Post-Transcriptional Dynamics of Fibroblasts and Keratinocytes During Skin Wound Healing

In this tutorial, we will examine isoform expression and alternative splicing events in fibroblasts and keratinocytes, comparing patterns between acute wounds and normal skin to better understand post-transcriptional dynamics in wound healing.

Glossary

PSI (Percent Spliced In): Proportion of transcripts that include a specific isoform or splicing event, ranging from 0 to 1.

dPSI (ΔPSI): Difference in PSI values between two conditions (e.g., WF–SF or WK–SK), used to quantify splicing changes.

Alternative Splicing Events: Types of splicing patterns such as SE (exon skipping), RI (intron retention), A3 (alternative 3′ splice site), A5 (alternative 5′ splice site), MX (mutually exclusive exons), AF (alternative first exon), and AL (alternative last exon).

Overview of the Tutorial

This app is organized into three major parts, each with an Expression view and a Differential Expression (DE) analysis view:

Part 1: Isoform Expression & DE Isoform

• Isoform Expression: Explore isoform expression in fibroblasts (SF vs. WF) and keratinocytes (SK vs. WK).
• DE Isoform: Identify differentially expressed isoforms between wound and skin. Heatmaps and data tables can be exported.

Part 2: IsoAS Expression & DE IsoAS

• IsoAS Expression: Investigate isoform-level splicing events with gene-level queries.
• DE IsoAS: Focus on IsoAS events significantly regulated between conditions. Export both plots and tables.

Part 3: ASbyEvent Expression & DE ASbyEvent

• ASbyEvent Expression: Explore alternative splicing events grouped by event type (e.g., A3, MX, SE, A5, RI, AL, and AF).
• DE ASbyEvent: Detect splicing events that differ between wound and skin. Heatmaps and tables include ΔPSI, p-values, and transcript details.

Abbreviations

DE: Differential Expression	Iso: Isoform
AS: Alternative Splicing	SF: Normal Skin Fibroblast
WF: Post-wounded Day 7 Fibroblast	SK: Normal Skin Keratinocyte
WK: Post-wounded Day 7 Keratinocyte