Nasal epithelium dataset - isoswitch report

This scRNA-Seq dataset consists of two samples collected by nasal brushing and biopsy in the context of the Human Cell Atlas (HCA) project.
It includes a total of 7.588 cells, clustered in 13 cell types. Annotated UMAP representation is shown below.

Marker search

ISO_SWITCH_ALL identifies isoform-level markers for each cluster and filters only events where two (or more) transcripts of the same gene show as markers of different clusters.

clusters <- levels(adult@active.ident)
markers_hc20_nomin <- ISO_SWITCH_ALL(adult, clusters, assay="multi", min.pct=0, logfc.threshold=0.40, verbose=TRUE)
head(markers_hc20_nomin)

Graphical representations of the genes with isoform switches found across the full dataset

• Left heatmap shows unique number of genes detected per contrast (tiles), per cell type (row annotation), and overall (n)
• Volcano plot (right) shows average log fold change and adjusted p-val (FDR) associated with each gene

This general plot shows highly significant switches (HYAL2, RPS24, MYL6 …)

The same plot can be split per cell type:

plot_marker_score(adult, markers_hc20_nomin, facet=TRUE, ncol=5, overlaps=16)

Or zoom at particular contrasts of interest:

Zoom at Deuterosomal vs Basal

Closer look at the hot spot (29 unique genes found) in the contrast “Deuterosomal vs Basal”

deut_vs_basal <- filter(markers_hc20_nomin, contrast == "Deuterosomal vs Basal")
plot_marker_score(adult, deut_vs_basal, facet=FALSE, overlaps=16) 

Zoom at Squamous vs Multiciliated

Closer look at the Deuterosomal vs Multiciliated contrast

deut_vs_basal <- filter(markers_hc20_nomin, contrast == "Squamous vs Multiciliated")
plot_marker_score(adult, deut_vs_basal, facet=FALSE, overlaps=16) 

Gene reports (top 10)

HYAL2

RPS24

MYL6

EEF1B2

LYPLA2

LGALS9

RTN4

GCHFR

VAMP5

LMNA

Full gene switch table

141 distinct genes with isoform-switches were found: