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
BMDM_ChIP_input_0hKLA
strain
C57BI/6 (Harlan Laboratories)
age
8-10 weeks
Sex
female
cell type
Primary BMDM
genotype/variation
WT
chip antibodies
N/A

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For human ChIP-seq, ~15 million wild-type HeLa S3 cells or the indicated hNDF knockout cells were collected and crosslinked with 1% formaldehyde. After cell lysis and genome fragmentation by sonication, samples were incubated with 20 μL of Dynabeads Protein A that were pre-bound with 1 μL of NDF antiserum. [Note that 1 μL of hNDF antiserum was optimal for hNDF antiserum #7. For hNDF antiserum #6, 2 μL was the optimal volume.] Bound DNA were isolated with MinElute columns (Qiagen). For human RNA-seq, total RNA was purified by using the PureLink RNA Mini RNA Kit (Thermo Fisher Invitrogen). Mouse BMDM ChIP-seq and RNA-seq were performed as described in Kaikkonen, M. U. et al. Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Mol. Cell 51, 310-325. Human ChIP-seq libraries were prepared by end-repair, A-tailing, and ligation of Illumina TruSeq adaptors, which was then followed by PCR amplification and size selection with AMPure beads (Beckman Coulter). Human RNA-seq libraries were prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina). Mouse ChIP-seq libraries were prepared from ChIP DNA and inputs by blunting, A-tailing, and adapter ligations were performed by using NextFlex barcode adapters. Mouse RNA-seq libraries were prepared from poly(A)-enriched mRNA, as described in Kaikkonen, M. U. et al. Mol. Cell 51, 310-325.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
9823025
Reads aligned (%)
97.5
Duplicates removed (%)
9.3
Number of peaks
270 (qval < 1E-05)

mm9

Number of total reads
9823025
Reads aligned (%)
97.4
Duplicates removed (%)
9.4
Number of peaks
235 (qval < 1E-05)

Base call quality data from DBCLS SRA