|
| Status |
Public on Oct 22, 2019 |
| Title |
BRCA1-/- AsiSI MEFS ENDseq rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse Embryonic Fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mouse Embryonic Fibroblasts
strain: C57BL/6
genotype: BRCA1-/-
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 |
MEFs were harvested and 9 million cells were embedded in agarose plugs, after which END-seq was performed as previously described (Canela et al., 2016)
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 |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Library strategy: END-seq
mouse reads were aligned to the GRCm38p2/mm10.Alignment done using bowtie version 1.1.2, with the parameters: -l 50 -n 3 -k 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) |
| GSE133806 |
53BP1 Enforces Distinct Pre- and Post-resection Blocks on Homologous Recombination (END-seq) |
| GSE133808 |
53BP1 Enforces Distinct Pre- and Post-resection Blocks on Homologous Recombination |
|
| Relations |
| BioSample |
SAMN12211980 |
| SRA |
SRX6403374 |
