Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HEXIM1

Cell type

Cell type Class
Epidermis
Cell type
A-375
Primary Tissue
Skin
Tissue Diagnosis
Melanoma

Attributes by original data submitter

Sample

source_name
A375 melanoma cell line
cell line
A375
cell type
malignant melanoma
chip antibody
HEXIM1 (Abcam)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
DNA was sonicated and chromatin immunoprecipitation was performed with either HEXIM1 (Abcam) or CDK9 (Santa Cruz) antibodies. DNA was then de-cross-linked from pulled down protein and purified by phenol:chloroform:isoamyl alcohol extraction. The NEBNext multiplex oligos for Illumina Kit (NEB) was used to make the samples suitable for multiplexing. The PCR reaction was run for 18 cycles. The indexed libraries were purified on a 2% agarose gel, and were cut out between 150 and 350 bp. The concentration of the isolated libraries was estimated with a high-sensitivity DNA chip from Agilent according to manufacturer’s protocol and libraries were mixed in equal quantities and sequenced on Illumina Hi-Seq2000. Index sequences from multiplexed primers were used to identify treatment group and reads were demultiplexed using a perl script.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
24469167
Reads aligned (%)
82.7
Duplicates removed (%)
12.3
Number of peaks
1402 (qval < 1E-05)

hg38

Number of total reads
24469167
Reads aligned (%)
84.2
Duplicates removed (%)
11.4
Number of peaks
1498 (qval < 1E-05)

Base call quality data from DBCLS SRA