Antigen

Antigen Class

ATAC-Seq

Antigen

ATAC-Seq

Cell type

Cell type Class

Blood

Cell type

Lymphocytes

MeSH Description

White blood cells formed in the body's lymphoid tissue. The nucleus is round or ovoid with coarse, irregularly clumped chromatin while the cytoplasm is typically pale blue with azurophilic (if any) granules. Most lymphocytes can be classified as either T or B (with subpopulations of each), or NATURAL KILLER CELLS.

Sample

source_name

Intraepithelial lymphocyte

microbial colonization state

conventionalized

cell type

Intraepithelial lymphocyte

strain

C57BL/6

tissue origin

Intestine

Sequenced DNA Library

library_strategy

ATAC-seq

library_source

GENOMIC

library_selection

other

library_construction_protocol

Peripheral T cells and IELs were isolated by FACS, with a target maximum of 50,000 cells per transposition reaction. Nuclei were isolated and prepared as described in Buenrostro et al., Nature Methods, 2013. Libraries were prepared using a modified version of the Illumina Nextera DNA Sample kit, based on the work of Buenrostro et al., Nature Methods, 2013 and outlined in the associated manuscript, Semenkovich et. al., 2016 (in submission).

Sequencing Platform

instrument_model

NextSeq 500

mm10

Number of total reads

20694381

Reads aligned (%)

81.2

Duplicates removed (%)

34.4

Number of peaks

28990 (qval < 1E-05)

mm9

Number of total reads

20694381

Reads aligned (%)

81.1

Duplicates removed (%)

34.5

Number of peaks

28997 (qval < 1E-05)