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Sample GSM3131788 Query DataSets for GSM3131788
Status Public on May 05, 2018
Title Kieffer-Kwon-2017-HIC075
Sample type SRA
 
Source name mouse ES cells
Organism Mus musculus
Characteristics genotype: WT
tissue: blastocyst
cell type: ES-E14TG2a
protocol: in situ Hi-C
treatment: N/A
Treatment protocol treatment protocol for specific samples are specified in the SAMPLES section
Growth protocol specificed in the SAMPLES section
Extracted molecule genomic DNA
Extraction protocol Cells were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads.
standard Illumina library construction protocol, Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeqX Ten, or HiSeq 2500 following the manufacturer's protocols
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Data processing The paired end reads were aligned separately using BWA against the mm9 mouse build
PCR duplicates, low mapping quality and unligated reads were removed using Juicer (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
Contact matrices were constructed at various resolutions and normalized using Juicer (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
loops were annotated using HiCCUPS (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016), domains were annotated using Arrowhead (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
Genome_build: mm9 (mouse)
Supplementary_files_format_and_content: .hic file (contains contact matrices at various resolutions in an easy to visualize and access format) (see Durand, Robinson, et al Cell Systems 2016)
 
Submission date May 04, 2018
Last update date May 09, 2019
Contact name Seolkyoung Jung
Organization name NIH
Department NIAMS
Lab biodata mining and discovery section
Street address 10 Center Dr
City bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL17021
Series (1)
GSE82144 Myc regulates chromatin decompaction and nuclear architecture during B cell activation
Relations
BioSample SAMN09076482
SRA SRX4044222

Supplementary file Size Download File type/resource
GSM3131788_Kieffer-Kwon-2017-HIC075.hic 1.6 Gb (ftp)(http) HIC
GSM3131788_Kieffer-Kwon-2017-HIC075_30.hic 1.4 Gb (ftp)(http) HIC
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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