|
| Status |
Public on Mar 25, 2018 |
| Title |
OCEAN-C GM12878 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Normal
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GM12878
tissue: peripheral blood
cell type: B lymphocyte
age: No data
disease state: Normal
gender: female
|
| Biomaterial provider |
Coriell https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM12878&Product=CC
|
| Growth protocol |
Cells were cultured in RPMI-1640 medium (ATCC, Catalog No. 30-2001) with 15% fetal bovine serum and air, 95%, carbon dioxide (CO2), 5% at 37℃.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For OCEAN-C, about 5M cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Formaldehyde was quenched by 0.2M glycine. Nuclear lysates were incubated with MboI. Fragment ends were filled with biotinylated nucleotides, then ligated with T4. Nuclei were then isolated and sonicated. Sonicate was extracted with phenol–chloroform–isoamyl alcohol (25:24:1) and reverse crosslinked. DNA were purified and size selected before Illumina libraries generation
Sequencing libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (E7645, NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
No treatment
Processed data for combined replicates is available at foot of this sample.
|
| Data processing |
Library strategy: OCEAN-C
Hi-C and OCEAN-C reads were aligned to hg19 using Bowtie2
genome build: hg19
processed data files format and content: bed files for Hi-C OCEAN-C sample with HOCIs
|
| |
|
| Submission date |
Jul 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
lumeng Jia |
| E-mail(s) |
[email protected]
|
| Organization name |
Peking university
|
| Street address |
Yiheyuan road
|
| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE100832 |
OCEAN-C: mapping hubs of open chromatin interactions across the genome reveals gene regulatory networks |
|
| Relations |
| BioSample |
SAMN07325862 |
| SRA |
SRX2986032 |
