Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Blood
Cell type
P493-6
NA
NA

Attributes by original data submitter

Sample

source_name
Human B lymphocyte P493-6 cells
treatment
-tet-DMS
cell type
B lymphocyte cells
cell line
P493-6
chip antibody
H3K4me3 antibody (Millipore, 07-473)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The ChIP was performed with an EZ-ChIP kit (Millipuro) following the manufacture's instruction. In this experiment, the DNA fragments were sonicated between 100bp to 500bp. For H3K4me3 ChIP, 2 X 107 cells were used. As to RNA-seq, total RNA was extracted using TRIZOL Reagent (Life technologies) following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100.Qualified total RNA was further purified by RNeasy micro kit and RNase-Free DNase Set. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample ChIP-sequencing libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). RNA-sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
10572686
Reads aligned (%)
95.6
Duplicates removed (%)
14.7
Number of peaks
20176 (qval < 1E-05)

hg19

Number of total reads
10572686
Reads aligned (%)
95.0
Duplicates removed (%)
14.8
Number of peaks
20887 (qval < 1E-05)

Base call quality data from DBCLS SRA