Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD4

Cell type

Cell type Class
Neural
Cell type
SK-N-BE(2)
Primary Tissue
Brain
Site of Extraction
Bone Marrow
Tissue Diagnosis
Neuroblastoma

Attributes by original data submitter

Sample

source_name
SK-N-BE(2)-C neuroblastoma cell line
chip antibody
BRD4
status
naïve
treatement
JQ1
cell line
SK-N-BE(2)-C

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were harvested, washed twice in ice cold PBS with protease inhibitors and then lysed in 50 mM Tris-HCl pH 8.1, 10 mM EDTA, 1% SDS supplemented with protease inhibitors (Roche). Chromatin was sheared to ~250 bp fragments using the Covaris ultra-sonication. The sonicated lysate was then diluted with ChIP dilution buffer (16.7 mM Tris-HCl pH 8.1, 16.7 mM NaCl, 1.2 mM EDTA, 1.1% Triton-X100, 0.01% SDS). Subsequently, 2.5% of the lysate was removed as the input control. The remaining lysate was incubated over night at 4°C with 3 µg of H3K27Ac antibody (ab4729, Abcam). The precipitated lysate was then incubated with protein A/G sepharose beads (Pierce, catalog #20423) for 2 hours and then washed sequentially in ice cold low salt buffer (20 mM Tris-HCl pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton-X100, 0.1% SDS), high salt buffer (20 mM Tris-HCl pH 8.1, 2 mM EDTA, 500 mM NaCl, 1% Triton-X100, 0.1% SDS), LiCl buffer (10 mM Tris-HCl pH 8.1, 0.25 M LiCl, 1 mM EDTA, 1% deoxycholic acid, 1% IGEPAL CA-630) and TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA). Samples were incubated at 65°C overnight with elution buffer (0.1 M NaHCO3, 1% SDS) supplemented with 0.2M NaCl to reverse crosslinking. ChIP libraries were prepared using the Rubicon Genomics Thruplex DNA-seq prep kit optimized for low input samples.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
63422585
Reads aligned (%)
79.0
Duplicates removed (%)
9.6
Number of peaks
1539 (qval < 1E-05)

hg38

Number of total reads
63422585
Reads aligned (%)
81.0
Duplicates removed (%)
7.9
Number of peaks
2233 (qval < 1E-05)

Base call quality data from DBCLS SRA