Antigen

Antigen Class

TFs and others

Antigen

Runx3

Cell type

Cell type Class

Blood

Cell type

Dendritic Cells

MeSH Description

ANTIGEN-PRESENTING CELLS of dendritic cell morphology found in the LYMPH NODES and other lymphoid tissues.

Sample

source_name

Splenic CD4+ dendritic cells

cell type

Splenic CD4+ dendritic cells

passages

Collected from approximately 15 mice. DC were freshly sorted, fixed and frozen -80c

strain

C57BL/6

chip antibody

Runx3poly clonal home made

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Isolated cells were fixed in 1% formaldehyde and sonicated to yield DNA fragments of ~300bp. For immunoprecipitation, 40ul of anti-Runx3 Ab were added to 15 mL of diluted, fragmented chromatin; whole cell extract fragmented chromatin served as control. DNA was purified using QIAquick spin columns (QIAGEN). For ChIP-seq analysis, indexed CiHP-seq libraries were prepared as published Blecher-Gonen et al. Nature Protocols 8, 539–554 (2013). Illumina sequencing of short reads (50 bp) was performed in one lane of Hiseq 2000 using v3 clustering and sequencing reagents.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

31941529

Reads aligned (%)

97.7

Duplicates removed (%)

18.8

Number of peaks

3691 (qval < 1E-05)

mm9

Number of total reads

31941529

Reads aligned (%)

97.4

Duplicates removed (%)

18.7

Number of peaks

3665 (qval < 1E-05)