Gene expression data across multiple timepoints are included in an online interactive display including:
- whole lung samples at 0, 2, 4, and 6 hours
- endothelial cells (ECs, sorted) at 2 hours
- conventional dendritic cells (cDCs, sorted) at 6 hours
- alveolar macrophages (AMs, sorted) at 6 hours
Each sample represents data in four cell line genotypes:
- wildtype (WT)
- cDC-specific knockout of MyD88 (DC.KO)
- EC-specific knockout of MyD88 (EC.KO)
- full knockout of MyD88 (KO)
Gene expression measurements were obtained using the Nanostring nCounter Mouse Immunology Gene Expression Codeset, processed using nCounter software, and further analyzed using R-3.6.1 as described in the publication below.
Supplementary Data Summary Page: MyD88/Asthma Expression Profiles. Click Web Visualizations to view the figures.
This repository contains static data and figures accompanying
"MyD88-dependent Dendritic and Epithelial Cell Crosstalk Orchestrates Immune Responses to Allergens"
authored by Dr. Seddon Y. Thomas et al, 2018, who is both a gifted scientist and a fantastic person.
Mucosal Immunol. 2018 May; 11(3): 796–810.
Figures were prepared using the R package Trelliscope to create a static HTML set of figures across all genes and samples. This novel interface provides interactivity without the need for an active R-shiny server, which is a remarkably useful consideration especially when used for supplementary data for a scientific publication.
The interface relies on only the Trelliscope javascript library and therefore is entirely encoded by fixed HTML file. The interface also provides interactive querying and filtering capabilities.