Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Ep300

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.

Attributes by original data submitter

Sample

source_name
Flt3L cultured dendritic cells
cell type
CD172+DC
chip antibody
anti-p300

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP of p300, sorted cells were incubated in fresh media with Flt3L for 2 hours before crosslinking; for ChIP of IRF8, Batf3, H3K27ac, and H3K4me1, cells fixed before purification. Cells were crosslinked with 1% formaldehyde, quenched with 1.25M Glycine, twice washed with PBS. Chromatin was sonicated for shearing DNA size from 140 to 500 bp. Chromatin fragments were immunoprecipitated overnight at 4 °C with Dynabeads Protein A or G bound to anti-p300 (sc-585X, Santa Cruz Biotechnology), anti-IRF-8 (sc-6058x, Santa Cruz Biotechnology), or anti-Batf3, anti-H3K27ac (Ab 4729, Abcam) and H3K4me1 (Ab 8895, Abcam). ChIPed DNA was eluted and reverse-crosslinked for 6 hr. DNA was purified with phenol:chloroform extraction followed by ethanol precipitation. Libraries for ChIP-seq were prepared using ThruPLEX-FD kit (Rubicon Genomics) and sequenced using Illumina HiSeq 2500 as single reads extending 50 bases.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
25251768
Reads aligned (%)
83.4
Duplicates removed (%)
27.0
Number of peaks
489 (qval < 1E-05)

mm9

Number of total reads
25251768
Reads aligned (%)
83.2
Duplicates removed (%)
27.1
Number of peaks
496 (qval < 1E-05)

Base call quality data from DBCLS SRA