Antigen

Antigen Class

Histone

Antigen

H3K4me3

Cell type

Cell type Class

Digestive tract

Cell type

GIST48

NA

NA

Sample

source_name

GIST48-siETV1-H3K4Me3

cell line

GIST48

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

GIST cells were transfected with siRNAs using DharmaFECT2 (GE healthcare) according to the manufacture's protocol. In brief, transfection was performed under serum free conditions, using 20nM siRNA in Opti-MEM. cells were crosslinked for 15 min in 1% paraformaldehyde, washed and lysed. Chromatin was sheared using Bioruptor (Diagenode) to fragments of approximately 150 base pairs and was incubated with anti-rabbit IgG Dynabeads (Invitrogen) pre-conjugated with primary antibody,  ChIP libraries were prepared for sequencing using standard Illumina protocols

Sequencing Platform

instrument_model

Illumina HiSeq 2500

hg38

Number of total reads

27026574

Reads aligned (%)

97.0

Duplicates removed (%)

6.1

Number of peaks

28488 (qval < 1E-05)

hg19

Number of total reads

27026574

Reads aligned (%)

95.1

Duplicates removed (%)

10.0

Number of peaks

27862 (qval < 1E-05)