Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Digestive tract
Cell type
LoVo
Primary Tissue
Colon
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
LoVo
cell line
LoVo
cell type
colon adenocarcinoma
hgn
CTCF
antibody
Santa Cruz Biotechnology, Inc. : sc-15914 X
control sample
LoVoSTTnocodazole0_IgG_Goat
blocking protocol
Thymidine block + nocodazole

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked by 1% formaldehyde, and DNA was sonicated to 200- 400 bp fragments. Antibodies (5 µg) were added and collected using protein G Sepharose (GE). Cross-links were reversed and proteins digested by incubation with proteinase K at 65 °C overnight. DNA was then purified using Qiagen PCR purification kit.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
30465536
Reads aligned (%)
62.0
Duplicates removed (%)
35.1
Number of peaks
12053 (qval < 1E-05)

hg38

Number of total reads
30465536
Reads aligned (%)
64.0
Duplicates removed (%)
33.7
Number of peaks
12035 (qval < 1E-05)

Base call quality data from DBCLS SRA