Dr. Peter Adams, Sanford Burnham Prebys Medical Discovery Institute
Dr. Geoffrey Wahl, Salk Institute for Biological Studies
Dr. Brian James, Sanford Burnham Prebys Medical Discovery Institute
Single Cell Sequencing Workshop Group/Social
Date: First Monday Monthly
Time: 4:00pm - 5:00pm
Sanford Burnham Prebys Medical Discovery Institute
Fishman Auditorium, Building #4
10901 North Torrey Pines Road
La Jolla, CA 92037
2018 Workshop Group/Social Dates
Monday, March 5, 2018
Presenter: Sebastian A. Preissl, Ph.D., Associate Director, Single Cell Genomics under Dr. Bing Ren at the UCSD Center for Epigenomics in the Department of Cellular and Molecular Medicine
Title: Single nucleus analysis of chromatin accessibility in mouse for brain development
Summary: The forebrain plays a key role in multiple higher-order brain functions including memory and consciousness. Transcriptional regulatory regions in the genome including promoters and distal acting enhancers play fundamental roles for forebrain development. Regulatory elements can be identified by the presence of open chromatin as measured by ATAC-seq (Assay for transposase-accessible chromatin using sequencing). However, unraveling the role of regulatory DNA elements has proven challenging for two main reasons: 1) regulatory DNA elements are dynamic and thus their activity must be studied across multiple stages; 2) tissues are heterogeneous and comprised of different cell types with cell-type-dependent chromatin accessibility patterns. To overcome these challenges we have optimized a combinatorial barcoding assisted assay for transposase accessible chromatin for frozen brain tissue samples. Analysis of more than 15,000 forebrain nuclei at eight developmental stages reveals 20 distinct cell populations corresponding to major neuronal and non-neuronal cell types. In addition, we define cell-type-specific transcriptional regulatory sequences, infer potential master transcriptional regulators and delineate developmental changes in forebrain cellular composition.
Monday, April 2, 2018 Cancelled
Monday, May 7, 2018 Cancelled
Presenter: Alain Domissy, Ph.D., Scientific Director, Center for Computational Biology and Bioinformatics at The Scripps Research Institute
Title: The Metadata is your Program
Summary: We will present a new way for experimental scientists to efficiently manage their experiments metadata and as a result gain the power to autonomously trigger and control both upstream compute intensive as well more interactive downstream analysis from the comfort of just their laptop's text editor, browser and email programs.
This will be illustrated with an example of a 10x single cell rna-seq experiment. We will use a tutorial dataset which is a downsized version of a published paper, and allows going through the complete pipeline experience in less then one hour.
Monday, June 4, 2018
Presenter Raj Giraddi, Ph.D., Research Associate, Gene Expression Laboratory, Salk Institute
Title: Single cell analysis of the stem cell states
Summary: We generated a single cell transcriptome data set encompassing fetal, postnatal and adult mouse mammary epithelium and paid special attention to the perinatal interval, over which the prevalent, multipotent fMaSC phenotype declines and differentiation ensues. We elucidate biological programs that distinguish bipotent stem cells from differentiating and lineage-committed cells. Our results reveal the surprising nature of the mammary stem cell states and changes how we view the mammary gland hierarchy and its subsequent implications in breast cancer.
Monday, July 2, 2018 CANCELLED
Monday, August 6, 2018 CANCELLED
Monday, September 3, 2018 CANCELLED
Monday, October 1, 2018
Monday, November 5, 2018
Monday, December 3, 2018