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Status |
Public on Oct 23, 2015 |
Title |
SanbornRao-2015-HIC047 |
Sample type |
SRA |
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Source name |
haploid fibroblast-like
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Organism |
Homo sapiens |
Characteristics |
cell line: Hap1 protocol: in situ HYbrid Capture Hi-C
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Growth protocol |
Cell lines were cultured according to manufacturer's instructions
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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
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
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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)
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Submission date |
Oct 15, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Suhas Rao |
E-mail(s) |
suhasrao@post.harvard.edu
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Organization name |
Baylor College of Medicine
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Department |
Molecular and Human Genetics
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Lab |
The Center for Genome Architecture
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Street address |
1 Baylor Plaza
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City |
Houston |
State/province |
TX |
ZIP/Postal code |
77030 |
Country |
USA |
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Platform ID |
GPL18573 |
Series (1) |
GSE74072 |
Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes |
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Relations |
BioSample |
SAMN04191952 |
SRA |
SRX1341917 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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