|
| Status |
Public on Feb 03, 2015 |
| Title |
HCT116 |
| Sample type |
SRA |
| |
|
| Source name |
human colorectal cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
fraction: TET2_bound
antibody: anti TET2 (SantaCruz, catalog# sc-136926, lot# H2412)
cell line: HCT116 colorectal cancer cell line
|
| Treatment protocol |
not applicable
|
| Growth protocol |
not applicable
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For hmeDIP-seq, Illumina libraries were prepared from sonicated genomic DNA followed by immunoprecipitation with anti-5hmC antibody (Active Motif, 39791) and sequenced.
For TET2 ChIP-seq, formaldehyde cross-linked material was immunoprecipitated with anti-TET2 antibody (SantaCruz sc-136926) followed by Illumina adapter ligation and sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
HCT116 human colorectal cancer cell line
HCT116
HCT116
|
| Data processing |
Alignments: For HCT116 TET2 ChIP-seq, Illumina reads were aligned to the Human Reference Genome (assembly hg18, NCBI Build 36.3, March 2008) using BWA version 0.5.9.
Peak calling: For HCT116 TET2 ChIP-seq, enriched regions (peaks) were identified using MACS version 1.4 (Zhang et al, 2008) with the default parameters and a p-value cut-off < 10-10. Peaks were then filtered to avoid significant overlaps (< 80%) with repetitive regions using the UCSC repeat marker tracks.
Genome_build: hg18
Supplementary_files_format_and_content: MACS peaks in .bed file format
|
| |
|
| Submission date |
Jun 03, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Chandra Chilamakuri |
| E-mail(s) |
[email protected]
|
| Organization name |
Cancer Research UK Cambridge Institute
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL15456 |
| Series (2) |
| GSE47590 |
5-hydroxymethylcytosine marks promoters in colon that resist hypermethylation in cancer [seq] |
| GSE47592 |
5-hydroxymethylcytosine marks promoters in colon that resist hypermethylation in cancer |
|
| Relations |
| BioSample |
SAMN02189738 |
| SRA |
SRX290521 |
| Named Annotation |
GSM1152879_HCT116_TET2_peaks.bed.gz |
