ChIP-Atlas: SRX5766122

Antigen

Cell type Class: Blood
Cell type: GM12878
Tissue: blood
Lineage: mesoderm
Description: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

library_strategy: ATAC-seq
library_source: GENOMIC
library_selection: other
library_construction_protocol: We isolated nuclei from three independent cultures for the PCR-variable experiment and six additional cultures for the PCR-constant experiment. We conducted ATAC-seq as described in (Buenrostro et al. 2015) using a home-made Tn5 that we synthesized as described in (Picelli et al. 2014). For each replicate we incubated 50,000 nuclei with various concentrations of enzyme (1/5X, 1/2X, 2/3X, 1X, 1.5X, 2X, 5X; 1X corresponds to 2.5 uL of 1:1 Tn5-A/B mix) at 37 degrees C for 30 minutes in a 50 uL reaction. We column-purified the tagmented DNA using the Zymo DNA Clean & Concentrator-5 kit (Zymo Research, Irvine, CA). In the PCR-variable experiment, we PCR-amplified the entire eluate until amplification curve reached its mid-log phase (1/3 to 1/2 of max signal); whereas in the PCR-constant experiment, we amplified the entire eluate with a fixed number of PCR cycles (16) for all samples. We purified the products using SPRI beads prepared as in (Rohland and Reich, 2012) and eluted in 20 uL of TE buffer with Tween-20 (10 mM Tris-HCl, 0.1 mM EDTA, 0.05% Tween-20, pH 8)