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Sample GSM1909124

Query DataSets for GSM1909124

Status

Public on Oct 23, 2015

Title

SanbornRao-2015-HIC004

Sample type

SRA

Source name

haploid fibroblast-like

Organism

Homo sapiens

Characteristics

cell line: Hap1
protocol: in situ Hi-C

Growth protocol

Cell lines were cultured according to manufacturer's instructions

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 MiSeq/HiSeq2500/HiSeqX following the manufacturer's protocols

Library strategy

OTHER

Library source

genomic

Library selection

other

Instrument model

HiSeq X Ten

Data processing

Library strategy: HiC-Seq
The paired end reads were aligned separately using BWA against the b37 human build or the mm9 mouse build
PCR duplicates, low mapping quality and unligated reads were removed using an in-house Hi-C analysis pipeline (see Rao, Huntley, et al)
Contact matrices were constructed at various resolutions and normalized using an in-house Hi-C analysis pipeline (see Rao, Huntley, et al)
loops were annotated using HiCCUPS (see Rao, Huntley, et al. Cell 2014), domains were annotated using Arrowhead (see Rao, Huntley, et al. Cell 2014),
genome build: b37 (human), mm9 (mouse)
processed data files format and content: HiCCUPS_looplist.txt files contain loop calls generated via HiCCUPS; first three fields represent the locus participating in the loop closer to the p-end of the chromosome; fields 4-6 represent the locus participating in the loop closer to the q-end of the chromosome; field 7 represents the color used to display the feature in Juicebox (a Hi-C data visualization software, see www.aidenlab.org/juicebox); field 8 represents the observed number of counts at the loop; fields 9-12 represent the expected number of counts at the loop using four different expected models; fields 13-16 are the q-values over each of the expected values; field 17 is the number of enriched pixels that was clustered into a particular loop; field 18-19 are the centroid of the loop; field 20 is the radius of the loop
processed data files format and content: Arrowhead_domainlist.txt files contain domain calls generated via Arrowhead; first 6 fields represent the boundaries of the domain; field 7 represents the color used to display the feature in Juicebox (a Hi-C data visualization software, see www.aidenlab.org/juicebox); field 8 is the corner score for the domain (see Rao, Huntley, et al. Cell 2014); fields 9-12 are the component scores used in the Arrowhead algorithm (see Rao, Huntley, et al. Cell 2014)

Submission date

Oct 15, 2015

Last update date

May 15, 2019

Contact name

Suhas Rao

E-mail(s)

suhasrao@post.harvard.edu

Organization name

Baylor College of Medicine

Department

Molecular and Human Genetics