Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RAD21

Cell type

Cell type Class
Digestive tract
Cell type
HCT 116
Primary Tissue
Colon
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
HCT116_RAD21_ChIPSeq
cell line
HCT116
tissue source
Colon
cell type
Colorectal carcinoma cell line
chip antibody
RAD21 (Santa Cruz #sc98784)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cultured cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with G (for Pol2-Ser2 and Pol2-Ser5) or A (for CTCF, RAD21, SMC1, and H3K27) agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 ug of antibody against each of the protein. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina's NextSeq 500 (75 nt reads, single end).

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
61818531
Reads aligned (%)
52.0
Duplicates removed (%)
45.6
Number of peaks
44116 (qval < 1E-05)

hg38

Number of total reads
61818531
Reads aligned (%)
53.3
Duplicates removed (%)
44.5
Number of peaks
44439 (qval < 1E-05)

Base call quality data from DBCLS SRA