Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

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
cell type
human colon cancer
chip antibody
ChIPAb+ Anti-H3K4me3 (Millipore #17-614)
culture media
(+) Methionine

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells grown on 15cm plates were crosslinked with 1% formaldyhyde in culture media. Cross-linked chromatin was collected and flash frozen before sonication with the Covaris M2. Lysates were clarified and protein-DNA complexes were immunoprecipitated with H3K4me3 antibody. Libraries were prepared according to standard Illumina protocols

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
31481265
Reads aligned (%)
90.5
Duplicates removed (%)
9.8
Number of peaks
24878 (qval < 1E-05)

hg19

Number of total reads
31481265
Reads aligned (%)
89.9
Duplicates removed (%)
10.5
Number of peaks
24671 (qval < 1E-05)

Base call quality data from DBCLS SRA