|
| Status |
Public on Aug 08, 2019 |
| Title |
2h_C |
| 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: 2h 4OHT
strain: E14tg2a
background strain: 129SV
Stage: embryonic
|
| Treatment protocol |
Cells were left untreated (0h), or treated with 250nM 4OHT (1h, 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 |
Nuclei were purified by incubation with 10mM TrisHCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.3% Igepal. Open DNA was tagged using the tn5 transposase kit (Illumina)
Fragments were indexed and amplidied using standard Illumina barcodes
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
2h_B_S6
|
| 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 (broad)
Genome_build: mm10
|
| |
|
| Submission date |
Jun 10, 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) |
| GSE132444 |
Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation |
| GSE132480 |
Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation [ATAC-Seq] |
|
| Relations |
| BioSample |
SAMN12006976 |
| SRA |
SRX6003743 |
