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Sample GSM3733959 Query DataSets for GSM3733959
Status Public on Aug 19, 2019
Title dCas9Control_GROSeq_rep3
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, Emu-Bcl2, RAG2 deficient
Treatment protocol 3 uM STI-571 treated for 4 days
Growth protocol RPMI1640+15% FBS
Extracted molecule nuclear RNA
Extraction protocol Briefly, 10 million cells were permeabilized with permeabilization buffer (10 mM Tris-HCl, pH 7.4, 300 mM sucrose, 10 mM KCl, 5 mM MgCl2, 1 mM EGTA, 0.05% Tween-20, 0.1% NP40 substitute, 0.5 mM DTT, one tablet of protease inhibitors per 50 ml and 4 units Rnase inhibitor per ml) and resuspended in 100 ul storage buffer (10 mM Tris-HCl, pHHH 8.0, 25% (vol/vol) glycerol, 5 mM MgCl2, 0.1 mM EDTA and 5 mM DTT). Permeabilized cells were subjected to nuclear run-on (2xRun-on mix: 5 mM Tris-Cl, PH 8.0, 2.5 mM MgCl2, 0.5 mM DTT, 150 mM KCl, 0.5 mM ATP, 0.5 mM CTP, 0.5 mM GTP, 0.5 mM BrUTP, 10 units of RNase inhibitor, 1% sarkosyl) at 37o for 5 min, followed by Trizol-based RNA extraction.
Illumina adapters were ligated to RNA followed by cDNA generation with reverse transcriptase. Libraries were PCR-amplified with Illumina primers and subjected to sequencing.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model NextSeq 550
 
Description aligned to mm9 genome
Data processing Library strategy: GRO-Seq
Reads were aligned to mm9 genome using bowtie 2.2.8 with --non-deterministic flag
Aligned reads were separated into positive and negative strand 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
Genome_build: mm9
Supplementary_files_format_and_content: wig files contain peak information for samples
 
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)
GSE130215 The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination [GRO-Seq]
GSE130224 The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination
Relations
BioSample SAMN11483961
SRA SRX5726872

Supplementary file Size Download File type/resource
GSM3733959_dCas9Control_rep3.neg.bw 444.0 Mb (ftp)(http) BW
GSM3733959_dCas9Control_rep3.pos.bw 457.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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