|
| Status |
Public on Aug 08, 2019 |
| Title |
8h_WT_clone B +DOX |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic stem cells
treatment: 8h 4OHT
strain: E14tg2a
background strain: 129SV
Stage: embryonic
genotype/variation: Med24 KO cells rescued with TET-Med24 cDNA
|
| Treatment protocol |
Cells were left untreated (0h DMSO), or treated with 250nM 4OHT (2h, DMSO), or treated with either PD302509 or PP1, or in combination with 4OHT for 2hrs. 15 minutes prior to RNA isolation cells were treated with 5mM ethynyl uridine to label newly synthesized RNA.
|
| 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 |
total RNA |
| Extraction protocol |
Total RNA was collected using the RNeasy Mini Kit (Qiagen). Genomic DNA was eliminated by DNAse treatment (Qiagen). Nascent RNA was purified using the Click-iT Nascent RNA Capture Kit (Invitrogen)
Libraries were prepared using the NEB Next Ultra 2 kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
nascent RNA
8h_WT_B
|
| Data processing |
Reads were mapped using STAR, removing multi-mappers
Count tables were generated using featureCounts
fold change vaues (0h/2h) (0h/8h) were determined using the Deseq package
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 |
| GSE132494 |
Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation [Med24_KO] |
|
| Relations |
| BioSample |
SAMN12009133 |
| SRA |
SRX6033301 |
