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

BTBR T+ Itpr3tf/J_BMDM_one dose LPS

strain

BTBR T+ Itpr3tf/J

Sex

male

cell type

bone marrow derived macrophage (BMDM)

biological replicate

2

treatment

one dose LPS

additional pcr cycles

7

sequencing lane

1

barcode

Index 2.5 5' GGACTCCT 3'

molecule subtype

Tn5 Transposase treated DNA

Sequenced DNA Library

library_strategy

ATAC-seq

library_source

GENOMIC

library_selection

other

library_construction_protocol

ATACseq was performed as described in(Buenrostro, et al., 2015). Briefly, cultures of 50,000 BMDM were washed once in ice cold 1xPBS and then resuspended gently in 100ul ATACseq lysis buffer (1 mM Tris·Cl, pH 7.4, 1 mM NaCl= 500ul 1M NaCl, 0.3 mM MgCl2, and 0.01% (v/v) Triton-X 100) to release nuclei. Nuclei were then pelleted (1,000xg, 10min, 4C) and transposed in 2.5ul Tn5 (Nextera Tn5 transposase, Illumina), 12.5ul TD reaction buffer and 10.5ul water for 40min at 37C with rotation. Following transposition, DNA was purified (MinElute PCR Purification Kit, Qiagen) and stored at -80C. Samples were then thawed on ice and unique barcodes(Buenrostro, et al., 2015) were added to each sample using 5 cycles of PCR(Buenrostro, et al., 2015). A side PCR reaction was then taken and used as input for qPCR for an additional 20 cycles to assess determine the optimal number of additional PCR cycles for each library (the cycle number that corresponds to one-third of the maximum fluorescent intensity). Each sample was then amplified by the determined number of PCR cycles and then purified (MinElute PCR Purification Kit, Qiagen). Final libraries were then size selected for fragments between 100-1000bp using AMPure XP beds (Beckman Coulter) and quality was checked by DNA High Sensitivity bioanalyzer. Libraries were pooled (6 per pool) and sequenced across four lanes of the HiSeq2500 to generate 50bp paired end reads.

Sequencing Platform

instrument_model

Illumina HiSeq 2500

mm10

Number of total reads

29692605

Reads aligned (%)

91.4

Duplicates removed (%)

15.2

Number of peaks

56188 (qval < 1E-05)

mm9

Number of total reads

29692605

Reads aligned (%)

91.2

Duplicates removed (%)

15.4

Number of peaks

56208 (qval < 1E-05)