Antigen

Antigen Class

ATAC-Seq

Antigen

ATAC-Seq

Cell type

Cell type Class

Blood

Cell type

Macrophages

MeSH Description

The relatively long-lived phagocytic cell of mammalian tissues that are derived from blood MONOCYTES. Main types are PERITONEAL MACROPHAGES; ALVEOLAR MACROPHAGES; HISTIOCYTES; KUPFFER CELLS of the liver; and OSTEOCLASTS. They may further differentiate within chronic inflammatory lesions to EPITHELIOID CELLS or may fuse to form FOREIGN BODY GIANT CELLS or LANGHANS GIANT CELLS. (from The Dictionary of Cell Biology, Lackie and Dow, 3rd ed.)

Sample

source_name

Large peritoneal macrophages (LPMs)

strain/background

C57BL/6

genotype/variation

RXRabfl/fl

developmental stage

9 weeks

cell type

Large peritoneal macrophages

library batch

1

Sequenced DNA Library

library_strategy

ATAC-seq

library_source

GENOMIC

library_selection

other

library_construction_protocol

40,000 sorted LPMs were lysed with lysis buffers (10 mM Tris-HCl pH 7.4, 10mM MgCl2, 0.1% IGEPAL CA-630), and the transposase reaction was performed incubating the isolated nuclei with 2.5 microl per sample of Tn5 (Nextera DNA Library Preparation Kit, Illumina) for 30 min at 37ºC. Transposed DNA was purified with the ChIP DNA Clean & Concentrator kit (Zymo) according to manufacturer´s instructions. PCR amplification and barcoding were done with the primers described by Buenrostro et al. Each PCR reaction included 11 ml NEB 2× PCR Mix (New England Biolabs), 10 ml of transposed DNA, 0.5 ml of X mM primer Ad_ no Mx (forward) and 0.5 ml of barcoded reverse primer (Ad_2.1 to Ad_2.4). PCR conditions were as follows: 72°C for 5 min, 98 °C for 30 s, 5 cycles of 98 °C for 10 s, 63 °C for 30 s, 72 °C for 1 min, followed by 4 ºC next to final 5th cycle. After first PCR DNA was size selected with 0.5X volume SPRI beads (Agencourt AMPure, Beckman Coulter), and cleaned up with 2X SPRI beads. Second PCR with same set of primers was done as follows: 98 °C for 30 s, followed by 6-9 cycles of 98 °C for 10 s, 63 °C for 30 s, 72 °C for 1 min. Each sample was amplified for a total of 11 to 14 cycles. Libraries were purified with SPRI beads, and concentration was measured by Qbit dsDNA HS Assay kit (ThermoFischer Scientific) and fragment profiles were analyzed with the Bioanalyzer DNA High Sensitivity Kit (Agilent).

Sequencing Platform

instrument_model

Illumina HiSeq 3000

mm10

Number of total reads

43398365

Reads aligned (%)

82.4

Duplicates removed (%)

26.6

Number of peaks

23650 (qval < 1E-05)

mm9

Number of total reads

43398365

Reads aligned (%)

82.3

Duplicates removed (%)

26.7

Number of peaks

23642 (qval < 1E-05)