|
| Status |
Public on Aug 08, 2019 |
| Title |
8h-2h Meki clone b input for RBP1 ChIP |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
treatment: 8h with 4OHT plus 2 hours with MEK inhibitor PD0325901
cell line: E14tg2a
background strain: 129SV
Stage: embryonic
chip antibody: none (input)
|
| Treatment protocol |
Cells were left untreated (0h), or treated with 250nM 4OHT (2h, 8h), or treated with 4OHT for 8hrs followed by a subsequent 2h Mek inhibitor treatment (8_2h).
|
| 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, nuclei extracted and chromatin sonicated using a bioruptor (10 cycles, 30s on 30s off). Cleared chromatin was incubated with anti-RBP1 antibody (Active Motif, 39097). 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 |
ChIP-seq
|
| Data processing |
reads were mapped uning bowtie2
duplicate reads were removed
reads were quality filtered
reads were counted using bedtools coverage
Genome_build: mm10
Supplementary_files_format_and_content: excel file
|
| |
|
| Submission date |
May 29, 2019 |
| Last update date |
Aug 08, 2019 |
| 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) |
| GSE131932 |
Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation [RBP1 ChIP-seq] |
| GSE132444 |
Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation |
|
| Relations |
| BioSample |
SAMN11885942 |
| SRA |
SRX5927400 |
