|
Status |
Public on May 11, 2020 |
Title |
CTCFChIP_parental_input_rep1 |
Sample type |
SRA |
|
|
Source name |
v-Abl transformed pro-B cell line
|
Organism |
Mus musculus |
Characteristics |
genotype: Emu-Bcl2, RAG2 deficient treatment: 3 uM STI-571 treated for 4 days antibody: none
|
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 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 |
Dec 31, 2019 |
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 |
SAMN13702937 |
SRA |
SRX7481996 |