ChIP-Atlas: SRX2613957

Antigen

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.)

library_strategy: ChIP-Seq
library_source: GENOMIC
library_selection: ChIP
library_construction_protocol: ChIP-Seq: Sequencing libraries were prepared from collected DNA by using NEB next Ultra DNA library prep kit for Illumina. Libraries were PCR-amplified for 12-15 cycles and sequenced on a Hi-Seq 1500 (Illumina) for 51 cycles. RNA-Seq: PolyA-tagged RNA was pulled down with oligo-dT magnetic beads from total RNA. RNA-seq libraries were multiplexed and prepared according to the manufacturer's protocol (NEB cat#E7530, Ipswich, MA). Libraries were paired-ended sequenced on a HiSeq 2000 sequencer (Illumina, San Diego, CA) Reads were aligned to mm9 genome using default parameter for RNA-star. Aligned reads read files were analyzed with HOMER (http://homer.salk.edu/homer/) to calculate RPKM from the gene bodies of RefSeq genes, perform motif analysis in the study. Reads counts were normalized using DESeq2.