Topic: Single Cell RNA SEQ

The Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) Office of the Scientific Director invites you to the Division of Intramural Research (DIR) Tenure-Track Investigator Virtual Symposia Series.

Speakers:

Timothy J. Petros, Ph.D.

Investigator, Unit on Cellular and Molecular Neurodevelopment, NICHD, NIH

“A comprehensive spatial epigenome atlas of the embryonic mouse brain”

Maria K. Lehtinen, Ph.D.

Hannah C. Kinney, M.D. Chair in Pediatric Pathology Research, Boston Children’s Hospital

Associate Professor, Harvard Medical School

“Signals making a splash: Choroid plexus – cerebrospinal fluid contributions to brain development”

Flora M. Vaccarino, M.D.

Professor, Child Study Center and Department of Neuroscience, Yale School of Medicine

“Organoid modeling of gene regulatory events during forebrain development”

Bing Ren, Ph.D.

Member of the Ludwig Institute for Cancer Research

Director of the Center for Epigenomics, Professor of Cellular and Molecular Medicine, University of California, San Diego

“Single cell epigenome atlases of the brain”

Arnold Kriegstein M.D., Ph.D.

Professor of Neurobiology, University of California, San Francisco

“Development and evolution of the human brain revealed by single cell transcriptomics”

About the series:

The NICHD DIR Tenure-Track Investigator Virtual Symposia Series provides tenure-track investigators within NICHD the opportunity to organize a virtual mini-symposium to showcase their area of science to the NICHD DIR and larger NIH intramural community. Symposia are held monthly on the second Thursday of the month at 1 pm ET, and are open to all NIH faculty, trainees, and staff.

American Sign Language interpreting services will be available only upon request. Individuals who need interpreting services and/or other reasonable accommodations to participate in this event, should contact Amaressa Abiodun (amaressa.abiodun@nih.gov), 301-435-6994.  Requests should be made five days in advance of the event.

Powerful and Intuitive Gene Expression Visualization Tools to Interpret Biological Signals – Bulk and Single Cell Data

The increasing use of genomic technologies, such as RNA-Seq and single cell RNA-Seq, to assess gene expression patterns has led to an unprecedented amount of data. For many, the size and complexity of these data sets make it challenging to see the biological signals. But not anymore.

The visualization tools in Partek^® Flow^® provide the flexibility needed to display gene expression results ready for publication. Our powerful, interactive plots also facilitate novel discovery and provide fast and accurate QAQC. Together with the easy-to-use point and click interface, Partek Flow allows you to answer more questions and move forward with your research.

In this webinar, you will learn how to visualize gene expression data using:

• Feature distribution plots
• Sample correlation plots
• Volcano plots
• Chromosome view
• Dot plots
• Violin plots
• Hierarchical clustering
• PCA
• t-SNE
• Customizable scatterplots

WebEx link: https://cbiit.webex.com/cbiit/j.php?MTID=m634db94c7c42f1eb6dcf1850c27bd2c6

This webinar will discuss the various single cell RNA-Seq data formats and how to process them with Partek Flow.

You will learn about:

• Single cell data file formats .h5, .fastq, .tsv, .mtx, .bcl
• Trimming tags
• Alignment
• Deduplicating UMI
• Filtering barcodes (cells)
• Knee plots

Sarah Teichmann, Ph.D., Fellow of the Academy of Medical Sciences (UK FMedSci), Fellow of the Royal Society (FRS), Wellcome Sanger Institute

Sarah Teichmann is co-founder and principal leader of the Human Cell Atlas (HCA) international consortium. The International Human Cell Atlas initiative aims to create comprehensive reference maps of all human cells to further understand health and disease.

The team’s research focuses on four complementary study areas:

• Transcriptional regulation and gene expression
• Single-cell genomics
• Immunology
• Protein complexes