Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
LDB1

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
differentiated macrophages - acute monocytic leukemia derived
cell type
differentiated macrophages - acute monocytic leukemia derived
chip antibody
LDB1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP and library construction were conducted essentially as described by using an unspecific IgG control antibody (rabbit, Merck Millipore #12-370) or LDB1 (rabbit, Abcam #ab96799). Tags for sequencing were mapped to the human reference genome (GRCh37.67/hg19) using BWA mem Aligner (arXiv:1303.3997) (LDB1 ChIPseq) and Bowtie software (all other).(PMID: 21154709) Downstream analysis of uniquely mapped tags, including quality control, peak calling, and motif analysis, was performed as described using MACS2 (PMID: 22936215) (LDB1 ChIP-seq) and Hypergeometric Optimization of Motif EnRichment (HOMER) software tools (all others). (PMID: 20513432) Motif enrichment in LDB1 binding peaks was calculated with findMotifsGenome.pl from the Homer suite.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
48242916
Reads aligned (%)
76.7
Duplicates removed (%)
13.1
Number of peaks
13665 (qval < 1E-05)

hg38

Number of total reads
48242916
Reads aligned (%)
78.2
Duplicates removed (%)
12.0
Number of peaks
13992 (qval < 1E-05)

Base call quality data from DBCLS SRA