|
| Status |
Public on Jun 12, 2015 |
| Title |
Hs_CTCF_X_ChIP_(20141204_25) |
| Sample type |
SRA |
| |
|
| Source name |
Crosslinked MNase digested chromatin
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562 cells
antibody: CTCF (Millipore catalog #07-729)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Human K562 cells were crosslinked using formaldehyde for 10 minutes at room temperature. Chromatin was fragmented using MNase and then sonicated to ensure complete extraction of chromatin and associated proteins. Chromatin was immunoprecipitated using an antibody against CTCF. DNA was extracted from the immunoprecipitated chromatin and subjected to Illumina (Solexa) sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
High-resolution X-ChIP-seq for CTCF was performed in human K562 celss using a specific antibody against CTCF.
library strategy: Modified ChIP-seq (see PMID 22025700)
|
| Data processing |
1. We used Bowtie2 (v2.2.3) with options "--no-unal --local --very-sensitive-local --no-discordant --no-mixed --contain --overlap --dovetail --phred33 -I 10 -X 700" to map paired-end 25bp reads to release hg19 of the human genomic sequence obtained from UCSC. 2. We extracted properly paired reads (Supplementary file .bed). 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig)
|
| |
|
| Submission date |
Mar 31, 2015 |
| Last update date |
Jul 13, 2020 |
| Contact name |
Jorja Henikoff |
| E-mail(s) |
jorja@fhcrc.org
|
| Phone |
206-667-4850
|
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Department |
Basic Sciences
|
| Lab |
Henikoff
|
| Street address |
1100 Fairview AV N, A1-162
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-1024 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE67454 |
A simple method for generating high-resolution maps of genome wide protein binding |
|
| Relations |
| BioSample |
SAMN03453194 |
| SRA |
SRX974395 |
