This interactive tool lets you explore our spatial isoforms data from Spl-ISO-Seq2 ONT, Visium HD ONT, and Visium HD PacBio datasets:

1) Spl-ISO-Seq2 ONT

Two consecutive slides of a P56 male mouse brain can be explored:

• Sample 1 was sequenced twice: once using a whole-exome approach (Sample 1 (Whole-Exome)) and once while enriching for 3378 genes (Sample 1 (3.3K Enriched)) .
• Sample 2 was sequenced only using the whole-exome approach (Sample 2 (Whole-Exome)) .

The 3378 genes that are enriched are linked to synaptic function, AD, TDP43 knockdown, Autism Spectrum Disorder (ASD), Schizophrenia and Amyotrophic Lateral Sclerosis (ALS) and genes with cell-type-specific splicing patterns in our human PFC8 data. Fore more information, Refer to previous paper

2) Visium HD ONT

One P56 male mouse brain slide sequenced using ONT.

3) Visium HD PacBio

One P56 male mouse brain slide sequenced using PacBio.

For details and citation, please see our Preprint . Visit the Tilgner Lab Website and GitHub .

Instructions:

• Please select the Explorer Plot tab to begin.
• You need to select the exploration option from the dropdown menu Gene / Transcript first.
• Input the Gene / Transcript identification to show the plot. There will be auto-suggestions in the dropdown menu . The input is case-insensitive. Both the name and ID of the transcript/gene can work .
• For the selected isoform, there will be a spatial hexplot and 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 gene.
• The bar chart shows the mean relative expression per region.
• Plots are only shown if at least 10 cells are expressing the gene corresponding to the isoform of interest.
• The bar chart brain region names are shown in abbreviation. CTX: Cortex, MB: Mid Brain, THA: Thalamus, STR: Striatum, HYP: Hypothalamus, PAL: Pallidus, WM: White Matter, HPC: Hippocampus, OFT: Optic Fiber Tract
• If you would like to show the stain in the background, tick the box for this option .
• If you would like to focus on a specific cell type / region / subregion, Choose from the dropdown menu . If there are not enough cells expression the gene corresponding to the isoform of interest (cells < 10) in the selected cell type / region / subregion, a message will be shown on the screen.
• Reset to Default option allows you to set everything before selecting Gene / Transcript.