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Series GSE73143 Query DataSets for GSE73143
Status Public on Aug 03, 2016
Title Differential Peak Calling of ChIP-Seq Signals with Replicates with THOR
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Dendritic cells (DC) are professional antigen presenting cells that develop from hematopoietic stem cells in bone marrow by successive steps of lineage commitment and differentiation. Different DC subsets were identified based on phenotype, localisation and function: (i) classical DC (cDC) and plasmacytoid DC (pDC) are found in lymphoid organs and (ii) migratory tissue DC are spread throughout peripheral organs, including Langerhans cells, the cutaneous contingent of DC. We have developed a two-step culture system that recapitulates DC development in vitro (Felker et al., J. Immunol. 185, 5326-5335, 2010). In this system multipotent hematopoietic progenitors (MPP) progress into DC-restricted common DC progenitors (CDP) and further into the two major DC subsets cDC and pDC. We employed chromatin immunoprecipitation (ChIP) with deep sequencing (ChIP-seq) to determine the dynamics of H3K27ac occupancy in MPP, CDP, cDC and pDC. Additionally, we monitored changes in gene expression in MPP, CDP, cDC and pDC by RNA-seq.
 
Overall design Histone modification H3K27ac and RNA-Seq in MPP, CDP, cDC and pDC
 
Contributor(s) Allhoff M, Seré K, Freitas J, Zenke M, Costa IG
Citation(s) 27484474
Submission date Sep 17, 2015
Last update date Mar 19, 2019
Contact name Manuel Allhoff
E-mail allhoff@aices.rwth-aachen.de
Organization name AICES
Street address Schinkelstr. 2
City Aachen
ZIP/Postal code 52062
Country Germany
 
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (16)
GSM1887715 MPP_H3K27ac_1
GSM1887716 MPP_H3K27ac_2
GSM1887717 CDP_H3K27ac_1
Relations
BioProject PRJNA296058
SRA SRP063865

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE73143_DC_CDP_cDC-diffpeaks.bed.gz 3.0 Mb (ftp)(http) BED
GSE73143_DC_CDP_cDC_THOR-1.bedGraph.gz 556.3 Kb (ftp)(http) BEDGRAPH
GSE73143_DC_CDP_cDC_THOR-2.bedGraph.gz 558.8 Kb (ftp)(http) BEDGRAPH
GSE73143_DC_CDP_pDC-diffpeaks.bed.gz 2.8 Mb (ftp)(http) BED
GSE73143_DC_CDP_pDC_THOR-1.bedGraph.gz 517.6 Kb (ftp)(http) BEDGRAPH
GSE73143_DC_CDP_pDC_THOR-2.bedGraph.gz 523.4 Kb (ftp)(http) BEDGRAPH
GSE73143_DC_MPP_CDP-diffpeaks.bed.gz 2.4 Mb (ftp)(http) BED
GSE73143_DC_MPP_CDP_THOR-1.bedGraph.gz 452.8 Kb (ftp)(http) BEDGRAPH
GSE73143_DC_MPP_CDP_THOR-2.bedGraph.gz 451.4 Kb (ftp)(http) BEDGRAPH
GSE73143_DC_cDC_pDC-diffpeaks.bed.gz 2.6 Mb (ftp)(http) BED
GSE73143_DC_cDC_pDC_THOR-1.bedGraph.gz 494.8 Kb (ftp)(http) BEDGRAPH
GSE73143_DC_cDC_pDC_THOR-2.bedGraph.gz 498.1 Kb (ftp)(http) BEDGRAPH
Raw data are available in SRA
Processed data is available on Series record

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