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Sample GSM1909121 Query DataSets for GSM1909121
Status Public on Oct 23, 2015
Title SanbornRao-2015-HIC001
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 Illumina HiSeq 2500
 
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 Oct 23, 2015
Contact name Suhas Rao
E-mail suhasrao@post.harvard.edu
Organization name Baylor College of Medicine
Department Molecular and Human Genetics
Lab The Center for Genome Architecture
Street address 1 Baylor Plaza
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL16791
Series (1)
GSE74072 Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
Relations
BioSample SAMN04192005
SRA SRX1341871

Supplementary data files not provided
Raw data provided as supplementary file
Processed data is available on Series record

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