Topic: Genomics

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NHGRI will host a new seminar series this year on the “Bold Predictions for Human Genomics by 2030” that are described in NHGRI’s “Strategic Vision for Improving Human Health at the Forefront of Genomics.” The July 12, 2021 seminar will focus on Bold Prediction #6: The regular use of genomic information will have transitioned from boutique to mainstream in all clinical settings, making genomic testing as routine as complete blood counts (CBCs). Dr. Jennifer Posey of Baylor College of Medicine and Dr. Katrina Armstrong of Massachusetts General Hospital & Harvard Medical School will use this prediction as an aspirational theme for their talks, highlighting their own work in the context of that theme and speculating about the next decade in their areas. The talks will be followed by a moderated question-and-answer session. All seminars will be open to the public and recorded for posting on GenomeTV.

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Attendees will learn how to use Partek Flow to identify cell subtypes using both gene and protein expression in a peripheral blood mononuclear cell (PBMC) sample using Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq) technology. CITE-Seq is a multimodal single cell phenotyping method. CITE-Seq data analysis starts with importing a count matrix file, followed by QC and filtering data. Clustering analysis and dimension reduction techniques are then used to visualize and identify subtypes of cells. Differential expression detection among different subtypes will be demonstrated, followed by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Basic knowledge of Partek Flow is required.

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Understanding the biology in transcription factor binding site data requires a comprehensive and integrated approach and must be supplemented with highly-curated data content from multiple sources. Genomatix is a computational biology company with a 22-year history of developing tools and data content for understanding the molecular mechanisms of eukaryotic gene expression. This two-day class will provide an easy-to-use bioinformatics software platform for the detailed analysis of promoters and transcription factor binding sites.

This two-day lecture and training workshop will introduce students to the rich applications for transcription factor binding site (TFBS) analysis using the Genomatix platform. This course is broken down into a morning and an afternoon session. NOTE: Registration and attendance for the day one session is required to attend the day two session.

The day one session will focus on promoter annotation, basic transcription factor binding site analysis, and comparative genomics. Covered topics: promoter annotation and alternative promoters; using tissue activity data to select promoters (programs: ElDorado, Gene2Promoter); TFBS analysis with additional lines of evidence (MatInspector, MatBase); promoter orthologs and analysis of conserved TFBSs (Common TFs, DiAlignTF).

The day two session will focus on regulatory cassettes and genome-wide analysis of ChIP-Seq data. Covered topics: analysis of conserved gene regulatory cassettes (FrameWorker, ModelInspector); TFBS and TFBS pattern overrepresentation in ChIP-Seq peaks (Overrepresented TFs); gene neighbor and promoter overlap annotation of ChIP-Seq peaks (Annotation & Statistics).

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