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Sample GSM3927552 Query DataSets for GSM3927552
Status Public on Oct 22, 2019
Title BRCA1-/- 53BP1_S25A 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-/-
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 (* and minus (* 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 National Cancer Institute
Department Center for Cancer Research
Lab Laboratory of Genome Integrity
Street address 9000 Rockville Pike
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
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
BioSample SAMN12211988
SRA SRX6403368

Supplementary file Size Download File type/resource 23.9 Mb (ftp)(http) BW 23.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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