Current Topics in Genomics - Fall, 2021

Date: November 22, 2021
Time: 1:30 pm
Mode: Zoom (link will be provided later)

Topic: Single-cell Genomics

Differential gene expression studies are critical to understand phenotype. Typically, in the past, these studies considered time expression at various time-points during the development of the phenotype and collected tissues in which the phenotype was being expressed. For example, to study root development, masses of roots were collected, mRNA extracted, and differential expression of all genes in the genome were considered. While the study just considered the root, the root itself consists of various cell types. Techniques have now been developed to harvest different cell types in roots (and other organs), and study expression at the single cell level. This field is called single cell genomics.

This session of Current Topics in Genomics will focus on the techniques and application of single cell genomics. One paper will describe the general experimental approaches to isolating single cell types and their analysis. Another paper will discuss the application of these techniques to lateral root development in Arabidopsis. The third paper will describe the development of a cis-regulatory atlas across six different maize organs from data collected at the single-cell level.

Presentation Instructions

Each participant needs to present a description of the paper that lasts 25-30 minutes. This presentation is required to be in the form of a MS Powerpoint presentation. The presentation should 1) provide an introduction of the importance of single-cell genomics; 2) outline the experimental methodology, and 3) include a discussion of the key tables and figures in the paper and how they relate to the theme of the paper.

Each student will also be required to lead the discussion of the paper after the presentation. As discussion leader, you must also be familiar with the content of the second paper. All assignments are below

Papers

Kennedy Lund: Marand and Schmitz - Single-cell analysis of cis-regulatory elements (Discussion leader: Gurminder Singh)

Peter Beerbower: Gala et al - A single-cell view of the transcriptome during lateral root initiation in Arabidopsis thaliana (Discussion leader: Kennedy Lund)

Gurminder Singh: Marand et al - A cis-regulatory atlas in maize at single-cell resolution (Discussion leader: Peter Beerbower)