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Single Cell Sequencing Techniques in Plant Biology
Part 2: Data Analysis
Virtual Workshop
November 30, 2023

 

Objectives

Registration

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 is closed for the Single Cell Sequencing Techniques in Plant Biology Part 2: Data Analysis workshop.

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)
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
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 (University of California, Berkeley, 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)

Tentative Agenda

7:55 AM - 8:00 AM PST
Opening Remarks
8:00 AM - 8:25 AM PST
Talk Topic: Introduction to scRNA-seq its applications
Speaker:
  • Bert de Rybel (VIB Center for Plant Systems Biology/Ghent University, Belgium)
8:30 AM - 8:45 AM PST
Talk Topic: Creating and reading metadata
Speaker:
  • Benjamin Cole (Joint Genome Institute, USA)
8:50 AM - 9:40 AM PST
Talk Topic: From raw data to count matrix
Speakers:
  • Irene Papatheodorou (EMBL-European Bioinformatics Institute, UK)
  • Che-Wei Hsu (Duke University, USA)
9:50 AM - 10:00 AM PST
Break
10:00 AM - 10:50 AM PST
Talk Topic: From count matrix to Clusters
Speakers:
  • Sina Booeshaghi (University of California, Berkeley, USA)
  • Hongyu Chen (Zhejiang University, China)
11:00 AM - 11:50 AM PST
Talk Topic: Beyond scRNA-seq
Speakers:
  • Andrew Farmer (National Center for Genome Resources, USA)
  • Robin Buell (University of Georgia, USA)
12:00 AM - 12:10 AM PST
Break
12:10 AM - 12:40 AM PST
Panel Discussion/Closing Remarks
Protein bodies in maize endosperm, Marisa Otegui
Electron tomographic reconstruction of protein bodies in maize endosperm. Photo Credit: Marisa Otegui
Arabidopsis cotyledon, Flavia Bossi
Reconstruction of an Arabidopsis first leaf from a six-day old seedling. Photo Credit: Flavia Bossi
Developing maize aleurone cell, Marisa Otegui
Electron tomographic reconstruction of a developing maize aleurone cell. Photo Credit: Marisa Otegui
MICHIGAN STATE UNIVERSITY LAND ACKNOWLEDGEMENT
“The Plant Cell Atlas operates predominantly out of Michigan State University. We acknowledge that Michigan State University occupies the ancestral, traditional, and contemporary Lands of the Anishinaabeg – the Three Fires Confederacy of Ojibwe, Odawa, and Potawatomi peoples. We affirm Indigenous sovereignty and hold Michigan State University accountable to the needs of American Indian and Indigenous peoples.”

For questions about the PCA Initiative please contact us at [email protected].

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  • Home
  • About
    • Annual Report
    • Newsletter
    • People
    • Motivation
    • Goals
    • Milestones
    • Affilations
    • News >
      • Breaking News
      • Past News
    • Code of Conduct
    • Bylaws
    • Contact
  • Resources
    • Publications >
      • 2022 Plant Physiology Focus Issue
    • Tools and Repositories
    • PCA Videos
  • Events
    • Upcoming Events >
      • Spatial Metabolomics Workshop - March 2025
    • Previous Events
  • Opportunities
    • Job Posts
    • Fellowships
  • Outreach
    • JR Biotek-PCA Best Talk Winner
    • PCA Art Exhibit >
      • About
      • Plant Biotechnology
      • Black Plant Scientists
      • Bowie State University
      • Howard University
      • Morgan State University
    • Futurum Brochure
  • Blog