Dataset features

Specifications


Application: ATAC-seq analysis
Number of samples: 8
Release date: Mar 10 2018
Last update date: Oct 24 2018
Access: Public
Diseases: Asthma
Dataset link 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

Experimental Protocol


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.

Repositories


GEO

GSE79062

ENA

SRP071571

BioProject

PRJNA314845

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Contact


Seddon Thomas

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