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Sample GSM3733935 Query DataSets for GSM3733935
Status Public on Aug 19, 2019
Title Rad21_Ig2bdel_rep2
Sample type SRA
 
Source name v-Abl transformed pro-B cell line
Organism Mus musculus
Characteristics cell type: v-Abl transformed pro-B cell line
genotype: JH-del, dCas9 expressing, Ig2b-del/del, Emu-Bcl2, RAG2 deficient
Treatment protocol 3 uM STI-571 treated for 4 days
Growth protocol RPMI1640+15% FBS
Extracted molecule genomic DNA
Extraction protocol Briefly, 20 million cells were crosslinked in 37oC prewarmed culture medium with 1% formaldehyde for 10 min at RT. Cells were then treated with cell lysis buffer (5 mM PIPES pH 8, 85 mM KCl, 0.5% NP-40) for 10 min on ice, followed by treatment with nuclei lysis buffer (50 mM TrisCl pH 8.1, 10 mM EDTA, 1% SDS) for 10 min at RT. Chromatin was subjected to sonication with Diagenode Bioruptor at 4oC to achieve an average size of 200-300 bp (30 sec on, 30 sec off, 20 cycles with high energy input). Chromatin was then precleared with Dynabeads Protein A at 4oC for 2 hours. 1/30 lysates were kept as input and the rest were incubated with 5 ug RAD21 antibody (Abcam, ab992) overnight at 4oC. IP samples were then captured by Dynabeads Protein A at 4oC for at least 2 hours, followed by bead washing and elution. IP and Input DNA were de-crosslinked at 65oC overnight and purified via Qiagen PCR purification columns. Purified DNA was subjected to ChIP-Seq library preparation with Illumina Truseq ChIP Sample Preparation Kit (Illumina, IP-202-1012).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model NextSeq 550
 
Description aligned to mm9 genome
Data processing Library strategy: ChIP-Seq
Reads were aligned to mm9 genome using bowtie 2.2.8 with --non-deterministic flag
Unmapped reads were filtered using samtools 1.8
wig files were produced using RSeQC tool 2.6.3 and normalized to a coverage of 10 million 100nt reads for display
Peak calling was performed using MACS2 with the following commands:
macs2 callpeak -t IP.bam -n Result_directory --nomodel --extsize 51 --nolambda -B --SPMR -g mm --verbose 0 –broad
Genome_build: mm9
Supplementary_files_format_and_content: wig files contain peak information for samples, bed files contain peak calling information.
 
Submission date Apr 23, 2019
Last update date Aug 20, 2019
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)
GSE130213 The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination [ChIP-Seq]
GSE130224 The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination
Relations
BioSample SAMN11483998
SRA SRX5726848

Supplementary file Size Download File type/resource
GSM3733935_Rad21_Ig2bdel_rep2.broadPeak.bed.gz 1.7 Mb (ftp)(http) BED
GSM3733935_Rad21_Ig2bdel_rep2.bw 4.6 Gb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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