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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 11, 2014 |
| Title |
HIC014 |
| Sample type |
SRA |
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| Source name |
B-lymphoblastoids
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| Organism |
Homo sapiens |
| Characteristics |
cell line: GM12878
protocol: in situ Hi-C
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| Biomaterial provider |
http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12878
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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/HiSeq2000/HiSeq2500 following the manufacturer's protocols
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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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), domains were annotated using Arrowhead (see Rao, Huntley, et al), subcompartments were annotated using a Gaussian HMM (see Rao, Huntley, et al)
Genome_build: b37 (human), mm9 (mouse)
Supplementary_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
Supplementary_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); fields 9-12 are the component scores used in the Arrowhead algorithm (see Rao, Huntley, et al)
Supplementary_files_format_and_content: the subcompartment bed file contains the coordinates of the 6 nuclear subcompartments identified in Rao, Huntley, et al.
Supplementary_files_format_and_content: HIC*_merged_nodups.txt files specify each Hi-C read pair (i.e., the mapping locations of each individual read pair).
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| Submission date |
Nov 20, 2014 |
| Last update date |
May 21, 2024 |
| Contact name |
Suhas Rao |
| E-mail(s) |
[email protected]
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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 |
GPL11154 |
| Series (1) |
| GSE63525 |
A three-dimensional map of the human genome at kilobase resolution reveals prinicples of chromatin looping |
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| Relations |
| Reanalyzed by |
GSE87112 |
| Reanalyzed by |
GSM2360324 |
| Reanalyzed by |
GSE167200 |
| Reanalyzed by |
GSE242815 |
| Reanalyzed by |
GSE255264 |
| Reanalyzed by |
GSE268050 |
| BioSample |
SAMN03203331 |
| SRA |
SRX764949 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1551563_HIC014.hic |
5.3 Gb |
(ftp)(http) |
HIC |
| GSM1551563_HIC014_30.hic |
4.0 Gb |
(ftp)(http) |
HIC |
| GSM1551563_HIC014_merged_nodups.txt.gz |
5.7 Gb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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