Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Digestive tract
Cell type
HCT-8
Primary Tissue
Colon
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
Cultured HCT8 5h with vesicles from C6706_Vibrio_cholerae
cell line
HCT8
chip antibody
H3K4me3 ( Abcam: ab8580; Lot no:GR188707-1)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Illumina TruSeq™ DNA Sample Preparation Twenty five microliters of immunoprecipitated, FAIRE or input DNA was used for library preparation. For CHIP samples Illumina (San Diego, CA) TruSeq™ DNA Sample Preparation reagents were used, with ligation of 1/10th the manufacturers recommended adapter amounts and agarose gel selection of DNA fragments in the 200-500 bp size range. For FAIRE samplesThruPLEX DNA-Seq reagents was used (Rubicon Genomics, Ann Arbor, MI, USA), following manufacturer’s instructions”.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
39723273
Reads aligned (%)
99.6
Duplicates removed (%)
56.7
Number of peaks
24720 (qval < 1E-05)

hg19

Number of total reads
39723273
Reads aligned (%)
99.3
Duplicates removed (%)
57.5
Number of peaks
24788 (qval < 1E-05)

Base call quality data from DBCLS SRA