|
| Status |
Public on May 11, 2020 |
| Title |
Rad21ChIP_HCT116spikingin_parental_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
v-Abl transformed pro-B cell line
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Emu-Bcl2, RAG2 deficient
antibody: Rad21 antibody (Abcam, #ab992)
treatment: 3 uM STI-571 treated for 4 days
|
| Growth protocol |
RPMI1640+15% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crosslinked cells were treated with cell lysis buffer (5mM PIPES pH 8, 85mM KCl, 0.5% NP-40) and nuclei lysis buffer (50mM TrisCl pH 8.1, 10mM EDTA, 1% SDS) and subjected to sonication. IP was performed using Rad21 antibody(Abcam, #ab992) or CTCF antibody (Millipore, #07-729). IP and Input DNA were de-crosslinked at 65o overnight and purified via Qiagen PCR purification columns.
ChIP-Seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB, #E7645)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
aligned to AJ851868/mm9 hybrid genome
|
| Data processing |
Reads were aligned using bowtie 2.2.8 with --non-deterministic flag
reads were quantified for specific loci using samtools version 1.8
bigwig files were produced using RseqQ package
Genome_build: AJ851868/mm9 hybrid genome,hg19
Supplementary_files_format_and_content: bigwig files contain peak information for samples
|
| |
|
| Submission date |
Jan 06, 2020 |
| Last update date |
May 12, 2020 |
| Contact name |
Frederick W Alt |
| E-mail(s) |
jianqiao.hu@childrens.harvard.edu
|
| Organization name |
Boston Children's Hospital
|
| Department |
PCMM
|
| Lab |
Alt
|
| Street address |
1 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE142779 |
CTCF orchestrates long-range cohesin-driven V(D)J recombinational scanning [ChIP-Seq] |
| GSE142781 |
CTCF orchestrates long-range cohesin-driven V(D)J recombinational scanning |
|
| Relations |
| BioSample |
SAMN13741194 |
| SRA |
SRX7508561 |
