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Sample GSM4556387 Query DataSets for GSM4556387
Status Public on May 16, 2020
Title HIC097_eB
Sample type SRA
 
Source name 63-12 RNP-eB
Organism Mus musculus
Characteristics tissue source: cell line - 63-12 pre B cell
protocol: Hi-C
rnp: eBeta (eB)
Extracted molecule genomic DNA
Extraction protocol 5x10^6 formaldehyde-cross-linked cells were lysed on ice for 15 minutes with 250 μl of ice-cold Hi-C lysis buffer (10mM Tris-HCl pH8.0, 10mM NaCl, 0.2% Igepal CA630) containing protease inhibitors (Roche). Chromatin was digested using DpnII (100 U) at 37°C for 6 hours. The digested DNA ends were then filled and marked with biotin using Klenow, followed by ligation with T4 DNA ligase. After reversing the cross-links, DNA was fragmented using a Covaris E220 Evolution Sonicator followed by size-selection for 300-500bp using AMPure XP Beads (Beckman Coulter).
DNA end-repair was performed using NEBNext Ultra II DNA Library Prep Kit according to the manufacturer’s instructions using 1μg of the Hi-C DNA. Adaptor-ligated DNA was then selected for 300-400bp using AMPure XP beads and the biotinylated DNA fragments were pulled down using MyOne Streptavidin T1 beads (Life Technologies). The final Hi-C library was generated with 5 PCR cycles using the NEBNext Ultra II DNA Library Prep Kit and NEBNext Dual Index primers (NEB) for Illumina sequencing.
Paired end using NEBNext Ultra II DNA Library Prep Kit and NEBNext Dual Index primers (NEB)
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description DNA - Hi-C DNA seq
Data processing HI-C Reads were processed using Juicer pipeline
Genome_build: mm9
Supplementary_files_format_and_content: hic files as produced by Juicer. The files are inter_30.hic.
 
Submission date May 15, 2020
Last update date May 18, 2020
Contact name Patrick Leonard Collins
E-mail(s) patrick.collins@osumc.edu
Phone 6156683538
Organization name Ohio State University
Department Microbial Infection and Immunity
Street address 770 BRT, 460 W 12th Ave
City Columbus
State/province OH
ZIP/Postal code 43210
Country USA
 
Platform ID GPL24247
Series (1)
GSE150384 DNA Double-Strand Breaks Induce H2Ax Phosphorylation Domains in a Contact-Dependent Manner
Relations
BioSample SAMN14933964
SRA SRX8350008

Supplementary file Size Download File type/resource
GSM4556387_HIC097_eB.hic 5.3 Gb (ftp)(http) HIC
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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