Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Spi1

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
Classical dendritic cell (cDC)
cell type
Classical dendritic cell (cDC)
chip antibody
PU.1 ( Santa Cruz, sc-352)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation (ChIP) was performed as described before (Dahl and Collas, 2008) with minor modifications. Briefly, sorted cells were cross-linked at a concentration of 2 million cells/ml with 1% formaldehyde for 6 min at room temperature. Cross-linking was stopped with 0.125 M glycine. Chromatin sonification into fragments of 200-400 bp in size was done by Diagenode Bioruptor with cooling device at 4°C for 10 min with 30 s pulse/pause cycles. Sheared lysates were clarified by centrifugation at 12,000g (10 mins, 4°C). 10 µl Dynabeads Protein A (Life Technologies) were preincubated with either 1 µg IgG control (Santa Cruz) or specific antibodies for H3K4me1, H3K4me3, H3K9me3, H3K27me3 or PU.1. For immunoprecipitation sheared chromatin of 1 million cells was added to the preincubated beads over night at 4°C. Chromatin complexes were isolated by magnetic bead selection and washed with RIPA and TE buffer. Chromatin complexes were digested with 50 µg/ml RNase (Roche) at 37°C for 30 min. Immunoprecipitated DNA was purified using QIAquick PCR Purification Kit according to the manufacturer's protocol (Qiagen). DNA concentration of immunoprecipitated DNA was determined by using Qubit dsDNA HS Assay kit (Life Technologies). Libraries were prepared and subjected to deep-sequencing on the Illunima platform according to then manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
20087924
Reads aligned (%)
97.4
Duplicates removed (%)
42.5
Number of peaks
13269 (qval < 1E-05)

mm9

Number of total reads
20087924
Reads aligned (%)
97.2
Duplicates removed (%)
42.6
Number of peaks
13267 (qval < 1E-05)

Base call quality data from DBCLS SRA