Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27ac

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
Jurkat cells
cell line
Jurkat
genotype/variation
ZBTB1 KO expressing FLAG-ZBTB1 cDNA
treatment
Asparagine deprivation
chip antibody
H3K27Ac

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RNA: Cells were harvested and RNA was isolated by Qiagen RNeasy kit. 1ug of total RNA was used for construction of sequencing libraries. ChIP: Cells were cross-linked with 1% paraformaldehyde for 10 minutes at 37C. Cross-linking was quenched with 125 mM glycine. Cells were pelleted and flash-frozen in liquid nitrogen. Nuclei were isolated and sonicated using a Covaris sonicator. Protein A/G beads were added to 2-4 ug of appropriate antibodies and bound at room temperature for 1.5 hours. Samples were immunoprecipitated with appropriate protein A/G-antibody complexes overnight at 4C. Immunoprecipitates were collected and washed twice each with low salt, high salt, and lithium chloride wash buffers. DNA was eluted, reverse-crosslinked and treated with RNase and proteinase K before being isolated with a PCR purification kit (Zymogen). ATAC: Cells were treated in the presence or absence of asparagine for 24 hours. Nuclear extracts were prepared from 100,000 cells for each cell line and condition, and incubated with 2.5 μl of transposase (Illumina) in a 50 μl reaction for 30 min at 37 °C. Transposase-fragmented DNA was purified, and the library was amplified by PCR. RNA, ATAC and ChIP libraries were prepared using standard Illumina protocols.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
44316958
Reads aligned (%)
97.0
Duplicates removed (%)
42.0
Number of peaks
31518 (qval < 1E-05)

hg19

Number of total reads
44316958
Reads aligned (%)
96.7
Duplicates removed (%)
42.4
Number of peaks
31491 (qval < 1E-05)

Base call quality data from DBCLS SRA