ChIP-Atlas: SRX1549371

Antigen

Cell type Class: Blood
Cell type: Natural Killer T-Cells
MeSH Description: A specific natural killer T-cell subtype that expresses an invariant T-cell receptor alpha-chain.

library_strategy: ChIP-Seq
library_source: GENOMIC
library_selection: ChIP
library_construction_protocol: ChIP Samples: Preparation of samples for ChIP was carried out as described (Brind'Amour et al, 2015). Pre-cleared chromatin was subjected to immunoprecipitation overnight at 4°C with acetylated H3K27 antibody or trimethylated H3K4 antibody, conjugated to Dynabeads coated with Protein-A. Samples were washed as described (Brind'Amour et al, 2015) and DNA was purified with phenol:chloroform:isoamylalcohol (25:24:1, pH 8) using Maxtract tubes (Qiagen), then precipitated overnight. ATAC Samples. Preparation of samples for ATAC was carried out as described (Buenrostro et al, 2015). Aliquots of 25,000 cells were lysed (10mM Tris-Cl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP40), pellets were resuspended in 50µl of transposition mix (Tagment DNA buffer, Tagment DNA enzyme, Illumina), and incubated at 37oC (30 min). Samples were purified using MinElute spin columns (Qiagen). ChIP Samples: ChIP or input DNA was used for indexed library preparation, pooled (4-6 samples), and subjected to 50 bp single-end sequencing per manufacturer’s protocol (Illumina HiSeq2500). ATAC Samples. Nextera index adapters (i7 and i5) were used to amplify transposed DNA fragments (Illumina). Libraries were purified using AMPure XP beans (Beckman-Coulter), pooled (2-3 samples) and subjected to PE50 sequencing on an Illumina HiSeq2500.