Venue: University of Nebraska at Lincoln – Red Cloud C ( Willa Cather Dining Complex)
Date: April 20th, 2018
Time: 1:00 pm to 4:00 pm CST
Biomedical datasets like RNA-Seq are rich with potential for knowledge discovery, especially when analyzed properly. In this workshop, expert bioinformaticians will share examples and practical approaches that you can put to use immediately utilizing the versatile and flexible T-BioInfo Bioinformatics platform (t-bio.info). The platform has dedicated sections to analyze Exome-Seq, RNA-Seq, Metagenomics and other data types. With a visual an intuitive interface that eliminates the need for coding, any clinician or biologist can prepare complex processing pipelines and deploy powerful machine learning algorithms to extract meaningful insights from large datasets. The approaches tested on this platform can be deployed independently and extended in a familiar environment like Excel or R for post-processing.
This workshop will address critical issues related to Transcriptomics data:
Processing raw Next Generation Sequencing (NGS) data:
1. Next Generation Sequencing data preprocessing:
- Trimming technical sequences
- Removing PCR duplicates
2. RNA-seq based quantification of expression levels:
- Conventional pipelines (looking at known transcripts)
- Identification of novel isoforms
Analysis of Expression Data Using Machine Learning:
3. Unsupervised analysis of expression data:
- Principal Component Analysis
4. Supervised analysis:
- Differential expression analysis
- Classification, gene signature construction
5. Gene set enrichment analysis
The workshop will include hands-on exercises utilizing public domain datasets:
- breast cancer cell lines transcriptomic profiles (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-10-r110),
- patient-derived xenograft (PDX) mouse model of tumor and stroma transcriptomic profiles (http://www.oncotarget.com/index.php?journal=oncotarget&page=article&op=view&path=8014&path=23533), and
processed data from The Cancer Genome Atlas samples (https://cancergenome.nih.gov/).
Team: The workshops are designed by the researchers at the Tauber Bioinformatics Research Center at University of Haifa, Israel in collaboration with academic centers across the US. Technical support for the workshops is provided by the Pine Biotech team.
Technical requirements: Participants must have a laptop/desktop computer with internet access. Spreadsheet analysis software is used for simple analyses of pipeline results in most of the exercises. A working version of Excel or other spreadsheet analysis software is necessary to follow these examples. Most of the analysis steps will be done using the t-bio.info platform. No coding or statistics background is required to participate in the workshop, however basic cell biology and biostatistics will be beneficial. In preparation for the workshop, everyone is encouraged to complete the online course material available at edu.t-bio.info.
Certification: Workshop participants will receive a certificate of participation from the Tauber Bioinformatics Research Center and Pine Biotech. The certificate will be emailed after the workshop.
Expected outcomes: Participants will have hands-on experience processing and analyzing Next Generation Sequencing data. After practical exercises and discussion of examples, we will open the discussion to address real-life challenges faced by participants with their own data or workflows for critical review.