Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CDK9

Cell type

Cell type Class
Neural
Cell type
KELLY
Primary Tissue
Brain
Tissue Diagnosis
Neuroblastoma

Attributes by original data submitter

Sample

source_name
Chromatin IP against CDK9 in DMSO KELLY
cell line
KELLY
cell type
Neuroblastoma
input
KELLY_DMSO_WCE
treatment
0.1% DMSO for 3HR
growth protocol
10% FBS, DMEM
barcode
TGGTCACA
antibody
CDK9-H169
antibody maker
santa-cruz
antibody catalog number
sc-8338

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared using Tn5 enzyme and amplified using 2x NEBNext HiFi master mix. ChIPmentation (Schmidl et a., 2015; PMC4589892)

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
45574966
Reads aligned (%)
49.2
Duplicates removed (%)
49.0
Number of peaks
835 (qval < 1E-05)

hg38

Number of total reads
45574966
Reads aligned (%)
50.9
Duplicates removed (%)
47.7
Number of peaks
991 (qval < 1E-05)

Base call quality data from DBCLS SRA