|
| Status |
Public on Aug 31, 2016 |
| Title |
HiChIP GM biological replicate 2 technical replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
GM12878
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Lymphoblastoid
gender: female
|
| Biomaterial provider |
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12878
|
| Treatment protocol |
Cells were crosslinked with 1% formaldehyde for 10 minutes, then quenched with 0.125M glycine for 5 minutes.
|
| Growth protocol |
mES cells were grown on gelatin plates with serum and LIF. GM cells were grown in RPMI-1640 with serum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Long-range contacts were generated and ChIP was performed.
Libraries were prepared using the Tn5 transposase.
Nextera
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Protein-enriched long-range contact.
Processed data file: HiChIP_GM_cohesin.hic
|
| Data processing |
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908).
Processed reads were then inputted into the Juicebox pipeline (PMID: 27467250) to allow for visualization of the interaction matrix.
Genome_build: hg19,mm9
Supplementary_files_format_and_content: *allValidPairs.txt: 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 pipeline. This file allows for visualization of the interaction matrix.
|
| |
|
| Submission date |
Apr 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ryan Alexander Flynn |
| E-mail(s) |
raflynn@stanford.edu
|
| Organization name |
Stanford University
|
| Street address |
380 Roth Way, Room 265
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE80820 |
HiChIP: Efficient and sensitive analysis of protein-directed genome architecture |
|
| Relations |
| BioSample |
SAMN04915625 |
| SRA |
SRX1736959 |
