Antigen

Antigen Class

ATAC-Seq

Antigen

ATAC-Seq

Cell type

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.

Sample

source_name

NKT1_SKG

strain

SKG

tissue

Thymus

cell type

NKT cell

cell population

NKT1

Sequenced DNA Library

library_strategy

ATAC-seq

library_source

GENOMIC

library_selection

other

library_construction_protocol

Cells were lysed in 50ul lysis buffer (10 mM TrisHCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Molecular biology-grade IGEPAL CA-630) to extract nuclei. Nuclei were pelleted at 500xg. Nuclei were resuspended in 50 μL 1× TD buffer containing 2.5 μL transposase (Nextera, Illumina). DNA was purified using MinElute PCR Purification columns and kit (Qiagen). Treatment with Nextera transposase for 40 minutes at 37°C, followed by PCR amplification.

Sequencing Platform

instrument_model

Illumina HiSeq 2500

mm10

Number of total reads

30298573

Reads aligned (%)

88.5

Duplicates removed (%)

31.1

Number of peaks

37775 (qval < 1E-05)

mm9

Number of total reads

30298573

Reads aligned (%)

88.4

Duplicates removed (%)

31.2

Number of peaks

37744 (qval < 1E-05)