GSM2544218: ATAC-seq macrophage1a; Homo sapiens; ATAC-seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
ATAC-Seq
Antigen
ATAC-Seq
Cell type
Cell type Class
Blood
Cell type
THP-1
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Acute Myelogenous
Attributes by original data submitter
Sample
source_name
THP-1 cells, + PMA exposure
cell line
THP-1
pma exposure
72 hr PMA exposure
cell type
derived macrophages
Sequenced DNA Library
library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Equal numbers of THP-1 monocytes and THP-1 derived macrophages were collected (50,000 cells per ATAC-seq experiment) and washed with 1x ice cold PBS. Cells were pelleted via centrifugation (500 xg, 5 minutes, 40C) and resuspended in cell lysis buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630), and immediately spun down (500 xg, 10 minutes, 40C). The supernatant was then discarded, and transposition reaction carried out for 30 minutes at 37C with Tn5 transposase in transposition buffer (Illumina, cat#FC-121-1030). DNA was immediately purified on a minElute column (Qiagen), followed by PCR amplification using the NEBNext high-fidelity master mix (NEB cat#M0541) with Nextera PCR primers and barcodes. PCR amplification was monitored as described (Buenrostro et al. 2015), and gel purified to remove contaminating primer-dimer species. Libraries were prepared for sequencing using standard Illumina protocols.