|
| Status |
Public on Mar 05, 2024 |
| Title |
E5.5_4h_clone4_1 |
| Sample type |
SRA |
| |
|
| Source name |
cRAFR26
|
| Organism |
Mus musculus |
| Characteristics |
cell line: cRAFR26
cell type: E5.5 Epiblast
genotype: Sox2Cre;CRAFR26
clone: clone 4
time: 4h
treatment: 4OHT 4h
|
| Treatment protocol |
E5.5 Sox2Cre; CRAFR26 embryos were cultured in IVC2 media (Bedzhov et al. 2014) supplemented with 250 nM 4OHT (4-Hydroxytamoxifen, Sigma, H7904) to induce ERK. To collect the Epiblast, the extraembryonic layers were removed by microdissection.
|
| Growth protocol |
E5.5 embryos were dissected from the uterus of timely pregnant females.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A group of 10 Epiblasts were placed into a 1.5 ml tube with 350 µl of lysis buffer of the Micro RNEasy Kit (Qiagen, 74004), used for RNA extraction according to manufacturer’s instructions.
Libraries were prepared from 7 ng of RNA per sample using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB, E6420).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw reads were processed with bcl2fastq (v 2.19.1) and STAR (v 2.5.3a) was used to map sequencing reads
Assembly: mm10
Supplementary files format and content: tab-delimited file with raw counts per sample
|
| |
|
| Submission date |
Feb 26, 2024 |
| Last update date |
Mar 05, 2024 |
| 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 (1) |
| GSE259236 |
Common modes of ERK induction resolve into context specific signalling via a combination of signal duration and cell type specific transcriptional repression [E5.5_RNA] |
|
| Relations |
| BioSample |
SAMN40136910 |
| SRA |
SRX23739564 |
