|
| Status |
Public on Apr 30, 2023 |
| Title |
FOXD3-endo-G1S-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
G1/S phase synchronized cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mESCs
culture conditions: L2i
tag insertion: endogenous
bait: streptavidin magnetic beads
|
| Treatment protocol |
For exogenous samples, cells were kept consistently on 0.05µg/ml doxycycline for expression of exogenous FOXD3-Avi.
|
| Growth protocol |
Mouse ESCs were seeded on a 10 cm plate (10^6 cells) in L2i containing growth medium and harvested 2 days after seeding.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and FOXD3-DNA complexes were isolated with streptavidin magnetic beads.
Libraries were prepared according to manufacturers' instructions (NEBNext Ultra II).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Bowtie 2 mapping
Deeptools bamCompare for bigwig file creation
Peak calling with MACS2
Assembly: mm10
Supplementary files format and content: bigwig
|
| |
|
| Submission date |
Mar 17, 2022 |
| 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 |
GPL21103 |
| Series (2) |
| GSE183418 |
Genome-wide binding of FOXD3 in mouse ESCs |
| GSE183420 |
Transcriptional repressor FOXD3 safeguards genome integrity in embryonic stem cells |
|
| Relations |
| BioSample |
SAMN26750479 |
| SRA |
SRX14491857 |
