This workshop covers how to search and download gene counts from gene expression studies (RNA-seq / microarray) by searching the Gene Expression Omnibus (GEO) database using Correlation Engine, iDEP R shiny app (RNA-Seq), and Geo2R (Microarray and RNASeq). We also cover how to prepare the data for NCBI GEO database submission.
Participants will learn how to
search and download data from GEO (ex: gene counts from an RNASeq study )
analyze the data using GEO2R and iDEP R shiny app
submit the data to NCBI GEO data repository
Experimental biologists seeking to analyze gene lists through omics experiments. The software covered in the workshop operates through a user-friendly, point-and-click graphical user interface, so neither programming experience nor familiarity with the command line interface is required.
GSE101788: CBFb-SMMHC inhibition triggers apoptosis by disrupting MYC chromatin dynamics in acute myeloid leukemia [RNA-seq] (software demonstration)
GSE52778: Human airway smooth muscle transcriptome changes in response to asthma medications (practice exercise)
GSE152075: In vivo antiviral host response to SARS-CoV-2 by viral load, sex, and age [dataset I] (Software demonstration)
GSE152075: raw_counts_upload_ready (.csv) (software demonstration)
GSE152075: Metadata_transposed (.csv) (software demonstration)
GSE101788: CBFb-SMMHC inhibition triggers apoptosis by disrupting MYC chromatin dynamics in acute myeloid leukemia [RNA-seq] (practice exercise)
GSE101788: Counts_fpkm (.csv)(practice exercise)
GSE101788:metadata_transposed (.csv)(practice exercise)
Preanalyzed Results:
GSE152075: DEG Sars-Cov-2 Pos vs Neg
GSE161805: Gene expression analysis of normal primary human bronchial epithelial cells (pHBEC) stimulated by glucocorticoid, long-acting β2-adrenoceptor agonist or both combined. (software demonstration)
GSE9008: Resveratrol action on A549 lung cancer cells. (practice exercise)
Venn Diagram Creator - Calculate and draw a custom Venn diagram