Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CDK9

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 cell lines
chip antibody
CDK9 Santa Cruz sc484

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
After chromatin immunoprecipitation, cross-link reversal is carried out and precipitated DNA is purified by phenol:chloform:isoamyl alcohol extraction. The End-It DNA End-Repair Kit (Epicentre) was used to turn DNA overhangs into phosphorylated blunt ends and the Agencourt AMPure XP PCR Purification Kit (Beckman Coulter) was used to purify the resulting samples using a 1.8X ratio of beads to sample. Next, a single A in the 3' end was added to samples using the Klenow Fragment enzyme (NEB) to allow for directional ligation and the AMPure Kit was again used to purify samples. Illumina adaptor oligos (1:10 dilution) were added to samples using the Quick Ligation Kit (NEB) and NEBNext Multiplex Oligos for Illumina Kit (NEB), and samples were purified with the AMPure Kit. Samples were then size-selected with the AMPure beads with a 0.9X bead to sample ratio. Multiplexing primers from the NEBNext Multiplex Oligos Kit were added during the 18-cycle PCR enrichment step, which utilized the Phusion High-Fidelity PCR Master Mix (NEB), to generate indexed libraries. Indexed libraries were beads purified. 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
31440730
Reads aligned (%)
83.8
Duplicates removed (%)
12.9
Number of peaks
2875 (qval < 1E-05)

hg38

Number of total reads
31440730
Reads aligned (%)
84.9
Duplicates removed (%)
12.1
Number of peaks
3037 (qval < 1E-05)

Base call quality data from DBCLS SRA