Spatial Transcriptomics Technology Workshop

June 25, 2018, 10 a.m. - June 25, 2018, 4:30 p.m.

Organizer -

UCSF Center for Advanced Technology

Contact -

Stefania Giacomello <>

Location -

UCSF Genentech Hall, Room N114

Speaker – Stefania Giacomello, Senior Scientist, Spatial Transcriptomics AB

The Spatial Transcriptomics technology allows you to perform 2D transcriptome-wide studies in intact tissue sections combining high-throughput sequencing and microscopy. This innovative type of information can be generated from both mammalian and plant tissues. The end result is a quantitative gene expression map of the polyadenylated transcripts expressed in your tissue of interest.

The workshop will be divided in two parts. The first one will provide key concepts of the Spatial Transcriptomics workflow, from data generation to visualization and quantitative analysis. It will also include a presentation on how to combine spatial and single-cell data to study the human fetal heart development.

The second part, after lunch, will guide you step-by-step through the molecular and computational aspects of Spatial Transcriptomics to generate and analyse your spatial data.

Please register so we can get an accurate headcount for seminar sessions, coffee breaks and lunch.

Workshop agenda

Part I

10:00 – 10:50

Spatial Transcriptomics technology overview. How does it work and what results will I obtain?

10:50 – 11:10  Coffee break

11:10 – 11:40

Combining Spatial Transcriptomics and single-cell RNA-sequencing data to study the development of the human fetal heart.

11:40 – 12:00  Discussion

12:00 – 13:00  Lunch


Part II

13:00 – 13:30

Tissue Optimisation: walk-through the protocol.

13:30 – 14:00

Library Preparation part I: walk-through the first (“on slide”) part of the protocol.

14:00 – 14:15  Short coffee break

14:15 – 14:45

Library Preparation part II: linear library preparation and sequencing - overview of the workflow.

14:45 – 16:00

Introduction to Spatial Transcriptomics data analysis.

16:00 – 16:30  Discussion

Registration is closed for this event