Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Rela

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.)

Attributes by original data submitter

Sample

source_name
Primary thioglycollate-elicited peritoneal macrophages
cell type
Macrophage
strain
C57BL/6
treatment
DMSO 7h, Kdo2 Lipid A (KLA) 6h
chip antibody
p65 (Santa Cruz sc-372)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Extraction-ChIP-Seq Extraction-Gro-Seq: Nuclei were extracted from 8-12 million cells grown on 10 cm plates and nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. RNA was extracted with Trizol, DNase-treated, base-hydrolyzed and dephosphorylated with PNK. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads and precipitated overnight. Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified on a denaturing 10% polyacrylamide TBE-urea gel. The recovered cDNA was circularized, linearized, amplified for 10-16 cycles. The final product was ran on 10% TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit. The final libraries were sequenced using an Illumina Genome Analyzer II or HiSeq 2000. Extraction-ChIP-seq: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Alternatively, lysates clarified from isolated nuclei were treated with MNase and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (minus exo) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3? end. After adapter ligation, ChIP DNA was PCR-amplified with Illumina Genomic adaptors or with NEXTflex DNA barcodes adaptors for 18 cycles and library fragments (ChIP) (insert plus adaptor and PCR primer sequences) were size-selected (150-250bp) from a 2% agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina Genome Analyzer II or Illumina HiSeq 2000 according to the manuactuere?s instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
14798619
Reads aligned (%)
77.5
Duplicates removed (%)
74.6
Number of peaks
1921 (qval < 1E-05)

mm9

Number of total reads
14798619
Reads aligned (%)
77.3
Duplicates removed (%)
74.9
Number of peaks
1917 (qval < 1E-05)

Base call quality data from DBCLS SRA