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Series GSE79062 Query DataSets for GSE79062
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
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).
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.
Contributor(s) Thomas SY, Cook DN
Citation(s) 29067999
Submission date Mar 10, 2016
Last update date May 15, 2019
Contact name Seddon Thomas
Organization name NIEHS
Street address 111 T. W. Alexander Dr.,
City RTP
State/province North Carolina
ZIP/Postal code 27709
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (8)
GSM2084788 Lung_cDC_CD11c_cre+_MyD88 fx_0h
GSM2084789 Lung_cDC_WT_MyD88 fx_0h
GSM2084790 Lung_cDC_MyD88_KO_0h
This SubSeries is part of SuperSeries:
GSE79615 MYD88-dependent dendritic and epithelial cell crosstalk in the lung orchestrates immune responses to inhaled allergens
BioProject PRJNA314845
SRA SRP071571

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Supplementary file Size Download File type/resource
GSE79062_RAW.tar 12.0 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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