Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K9K14ac

Cell type

Cell type Class
Blood
Cell type
NB-4
Primary Tissue
Blood
Site of Extraction
Bone Marrow
Tissue Diagnosis
Leukemia

Attributes by original data submitter

Sample

source_name
MS275 treated NB4 cells, 4h ChIP
cell type
NB4 promyelocytic leukaemia cell line
treatment
MS275 4h
chip antibody
H3K9K14ac (Diagenode)
reference genome
HG18

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was sonicated and used for ChIP-seq using H3K9K14ac (Diagenode). RNA was extracted using qiagen RNeasy kit according to manufacturer. cDNA first and Ds-cDNA synthesis then, was performed following supplier’s instructions (Invitrogen). Ds-cDNA samples were prepared for sequencing by end repair of 20 ng DNA as measured by Qubit (Invitrogen). Adaptors were ligated to DNA fragments, followed by size selection (~300 bp) and limited PCR amplification (14 cycles). The resulting sample libraries were subjected to DSN treatment (Evrogen) according to the manufacturer’s recommendations. ChIP and RNA seq libraries were preapared according to Illumina's standard protocol.

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg38

Number of total reads
33952130
Reads aligned (%)
98.2
Duplicates removed (%)
30.8
Number of peaks
34574 (qval < 1E-05)

hg19

Number of total reads
33952130
Reads aligned (%)
97.8
Duplicates removed (%)
31.1
Number of peaks
34535 (qval < 1E-05)

Base call quality data from DBCLS SRA