Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CDK9

Cell type

Cell type Class
Breast
Cell type
T-47D
Primary Tissue
Breast
Tissue Diagnosis
Adenocarcinoma Ductal

Attributes by original data submitter

Sample

source_name
T47D cells
r5020 treatment
Untreated
chip antibody
CDK9

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
T47D-MTVL cells, without treatment or transfected with alpha-amanitin resistant HA-tagged wild type (WTr) versus R1810Ar mutant RNAP2 were cross-linked for 10 minutes with 1% formaldehyde. Lysate were sonicated to a DNA fragment size range of 200-300bp using a Biorupter sonicator (Diagenode). CDK9 Immunoprecipitated from , 150 μg chromatin with 15μg of anti-CDK9 (H-169.SC-8338)) antibody followed by 42μl of Protein A-Agarose Beads (Diagenode). Libraries were prepared using standadr Illumina instruction of NEBNext® ChIP-Seq Library Prep Reagent.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
89307088
Reads aligned (%)
86.5
Duplicates removed (%)
43.5
Number of peaks
2615 (qval < 1E-05)

hg38

Number of total reads
89307088
Reads aligned (%)
87.9
Duplicates removed (%)
43.0
Number of peaks
3588 (qval < 1E-05)

Base call quality data from DBCLS SRA