|
| Status |
Public on Oct 22, 2019 |
| Title |
BRCA1-/- AsiSI MEFS Rad51 ChIP-seq without FHA-PALB2 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse Embryonic Fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mouse Embryonic Fibroblasts
strain: C57BL/6
genotype: BRCA1-/- 53BP1_S25A
chip antibody: RAD51 Abcam #176458
treatment: -FHA-PALB2
expression: AsiSI
|
| Treatment protocol |
Exponentially AsiSI-expressing MEFs were treated with 1uM doxocyclin (DOX) for 24 hours and then, for 5 hours with 4-OHT, resulting in the nuclear translocation of AsiSI
|
| Growth protocol |
Cells are grown in DMEM containing 10% FBS and 1% P/S
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Twenty million cells were harvested for chromatin immunoprecipitation (ChIP) using an anti-RAD51 (10ug/sample) or anti-RPA antibody (10ug/sample). ssDNA that spontaneously forms hairpins after heat renaturation was then enriched and sequenced as described (Brick et al., 2018)
Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads). libraries were prepared and sequenced following standard Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
adapters was removed by trimmomatic version 0.36
mouse reads were aligned to the GRCm38p2/mm10.Alignment done using bowtie version 1.1.2, with the parameters: -l 50 -n 2 -m 1.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were made for plus (*.plus.bw) and minus (*.neg.bw) strand separately using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig
|
| |
|
| Submission date |
Jul 03, 2019 |
| Last update date |
Oct 23, 2019 |
| Contact name |
Wei Wu |
| Organization name |
Center for Excellence in Molecular Cell Science
|
| Department |
Center for Excellence in Molecular Cell Science
|
| Street address |
320 yueyang road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE133805 |
53BP1 Enforces Distinct Pre- and Post-resection Blocks on Homologous Recombination (ChIP-seq) |
| GSE133808 |
53BP1 Enforces Distinct Pre- and Post-resection Blocks on Homologous Recombination |
|
| Relations |
| BioSample |
SAMN12211987 |
| SRA |
SRX6403369 |
