Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Digestive tract
Cell type
COLO 829
Primary Tissue
Skin
Tissue Diagnosis
Melanoma

Attributes by original data submitter

Sample

source_name
COLO829 cells
chip antibody
CTCF (Millipore 07-729)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Early passage cells were cross-linked in 1% formaldehyde and nuclei were extracted. Nuclei were lysed and DNA was sonicated for 6 hours in a Diagenode Pico Bioruptor (30 seconds on/ 30 seconds off). Chromatin was divided across two samples and incubated with polyclonal rabbit anti-CTCF antibody (Millipore 07-729) and rabbit immunoglobulin G (IgG; Sigma I5006) respectively. DNA was then purified, size selected and sequenced. Library construction was performed as per Illumina protocol Rev A 11257047

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
65282512
Reads aligned (%)
67.2
Duplicates removed (%)
31.5
Number of peaks
44202 (qval < 1E-05)

hg38

Number of total reads
65282512
Reads aligned (%)
69.1
Duplicates removed (%)
30.1
Number of peaks
44590 (qval < 1E-05)

Base call quality data from DBCLS SRA