|
| Status |
Public on Apr 30, 2023 |
| Title |
EtOH-Thy-4h-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
mESCs
|
| Organism |
Mus musculus |
| Characteristics |
culture conditions: L2i
genotype: FOXD3-iKO
treatment time: 24h
molecule subtype: 4SU-labeled RNA
|
| Treatment protocol |
Synchronization was achieved using a double thymidine block strategy and cells were release at 24h post tamoxifen treatment. 4SU was added for 30min or 15min for non-synchronized and synchronized cells, respectively.
|
| Growth protocol |
Mouse ESCs were seeded on a 10 cm plate (10^6 cells) or for synchronized cells on a well of a 6well plate (170k cells) in L2i containing growth medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were extracted using Trizol LS.
Libraries were prepared according to manufacturers' instructions (KAPA RNA Hyperprep).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
counts_foxd3_thymidine_sychronized.txt
DG124
|
| Data processing |
Library strategy: 4SU-seq
STAR mapping
featureCounts read count
Genome_build: mm10
Supplementary_files_format_and_content: count matrices
|
| |
|
| Submission date |
Sep 03, 2021 |
| Last update date |
Apr 30, 2023 |
| Contact name |
Robert Blelloch |
| Organization name |
UCSF
|
| Department |
Urology
|
| Street address |
35 Medical Center Way
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL28457 |
| Series (2) |
| GSE183416 |
Nascent RNA sequencing of FOXD3 KO and WT mouse ESCs |
| GSE183420 |
Transcriptional repressor FOXD3 safeguards genome integrity in embryonic stem cells |
|
| Relations |
| BioSample |
SAMN21218254 |
| SRA |
SRX12010361 |
