|
| Status |
Public on Aug 08, 2019 |
| Title |
Clone b, 4OHT treated for 1hr [mRNA_TC] |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic stem cells expressing a cRAF-ERT2 construct allowing ERK activation upon the addition of 4OT
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic stem cells expressing a cRAF-ERT2 construct allowing ERK activation upon the addition of 4OT
treatment: 4OHT treated for 1hr
strain: E14tg2a
background strain: 129SV
Stage: embryonic
|
| Treatment protocol |
Cells were left untreated (0h), or treated with 250nM 4OHT (2h). 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). rRNA was removed using the RiboGold kit (Illumina)
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 |
rRNA depleted RNA
1h_b
|
| Data processing |
Reads were mapped using STAR, removing multi-mappers
Count tables were generated using featureCounts
fold change vaues 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 |
| GSE132497 |
Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation [mRNA_TC] |
|
| Relations |
| BioSample |
SAMN12009240 |
| SRA |
SRX6035600 |
