This interactive tool lets you explore isoform expression in space across seven long-read spatial datasets from five mouse brain sections, generated with two spatial platforms (Stereo-seq and Visium HD) and two long-read sequencing technologies (Oxford Nanopore and PacBio).

1) Stereo-seq (Spl-ISO-Seq2)

Two consecutive slides, S1 and S2, from the same P56 male mouse brain. Because they are neighbouring sections, they show almost the same anatomy and are the most direct comparison in this collection.

• Stereo-seq S1 was sequenced twice: once with a whole-exome approach (S1, whole exome, ONT) and once enriching for 3378 genes (S1, 3.3K enriched, ONT) .
• Stereo-seq S2 was sequenced with the whole-exome approach only (S2, whole exome, ONT) .

The 3378 enriched genes are linked to synaptic function, Alzheimer's disease, TDP43 knockdown, Autism Spectrum Disorder (ASD), Schizophrenia and Amyotrophic Lateral Sclerosis (ALS), together with genes showing cell-type-specific splicing in our human PFC data. For more information, refer to our previous paper .

2) Visium HD

Three slides, V1, V2 and V3, each from a different P56 male mouse. They are cut at a slightly different plane from the Stereo-seq S1/S2 pair, so the set of annotated brain regions is not identical between sections.

• Visium HD V1 was sequenced with both technologies from the same section (V1, whole exome, ONT and V1, whole exome, PacBio) , which makes it a direct ONT-versus-PacBio comparison on identical tissue.
• Visium HD V2 was sequenced with ONT (V2, whole exome, ONT) .
• Visium HD V3 was sequenced with PacBio (V3, whole exome, PacBio) .

V1 is annotated at the level of segmented cells; V2 and V3 are annotated on the 8 µm binned grid. All sections have been re-oriented so the hemisphere sits the same way up, and only the annotated hemisphere is shown.

For details and citation, please see our Nature Methods paper . The analysis package behind this app is Spl-IsoFind ( documentation ). Visit the Tilgner Lab website and GitHub .

Instructions:

• Select the Explorer Plot tab to begin.
• Choose one to four datasets to view side by side. Any combination is allowed, so you can compare enrichment strategies, sequencing technologies, or sections.
• Pick whether to search by Gene or Transcript , then start typing. There will be auto-suggestions in the dropdown menu . The input is case-insensitive, and both the name and the ID work. Novel isoforms and novel genes, which have no name, are listed under their identifier (for example transcript16593.chr9.nnic ).
• For each selected dataset you get a spatial hexplot and a bar chart .
  • The spatial hexplot shows the relative expression of the isoform of interest. Every hexagon shows the mean relative expression of the underlying cells. Relative expression indicates the fraction of long reads for that gene that are assigned to the isoform of interest. A hexagon is only plotted when there are underlying cells expressing the gene.
  • The bar chart shows the mean relative expression per brain region.
• Plots are only shown if at least 10 cells express the gene corresponding to the isoform of interest.
• Bar chart regions are abbreviated. CTX cortex, MB midbrain, THA thalamus, STR striatum, HYP hypothalamus, PAL pallidus, WM white matter, HPC hippocampus, OFT optic fiber tract, FT fiber tracts, LV lateral ventricle, 3V/CP third ventricle and choroid plexus, CP1 / CP2 choroid plexus. Region annotations were made per section, so the available regions differ slightly between slides.
• Show brain region annotation adds a colour-coded map of the annotated regions above each panel, drawn from the same coordinates as the hexplot.
• If you would like to show the stain in the background, tick the box for this option .
• Hexagon size is given in microns, so a hexagon covers the same physical area on every panel even though the underlying image resolutions differ.
• To focus on a specific cell type, region or subregion, choose from the dropdown menus . A cell counts towards a cell type only if it is a singlet. If fewer than 10 cells expressing the gene remain, a message is shown instead of a plot. Subregions are only available for the Stereo-seq sections.
• The control panel on the left can be collapsed with the arrow next to its heading, which gives the plots the full width of the window. Your settings are kept while it is hidden.
• Reset to Default puts every option back to its starting value.