GSM4332934: ZBTB1 KO ATF4 No Asparagine; Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
TFs and others
Cell type Class
Leukemia Acute Lymphocytic
Attributes by original data submitter
Sequenced DNA Library
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.