreated (0h), or treated with 250nM 4OHT for 2h, 4h or 8h
|
| Growth protocol |
mESCs were grown in serum containing medium, supplemented with 1x LIF (made in house) and 2uM Chir99021. 24hrs prior to treatment, media was changed to serum containing media supplemented with 1x LIF and 250nM PD173074.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells we fixed in 1% formaldehyde at RT for 10 minutes and subsequently 2mM disuccinimidyl glutarate , nuclei extracted and chromatin sonicated using a bioruptor (10 cycles, 30s on 30s off). Cleared chromatin was incubated with anti-ESRRB (R&D, PP-H6705-00), or anti SOX2 antibody (R&D, AF2018). Input DNA serves as negative control for antibody enrichment.
Libraries were prepared using the NEB Next Ultra 2 kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
B_E_8h
|
| Data processing |
reads were mapped uning bowtie2
duplicate reads were removed
reads were quality filtered
reads were counted using bedtools coverage
peaks were called using MACS2 (narrow)
Genome_build: mm10
Supplementary_files_format_and_content: MACS PEAK BED
|
| |
|
| Submission date |
Jun 10, 2019 |
| Last update date |
Feb 27, 2020 |
| Contact name |
Josh M Brickman |
| E-mail(s) |
joshua.brickman@sund.ku.dk
|
| Organization name |
Copenhagen University
|
| Department |
reNEW
|
| Lab |
Brickman
|
| Street address |
3B Blegdamsvej
|
| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE132444 |
Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation |
| GSE132483 |
Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation [ESRRB_SOX2] |
|
| Relations |
| BioSample |
SAMN12008717 |
| SRA |
SRX6032066 |
