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Sample GSM3733969 Query DataSets for GSM3733969
Status Public on Aug 19, 2019
Title JHdel_GROSeq_rep1
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, 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 Illumina HiSeq 2500
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
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 GPL17021
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
BioSample SAMN11483988
SRA SRX5726882

Supplementary file Size Download File type/resource 262.9 Mb (ftp)(http) BW 274.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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