|
| Status |
Public on Jan 12, 2019 |
| Title |
Control_CTCF-HiChIP_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Hela S3 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Hela S3 cells
genotype/variation: stably expressed FLAG tag alone
antibody: CTCF(Active motif, 61311)
|
| Treatment protocol |
Cells were crosslinked with 1% formaldehyde for 10 minutes, then quenched with 0.125M glycine for 5 minutes.
|
| Growth protocol |
HeLa-S3 cells were cultured in DMEM (Hyclone) supplemented with 10% fetal bovine serum. Cultured cells were maintained at 37°C in a 5% CO2 incubator.
|
| 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 |
HiSeq X Ten |
| |
|
| Description |
Control_CTCF-HiChIP_combine_allValidPairs.hic
|
| Data processing |
Library strategy: HiChIP-seq
HiChIP paired-end reads were first subjected to Trim Galore to remove adaptors.
Trimmed reads were aligned to the hg19 genome using the HiC-Pro software with default settings except that reads were assigned to MboI restriction fragments.
Valid reads generated by HiC-Pro were transformed to .hic format for juice tools with KR normalization using hicpro2juicebox function, then contact domains were identified using juice tools arrowhead function with 10kb resolution.
Genome_build: hg19
Supplementary_files_format_and_content: hic format for CTCF-mediated chromatin looping in Control and CTCF-s OE cells
|
| |
|
| Submission date |
Jan 31, 2018 |
| Last update date |
Jan 12, 2019 |
| Contact name |
Kaimeng Huang |
| E-mail(s) |
Kaimeng_huang@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Street address |
4 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE108869 |
An alternative CTCF isoform antagonizes canonical CTCF occupancy and changes chromatin architecture to promote apoptosis |
|
| Relations |
| BioSample |
SAMN08446814 |
| SRA |
SRX3634853 |
