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GEO help: Mouse over screen elements for information. |
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Status |
Public on Mar 10, 2018 |
Title |
ATAC-seq of sorted lung cDCs (conventional dendritic cells) from cell-specific MyD88 KO at 0h and 6h in vivo sensitization with OVA/standard flagellin |
Organism |
Mus musculus |
Experiment type |
Other
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Summary |
Allergic asthma is a chronic disease of the airways characterized by eosinophilic and neutrophilic inflammation. MYD88, the adaptor molecule for TLR and IL-1 family member signaling, is required for allergic sensitization through the airway in animal models of allergic asthma. We generated conditionally mutant mice separately lacking Myd88 in airway epithelial cells (ECs) or dendritic cells (DCs) to define the contribution of Myd88 expression in each of these cell types. To examine epigenetic crosstalk from ECs to conventional (c)DCs in vivo, we examined ATAC-seq data from lung cDCs sorted at baseline or following 6h in vivo lung allergic sensitization through the airways from WT MyD88 fx/fx, SPC cre+ MyD88 fx/fx (EC-MYD88 KO), CD11c cre+ MyD88 fx/fx (DC-MYD88 KO), and full MyD88 KO mice. We observed specific epigenetic changes in chromatin conformation in cDCs that were cell-intrinsic as well as resulting from in vivo crosstalk from ECs. We also observed transcriptional changes in cDCs by Affymetrix Whole Transcriptome Array (linked data set) as well as changes in immune-specific whole lung RNA, sorted EC RNA, sorted alveolar macrophage RNA, and sorted cDC RNA changes by Nanostring nCounter Immunology Codeset Analysis (additional linked files).
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Overall design |
Lung cDCs from all genotypes were flow cytometry sorted at baseline or following 6h of in vivo allergic sensitization with 100 micrograms ovalbumin (OVA)/ 1250 ng standard flagellin (stFLA). Samples from all 4 genotypes (WT MyD88 fx, SPC cre+ MyD88 fx, CD11c cre+ MyD88 fx, MyD88 KO) x 2 timepoints (0h baseline, 6 h OVA/stFLA) = 8 conditions. 8 conditions x 2 replicates per genotype-timepoint = 16 total samples. Analysis of baseline (0h) timepoint is a control for induced chromatin conformation changes as compared to those at baseline. WT MyD88 fx/fx mice are a positive control for all potential chromatin-induced at baseline and following allergen sensitization, while MyD88 KO is a negative control for epigenetic changes that are not dependent on MYD88 expression in any cell-type or tissue. SPC cre+ MyD88 fx/fx mice test for epigenetic changes that require EC-dependent MYD88 signaling, whereas CD11c cre+ MyD88 fx/fx mice test for epigenetic changes that require CD11c-expressing cell-dependent MYD88 expression. ATAC-seq analysis was conducted as described.
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Contributor(s) |
Thomas SY, Cook DN |
Citation(s) |
29067999 |
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Submission date |
Mar 10, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Seddon Thomas |
E-mail(s) |
sythomas@gmail.com
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Organization name |
NIEHS
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Street address |
111 T. W. Alexander Dr.,
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City |
RTP |
State/province |
North Carolina |
ZIP/Postal code |
27709 |
Country |
USA |
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Platforms (1) |
GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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Samples (8)
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This SubSeries is part of SuperSeries: |
GSE79615 |
MYD88-dependent dendritic and epithelial cell crosstalk in the lung orchestrates immune responses to inhaled allergens |
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Relations |
BioProject |
PRJNA314845 |
SRA |
SRP071571 |
Supplementary file |
Size |
Download |
File type/resource |
GSE79062_RAW.tar |
12.0 Mb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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