Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

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
Peripheral blood cells
cell line
Jurkat
chip antibody
None
syros_id
20140404_1219
drug
DMSO / EPZ
duration
4 days
concentration
20 uM

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
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. 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. Lysates were clarified from sonicated cells and target bound fragments were isolated with antibody.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
9249758
Reads aligned (%)
43.6
Duplicates removed (%)
5.8
Number of peaks
495 (qval < 1E-05)

hg19

Number of total reads
9249758
Reads aligned (%)
43.1
Duplicates removed (%)
6.1
Number of peaks
478 (qval < 1E-05)

Base call quality data from DBCLS SRA