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Sample GSM4240118 Query DataSets for GSM4240118
Status Public on May 11, 2020
Title CTCFChIP_CTCFdegron_IAA_rep1
Sample type SRA
 
Source name v-Abl transformed pro-B cell line
Organism Mus musculus
Characteristics genotype: CTCFdegron, Emu-Bcl2, RAG2 deficient
treatment: 500 uM IAA 6h, 3 uM STI-571 with 500uM IAA treated for 4 days
antibody: CTCF antibody (Millipore, #07-729)
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 SAMN13702940
SRA SRX7481993

Supplementary file Size Download File type/resource
GSM4240118_CTCFChIP_CTCFdegron_IAA_rep1.broadPeak.gz 356.0 Kb (ftp)(http) BROADPEAK
GSM4240118_CTCFChIP_CTCFdegron_IAA_rep1.bw 223.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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