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Single-Cell Transcriptomics Training @ HSLS

On July 10, the HSLS Molecular Biology Information Service (HSLS-MBIS), in partnership with the Genomics Research Core (GRC) and the Center for Research Computing (CRC), offered a day-long workshop on single-cell transcriptomics research. Single-cell transcriptomics is a next-generation sequencing methodology that simultaneously measures, in individual cells and in high resolution, the messenger RNA concentrations of thousands of genes. The ultimate goal is to better understand individual cell functions, even in mixed cell populations.

During the morning session, Deborah Hollingshead, MS, GRC Assistant Director, shared GRC experience with single-cell sequencing projects over the past year and discussed best practices for sample handling. Two Pitt researchers then gave short presentations based on their research with single-cell RNA-Seq data (scRNA-Seq). Khodor Abou Daya, MD, Department of Surgery, spoke on “Transcription Profile of Tissue Resident Memory CD8 T Cells.”  Itay Raphael, PhD, Department of Medicine, spoke on “Transcriptional Features Associated with Response to Immunotherapy in Melanoma.”

The afternoon session, taught by Ansuman Chattopadhyay, PhD, and Sri Chaparala, MS, from HSLS-MBIS, focused on data analysis using the library-licensed point-and-click software, Partek Flow. Attendees learned the basic steps involved in scRNA-Seq data analysis, including quality assurance/quality control, aligning the reads to a reference genome, quantification, t-SNE and UMA plots, biological applications such as identifying biomarkers or cell populations, and how to access the Partek Flow server via the CRC HTC cluster.

The day exceeded expectations, with 46 attendees in the morning and 48 in the afternoon. HSLS-MBIS will continue to offer classes on scRNA-Seq each semester—check here for the fall 2019 workshop schedule.

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Posted in the September 2019 Issue