Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Neural
Cell type
D458
NA
NA

Attributes by original data submitter

Sample

source_name
D458
cell type
D458 sensitive
treatment
DMSO
ip antibody
H3K4me3

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Sensitive and drug-tolerant D425 and D458 were passaged in DMSO or JQ1 (1 µM) for 24 hours. Sheared chromatin from each cell line was subjected to ChIP-sequencing as previously described62 , enriching for H3K27ac (Cell Signaling Technologies, 8173S)), H3K4me3 (Cell Signaling Technologies, 9751S), Histone H3 (Cell Signaling 4499S) and BRD4 (Bethyl, A301-985A100). ChIP libraries were indexed, pooled and sequenced on Illumina Hi-seq-2000 sequencers.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
15407259
Reads aligned (%)
98.7
Duplicates removed (%)
5.7
Number of peaks
23988 (qval < 1E-05)

hg19

Number of total reads
15407259
Reads aligned (%)
98.4
Duplicates removed (%)
5.7
Number of peaks
23939 (qval < 1E-05)

Base call quality data from DBCLS SRA