|
| Status |
Public on Dec 04, 2018 |
| Title |
GM12878 HiChIP CTCF biological replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
GM12878 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GM12878
cell type: Lymphoblastoid
gender: female
|
| Biomaterial provider |
GM12878
https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM12878&Product=CC
|
| 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 DNA contact
GM_HiChIP_CTCF.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,mm10
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.
Supplementary_files_format_and_content: bigwig: Bam files were read into R through rsamtools and converted to a 250bp bin coverage object exported by rtracklayer.
|
| |
|
| Submission date |
Oct 09, 2018 |
| Last update date |
May 09, 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) |
| GSE115524 |
HiChIRP reveals RNA-associated chromosome conformation |
|
| Relations |
| BioSample |
SAMN10225262 |
| SRA |
SRX4821796 |
