Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

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
Spleen red pulp macrophages
strain
C57BL/6
tissue
Spleen
cell type
Spleen red pulp macrophages
chip antibody
None

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was eluted from the beads, then treated with RNase (Roche) for 30 min at 37°c and with Proteinase K (NEB) for 2 hrs at 37°c. Reverse cross-linking was performed at 65°c overnight. DNA was purified with SPRI beads (Agencourt AMPure XP beads, Beckman Coulter) at 2.3x ratio. Sequential steps of end-repair, A-base addition, adapter-ligation and amplification were performed, with DNA purification with SPRI beads after each step. Following the amplification step, DNA concentration was measured, and equivalent amounts of barcoded ChIPed DNA from each sample were pooled together. An additional size-selection step was performed Libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science Nat Protoc. 2013 Mar;8(3):539-54. doi: 10.1038/nprot.2013.023. PMID: 23429716

Sequencing Platform

instrument_model
Illumina HiSeq 1500

mm10

Number of total reads
9750873
Reads aligned (%)
92.0
Duplicates removed (%)
13.7
Number of peaks
300 (qval < 1E-05)

mm9

Number of total reads
9750873
Reads aligned (%)
91.8
Duplicates removed (%)
13.9
Number of peaks
279 (qval < 1E-05)

Base call quality data from DBCLS SRA