Antigen

Antigen Class

Histone

Antigen

H3K4me3

Cell type

Cell type Class

Liver

Cell type

97L

NA

NA

Sample

source_name

hepatoma cell line

cell line

97L

tissue

liver

chip antibody

H3K4me3 (human, Abcam, ab8580)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Methylation: Genomic DNA from tissues and cell lines was extracted using QIAamp DNA Mini Kit (Qiagen, 51306, Valencia, CA). 3μg genomic DNA was fragmented into 300-500bp by sonication. ChIP:Approximate 300 ug fixed chromatin and 5 ug antibody were used for each ChIP pull-down. RNA-seq: We extracted approximate 6 micrograms of total RNA, removed ribosomal RNA (rRNA) according to the manufacturer's instructions with minor modifications. Libraries were prepared for sequencing using standard Illumina protocols DNA Methylation sequencing, ChIP-seq and RNA-seq

Sequencing Platform

instrument_model

Illumina HiSeq 2500

hg38

Number of total reads

16208793

Reads aligned (%)

98.7

Duplicates removed (%)

9.6

Number of peaks

560 (qval < 1E-05)

hg19

Number of total reads

16208793

Reads aligned (%)

97.9

Duplicates removed (%)

9.9

Number of peaks

451 (qval < 1E-05)