Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

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 cells
cell line
HCT116
cell type
colorectal carcinoma
passages
19
treatment
24hr after methionine/SAM depletion
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated whole-cells and histone-DNA complexes were isolated with H3K9me3 antibody. Libraries were prepared by the University of Wisconsin-Madison Biotechnology Center using an Illumina TruSeq DNA Nano kit.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
28393649
Reads aligned (%)
98.9
Duplicates removed (%)
3.5
Number of peaks
680 (qval < 1E-05)

hg19

Number of total reads
28393649
Reads aligned (%)
98.1
Duplicates removed (%)
4.7
Number of peaks
624 (qval < 1E-05)

Base call quality data from DBCLS SRA