Antigen

Antigen Class

TFs and others

Antigen

CTCF

Cell type

Cell type Class

Digestive tract

Cell type

Colon cancer cell line

NA

NA

Sample

source_name

DKO

cell type

colon cancer cell line

treatment

none

Sex

male

antibody

anti-CTCF (CST:#3418)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

All ChIP-seq experiments used the SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) #9005 from Cell Signaling Technologies following the manufacturer's recommended protocol. Four million cells per IP. MNase digested chromatin was pooled into a single tube for brief sonication to lyse nuclei. Supernatant was then split evenly between IPs (minus 2% input). Antibodies and chromatin were incubated overnight at 4°C, rotating. DNA was purified using spin columns. Libraries were prepared using NEB UltraII DNA library kit

Sequencing Platform

instrument_model

NextSeq 500

hg38

Number of total reads

48784061

Reads aligned (%)

97.7

Duplicates removed (%)

5.9

Number of peaks

1237 (qval < 1E-05)

hg19

Number of total reads

48784061

Reads aligned (%)

96.6

Duplicates removed (%)

8.3

Number of peaks

1109 (qval < 1E-05)