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| 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
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| 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.
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| Overall design |
Histone modification H3K27ac and RNA-Seq in MPP, CDP, cDC and pDC
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| Contributor(s) |
Allhoff M, Seré K, Freitas J, Zenke M, Costa IG |
| Citation(s) |
27484474 |
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| Submission date |
Sep 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Manuel Allhoff |
| E-mail(s) |
allhoff@aices.rwth-aachen.de
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| Organization name |
AICES
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| Street address |
Schinkelstr. 2
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| City |
Aachen |
| ZIP/Postal code |
52062 |
| Country |
Germany |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA296058 |
| SRA |
SRP063865 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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