Antigen

Antigen Class

Histone

Antigen

H3K4me3

Cell type

Cell type Class

Digestive tract

Cell type

HCT-8

Primary Tissue

Colon

Tissue Diagnosis

Adenocarcinoma

Sample

source_name

Cultured HCT8 control

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

32854108

Reads aligned (%)

99.4

Duplicates removed (%)

83.3

Number of peaks

10202 (qval < 1E-05)

hg19

Number of total reads

32854108

Reads aligned (%)

99.0

Duplicates removed (%)

84.5

Number of peaks

10027 (qval < 1E-05)