 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 05, 2020 |
| Title |
Cremer-2019-HIC005 |
| Sample type |
SRA |
| |
|
| Source name |
HCT-116 cmvOsTIR1 RAD21-mAC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line background: HCT-116
genotype/variation: cmvOsTIR1, RAD21-mAC
treatment: 500uM IAA, 6hrs
|
| 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 NextSeq 500 following the manufacturer's protocols
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Cremer-2019-HIC005_HIC10453_S6
|
| Data processing |
The paired end reads were aligned separately using BWA against the hg19 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)
Genome_build: hg19
Supplementary_files_format_and_content:
*.hic file contains contact matrices at various resolutions in an easy to visualize and access format (Durand, Robinson, et al Cell Systems 2016)
Bedgraph containing deduplicated counts (early and late bedgraphs) or log-2 ratios of early to late binned at 5kb or 50kb resolution (ELratio bedgraph)
|
| |
|
| Submission date |
Feb 11, 2020 |
| Last update date |
Oct 05, 2020 |
| Contact name |
Suhas Rao |
| E-mail(s) |
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 |
GPL18573 |
| Series (1) |
| GSE145099 |
Cohesin depleted cells rebuild active and inactive nuclear compartments after mitosis |
|
| Relations |
| BioSample |
SAMN14083377 |
| SRA |
SRX7708020 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4306485_Cremer-2019-HIC005.hic |
63.3 Mb |
(ftp)(http) |
HIC |
| GSM4306485_Cremer-2019-HIC005_30.hic |
60.6 Mb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
