Antigen

Antigen Class

Input control

Antigen

Input control

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

Conventional dendritic cells

cell type

Conventional dendritic cells

strain

C56BL/6

chip antibody

none

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

10^7 cells were crosslinked 1% paraformaldehyde (Sigma-Aldrich) in PBS then lysed (1%SDS + 1mM EDTA + proteases inhibitors). Cross-linked DNA was sonicated with the Bioruptor (Diagenode). Protein G Dynabeads (Invitrogen) were incubated with 20 μg of PU.1 antibody (Santa Cruz, T-20) according to the manufacturer's protocol. Coupled antibody was added to 100 μg of chromatin and incubated overnight at 4°C. Unbound chromatin was removed using a series of four washes. Following elution, bound chromatin was reverse cross-linked and subjected phenol/chloroform immunoprecipitation. Libraries were prepared at the Beijing Genomic Institute (BGI) according to Illumina's instructions and standard BGI ChIP-seq protocols.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

25820698

Reads aligned (%)

97.9

Duplicates removed (%)

11.8

Number of peaks

495 (qval < 1E-05)

mm9

Number of total reads

25820698

Reads aligned (%)

97.7

Duplicates removed (%)

11.8

Number of peaks

533 (qval < 1E-05)