Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ATF4

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
treatment
Normal media conditions
chip antibody
ATF4

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

hg19

Number of total reads
20160819
Reads aligned (%)
43.4
Duplicates removed (%)
54.0
Number of peaks
1639 (qval < 1E-05)

hg38

Number of total reads
20160819
Reads aligned (%)
45.8
Duplicates removed (%)
51.8
Number of peaks
1706 (qval < 1E-05)

Base call quality data from DBCLS SRA