Antigen

Antigen Class

ATAC-Seq

Antigen

ATAC-Seq

Cell type

Cell type Class

Blood

Cell type

Th1 Cells

MeSH Description

A subset of helper-inducer T-lymphocytes which synthesize and secrete INTERLEUKIN-2; INTERFERON-GAMMA; and INTERLEUKIN-12. Due to their ability to kill antigen-presenting cells and their lymphokine-mediated effector activity, Th1 cells are associated with vigorous delayed-type hypersensitivity reactions.

Sample

source_name

WT Th1

genotype/variation

WT

tissue

Spleen

cell type

SMARTA CD4 T cells

cell subtype

Th1

molecule subtype

Tn5 transposase treated nuclei DNA

Sequenced DNA Library

library_strategy

ATAC-seq

library_source

GENOMIC

library_selection

other

library_construction_protocol

The nuclear pellet was resuspended into transposition reaction mixture containing Tn5 transposase from Illumina Nextera DNA Sample Prep Kit and incubated at 37 °C for 30 min. Then the transposase-associated DNA was purified using Qiagen MinElute Purification kit. The DNA was amplified for twelve cycles using KAPA Real-Time Library amplification kit (KAPAbiosystems) with Nextera indexing primers as per Buenrostro et al, 2015. The total amplified DNA was purified using AmPureXP beads.

Sequencing Platform

instrument_model

Illumina HiSeq 4000

mm10

Number of total reads

27617124

Reads aligned (%)

63.3

Duplicates removed (%)

34.9

Number of peaks

17496 (qval < 1E-05)

mm9

Number of total reads

27617124

Reads aligned (%)

63.2

Duplicates removed (%)

35.0

Number of peaks

17470 (qval < 1E-05)