Lower airway mucosa of allergen-induced asthma exacerbation

Jehan Alladina1, Neal P. Smith1, Tristan Kooistra1, Kamil Slowikowski1, Isabela J. Kernin1, Jacques Deguine2, Henry L. Keen3, Kasidet Manakongtreecheep2, Jessica Tantivit2, Rod A. Rahimi1, Susan L. Sheng1, Nhan D. Nguyen1, Alexis M. Haring1, Francesca L. Giacona1, Lida P. Hariri1, Ramnik J. Xavier2, Andrew D. Luster1, Alexandra-Chloé Villani1, Josalyn L Cho3, Benjamin D. Medoff1
1Harvard Medical School, 2The Broad Institute, 3University of Iowa Carver College of Medicine, *Corresponding author
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Description Bronchoscopic SAC and single-cell RNA sequencing (scRNA-seq) was used to define the airway mucosal microenvironment and identified transcriptional programs that were only observed after allergen exposure. These data distinguished cellular and molecular pathways that define asthma from those associated with allergy alone.
Dataset ID LMEX0000004410
Assay Type Single-cell RNA-seq
Organism Human
Stages Adult
Cell Count 52152
Technology 10x Genomics Chromium Single Cell Gene Expression
Reference Alladina et al. (2023)
External databases dbGaP: phs003101.v1.p1 GEO: GSE193816
FileDescriptionSize
GSE193816_all_cells_data.h5ad.gzThe authors' own object for this study, HDF5 AnnData, gzip compressed. 52,152 cells x 28,304 genes over 7 author cell states, 8 donors and 21 bronchoscopy libraries. X holds the natural log of one plus counts per hundred thousand, the authors' own normalisation. The site viewers read a log2 counts per TEN thousand matrix converted from it.558.3 MB
GSE193816_library_metadata.tsvLibrary metadata for the 21 bronchoscopy libraries, one row each. Carries the library, its donor, the challenge it followed (segmental allergen, diluent control, or baseline before challenge), the donor's health status, and the number of cells the library contributes. The Samples tab shows the donor level, so this file carries the library level.1.7 KB
LungMAP IDAlt IDSpeciesAge GroupHealth Status
LMSPASTH0000001500008Homo sapiensAdultAllergic non-asthmatic
LMSPASTH0000002500012Homo sapiensAdultAllergic non-asthmatic
LMSPASTH0000003500015Homo sapiensAdultAllergic non-asthmatic
LMSPASTH0000004500021Homo sapiensAdultAllergic asthmatic
LMSPASTH0000005500023Homo sapiensAdultAllergic asthmatic
LMSPASTH0000006500024Homo sapiensAdultAllergic non-asthmatic
LMSPASTH0000007500030Homo sapiensAdultAllergic asthmatic
LMSPASTH0000008500035Homo sapiensAdultAllergic asthmatic