Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD4

Cell type

Cell type Class
Epidermis
Cell type
CHL-1
Primary Tissue
Skin
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
melanoma cancer cell line CHL-1
cell line
CHL-1
tumor type
melanoma
tissue
skin
chip antibody
anti-BRD4 (Bethyl Labs, A301-985A100)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
One 15 cm cell culture dish with 80% confluent cells was used per IP. ChIP DNA preparation for sequencing was carried out as described previously in Nagarajan et al. (Cell Rep. 2014 Jul 24;8(2):460-9) with the following changes: cross-linked chromatin was sheared to 200-800 base pair fragments using sonication (30 sec on/30 sec off, high power, 2 x 7.5 minutes with a water bath change between the two cycles) in a Biorupter sonicator UCD-200. 1.5 µg antibodies (anti-BRD4 [Bethyl Labs, A301-985A100]; anti-H3K27ac [Diagenode, C15410174]) were used per IP. DNA was purified using a PCR purification kit (Qiagen) TrueSeq® ChIP Sample Preparation Guide (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
80550425
Reads aligned (%)
136.8
Duplicates removed (%)
28.8
Number of peaks
1127 (qval < 1E-05)

hg38

Number of total reads
80550425
Reads aligned (%)
138.8
Duplicates removed (%)
28.3
Number of peaks
3212 (qval < 1E-05)

Base call quality data from DBCLS SRA