Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27ac

Cell type

Cell type Class
Blood
Cell type
SU-DHL-4
Primary Tissue
Blood
Tissue Diagnosis
Lymphoma B-cell

Attributes by original data submitter

Sample

source_name
SUDHL4 cell line, CREBBP WT
cell line
SUDHL4
cell type
DLBCL cells
genotype
CREBBP WT
antibody
anti-H3K27Ac (Diagenode, C15410196, Lot. A1723-0041D)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Purified cells were cross-linked with 1% formaldehyde for 10 min at room temperature, quenched by the addition of glycine to a final concentration of 0.125 M, and frozen. Cell lysis and nuclei isolation was performed using the TruChIP Chromatin Shearing Kit High Cell SDS (Covaris). Nuclei were sonicated using the S220 Ultrasonicator (Covaris) in order to obtain chromatin fragments of 200-500bp. ChIP-seq libraries were constructed starting from 3ng of ChIP or Input DNA as reported in Blecher-Gonen et al., 2013, Nature protocol. Libraries were quantified using the KAPA SYBR FAST Universal qPCR Kit (KAPA Biosystems), normalized to 15nM, pooled and sequenced in an Illumina HiSeq 4000 instrument as paired-end 150 bp reads, obtaining on average 25x10^6 reads/sample.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
104690188
Reads aligned (%)
97.8
Duplicates removed (%)
22.4
Number of peaks
40594 (qval < 1E-05)

hg19

Number of total reads
104690188
Reads aligned (%)
97.2
Duplicates removed (%)
23.0
Number of peaks
39985 (qval < 1E-05)

Base call quality data from DBCLS SRA