|
| Status |
Public on Aug 28, 2017 |
| Title |
K562 HiChIP H3K27ac biological replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
K562 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
cell type: Chronic Myelogenous Leukemia
Sex: female
|
| Treatment protocol |
Crosslinked with 1% formaldehyde
|
| Growth protocol |
Grown in RPMI-1640 with 15% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Protein enrichment of 3C library
Nextera
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Protein-enriched long-range contact
K562_HiChIP_H3K27ac.hic
K562_HiChIP_H3K27ac_B2.hic
|
| Data processing |
Library strategy: HiChIP
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908)
Filtered reads were converted to a .hic file for visualization with Juicebox (PMID: 25497547)
Genome_build: hg19,mm9
Supplementary_files_format_and_content: validPairs output from the HiC-Pro pipeline. Aligned, filtered, and unique long-range contacts to call loops with.
Supplementary_files_format_and_content: HiC output from the Juicebox Tools pipeline. Matrix file to visualize long-range interactions with Juicebox.
|
| |
|
| Submission date |
Jul 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Howard Y Chang |
| Organization name |
Stanford University
|
| Street address |
269 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE101498 |
Enhancer connectome in primary human cells reveals target genes of disease-associated DNA elements |
|
| Relations |
| BioSample |
SAMN07357449 |
| SRA |
SRX3008798 |
