Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CDK12

Cell type

Cell type Class
Blood
Cell type
Jurkat
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Acute Lymphocytic

Attributes by original data submitter

Sample

source_name
T-ALL
cell line
Jurkat
chip antibody
CDK12
antibody manufacturer
Greenleaf Lab
antibody catalog
NA
antibody lot
NA
young_id
20141010_3201
system
Blood
cell number
300 million
drug
DMSO
concentration
0.1%
treatment duration
6h

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified. Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
33259647
Reads aligned (%)
89.2
Duplicates removed (%)
5.5
Number of peaks
2298 (qval < 1E-05)

hg38

Number of total reads
33259647
Reads aligned (%)
91.5
Duplicates removed (%)
4.0
Number of peaks
2450 (qval < 1E-05)

Base call quality data from DBCLS SRA