Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Blood
Cell type
CA46
Primary Tissue
Blood
Tissue Diagnosis
Malignant Lymphoma - Burkitts Type

Attributes by original data submitter

Sample

source_name
cell line: Human B lymphocyte CA46 cells; spike-in reference organism: Drosophila melanogaster; spike-in cell line: S2
cell type
Human B lymphocyte cell line
cell line
CA46
genotype/variation
Myc shRNA
treatment
exposed to 10mM dimethyl succinate (DMS, sigma) for 20h
chip antibody
ChIP antibody: H3K4me3 antibody (Millipore, 07-473) ;spike-in ChIP antibody: H2Av (Active Motif, 61686)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The CA46 cells' ChIP-seq experiments with spike-in control was referred to the manufacturer's instruction (Active Motif). In this experiment, the DNA fragments were sonicated between 200bp to 500bp. For H3K4me3 ChIP and a Drosophila-specific antibody (Active Motif 61686), 1.5 X 107 CA46 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 generated using NEBNext® Ultra™ IIDNA Library Prep Kit (#E7645). 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 NovaSeq 6000

hg38

Number of total reads
30358612
Reads aligned (%)
95.9
Duplicates removed (%)
12.9
Number of peaks
17170 (qval < 1E-05)

hg19

Number of total reads
30358612
Reads aligned (%)
95.6
Duplicates removed (%)
12.9
Number of peaks
16971 (qval < 1E-05)

Base call quality data from DBCLS SRA