Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SOX9

Cell type

Cell type Class
Digestive tract
Cell type
HT-29
Primary Tissue
Colon
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
HT29 cells
cell type
Human colorectal cancer
cell line
HT29
chip antibody
SOX9 (Millipore, AB5535)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. ChIP and Input DNAs were prepared for amplification by converting overhangs into phosphorylated blunt ends and adding an adenine to the 3’ ends. Illumina adaptors were added and the library was size-selected (175-225 bp) on an agarose gel. The adaptor-ligated libraries were amplified for 18 cycles. The resulting amplified DNAs were purified, quantified, and tested by QPCR at the same specific genomic regions as the original ChIP DNA to assess quality of the amplification reactions.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
44617230
Reads aligned (%)
35.6
Duplicates removed (%)
62.8
Number of peaks
11902 (qval < 1E-05)

hg38

Number of total reads
44617230
Reads aligned (%)
36.8
Duplicates removed (%)
61.8
Number of peaks
11981 (qval < 1E-05)

Base call quality data from DBCLS SRA