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Status |
Public on May 16, 2020 |
Title |
HIC097_eB |
Sample type |
SRA |
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Source name |
63-12 RNP-eB
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Organism |
Mus musculus |
Characteristics |
tissue source: cell line - 63-12 pre B cell protocol: Hi-C rnp: eBeta (eB)
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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)
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Library strategy |
Hi-C |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
DNA - Hi-C DNA seq
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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.
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Submission date |
May 15, 2020 |
Last update date |
May 18, 2020 |
Contact name |
Patrick Leonard Collins |
E-mail(s) |
patrick.collins@osumc.edu
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Phone |
6156683538
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Organization name |
Ohio State University
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Department |
Microbial Infection and Immunity
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Street address |
770 BRT, 460 W 12th Ave
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City |
Columbus |
State/province |
OH |
ZIP/Postal code |
43210 |
Country |
USA |
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Platform ID |
GPL24247 |
Series (1) |
GSE150384 |
DNA Double-Strand Breaks Induce H2Ax Phosphorylation Domains in a Contact-Dependent Manner |
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Relations |
BioSample |
SAMN14933964 |
SRA |
SRX8350008 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4556387_HIC097_eB.hic |
5.3 Gb |
(ftp)(http) |
HIC |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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