Objectives

The second part of the two-part workshop on Single Cell Sequencing Techniques in Plant Biology. This workshop aims to introduce well-established methods and approaches to analyzing scRNA-seq data. Specifically, it seeks to present a compilation of minimum considerations required to analyze and store scRNA-seq results, including QC assessment of the raw and processed data, clustering, differential gene expression, and annotation. It will also provide a look at cutting-edge strategies for multi-modal data integration and its application. Finally, the workshop will offer opportunities for speakers and participants to discuss sc-RNA-seq technologies in plant-specific systems.

Registration

Register

Date: November 30, 2023
Workshop Times
PST - 7:55am - 12:40pm
MST - 8:55am - 1:40pm
CST - 9:55am - 2:40pm
EST - 10:55am - 3:40pm
CET - 4:55pm - 9:40pm
GMT+8 - 11:55am  (12/1/23)- 4:40am (12/1/2023)
Search for your time zone here.

Workshop Organizers and Speakers

Epidermal plasma membrane in green and nuclei (H2B-TFP) in blue, together with chlorophyll autofluorescence in red below in the mesophyll. Photo credit: Kate Harline (Roeder Lab)

Pin1-YFP (yellow) and DR5::RFP (red) in the maize shoot apex. Photo credit: Leiboff Lab

Depth-coded image of microtubules in root hairs of the model grass, Brachypodium distachyon. Photo credit: Elison Blancaflor

Speakers

• Sina Booeshaghi (California Institute of Technology, USA)
• Robin Buell (University of Georgia, USA)
  
• Hongyu Chen (Zhejiang University, China)
• Benjamin Cole (Joint Genome Institute, USA)
• Bert de Rybel (VIB Center for Plant Systems Biology/Ghent University, Belgium)
• Andrew Farmer (National Center for Genome Resources, USA)
• Che-Wei Hsu (Duke University, USA)
• Irene Papatheodorou (EMBL-European Bioinformatics Institute, UK)

Agenda

7:55 AM - 8:00 AM PT

Opening Remarks

8:00 AM - 8:20 AM PT

Bert de Rybel (VIB-PSB /Ghent University, Belgium)
Talk Topic: Introduction to scRNA-seq its applications in plants

8:30 AM - 8:45 AM PT

Benjamin Cole (Joint Genome Institute, USA)
Talk Topic: Creating and reading metadata

8:50 AM - 8:15 AM PT

Irene Papatheodorou (EMBL-European Bioinformatics Institute, UK)
Talk Topic: Tools for QC analysis, processing scRNA-seq raw data, and generation of  count matrices

9:20 AM - 9:45 AM PT

Che-Wei Hsu (Duke University, USA)
Talk Topic: Pipelines automatization for sc/snRNA-seq analysis

9:50 AM - 10:00 AM PT

Break

10:00 AM - 10:25 AM PT

Sina Booeshaghi (California Institute of Technology, USA)
Talk Topic: Identification of cell clusters after generation of count matrices

10:30 AM - 10:55 AM PT

Hongyu Chen (Zhejiang University, China)
Talk Topic: Identification and annotation of cell clusters using  PlantscRNAdb

11:00 AM - 11:25 AM PT

Andrew Farmer (National Center for Genome Resources, USA)
Talk Topic: Integrating multimodal datasets

11:30 AM - 11:55 AM PT

Robin Buell (University of Georgia, USA)
Talk Topic: Integrating multimodal data and single-cell biology in nonmodel organisms

12:00 PM - 12:10 PM PT

Break

12:10 PM - 12:40 PM PT

Panel Discussion

Electron tomographic reconstruction of protein bodies in maize endosperm. Photo Credit: Marisa Otegui

Reconstruction of an Arabidopsis first leaf from a six-day old seedling. Photo Credit: Flavia Bossi

Electron tomographic reconstruction of a developing maize aleurone cell. Photo Credit: Marisa Otegui