HSLS MolBio Workshops

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

Target Audience

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.

PowerPoints

• Workshop Presentation (February 21, 2024)
• Practice Exercise 

Lecture Videos

• Transcriptomic analysis - GEO Datamining and Tools-  covers how to search gene expression data in GEO and analyze it using GEO2R, Correlation Engine and iDEP Tools. 

Data 

Correlation Engine

• 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)

iDEP

• 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)
• GSE152075: DEG Sars-Cov-2 Pos vs Neg (preanalyzed results)

GEO2R

• 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)

• How to transfer SRA data from GEO to CRC servers
• How to transfer files using Globus connect software
• How to use Pitt-CRC hosted shiny apps - iDEP
• Understanding the p-value of overlap statistics (18 min) 

• GEO tools - drag and drop it to your web browser 
• NCBI GEO -a public functional genomics data repository supporting MIAME-compliant data submissions.
• Search Engine for Gene Expression Data
• BioJupies - BioJupies Automatically Generates RNA-seq Data Analysis Notebooks.
• GREIN- GEO RNA-seq Experiments Interactive Navigator
• GEO2R - Use GEO2R to compare two or more groups of samples in order to identify genes that are differentially expressed across experimental conditions.
• Correlation Engine* - Find pre-analyzed results from GEO hosted RNA-seq and microarray experiments.
• iDEP (R shiny app) webtool -  iDEP (integrated Differential Expression and Pathway analysis)  is a web-based tool for analyzing RNA-seq data
• CRC-hosted iDEP via OnDemand (Pitt IT)
• iDEP (R shiny app) - Overview of iDEP for analyzing RNASeq data
• GSE101788 (RNA-Seq) - CBFb-SMMHC inhibition triggers apoptosis by disrupting MYC chromatin dynamics in acute myeloid leukemia [RNA-seq]
• GSE11352 (Microarray) - Timecourse of estradiol (10nM) exposure in MCF7 breast cancer cells.
• GSE101789 (ChIP-Seq) - CBFb-SMMHC inhibition triggers apoptosis by disrupting MYC chromatin dynamics in acute myeloid leukemia
• GSE56192 (RNA-Seq, Hands-on) - GEO dataset for hands-on practice exercise
• GEO data submission - NCBI GEO website to submit high throughput sequencing data
• BioRender - Scientific illustrations creating tool

• Venn Diagram Creator - Calculate and draw a custom Venn diagram

Key References

• BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud
• Pulikkan JA, Hegde M, Ahmad HM, et al. CBFβ-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia. Cell. 2018;174(1):172-186.e21. doi:10.1016/j.cell.2018.05.048
• Mahi NA, Najafabadi MF, Pilarczyk M, Kouril M, Medvedovic M. GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data. Sci Rep. 2019;9(1):7580. doi:10.1038/s41598-019-43935-8
• Kupershmidt I, Su QJ, Grewal A, et al. Ontology-based meta-analysis of global collections of high-throughput public data. PLoS ONE. 2010;5(9). doi:10.1371/journal.pone.0013066
• Ge X. iDEP Web Application for RNA-Seq Data Analysis. Methods Mol Biol. 2021;2284:417-443. doi:10.1007/978-1-0716-1307-8_22
• Mei S, Qin Q, Wu Q, et al. Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse. Nucleic Acids Res. 2017;45(D1):D658-D662. doi:10.1093/nar/gkw983
• Preprint: Chaparala S, Iwema CL, Chattopadhyay A. SARS-CoV-2 Infections - Gene Expression Omnibus (GEO) Data Mining, Pathway Enrichment Analysis, and Prediction of Repurposable Drugs/Compounds. September 2020. doi:10.20944/preprints202009.0459.v1

Feedback

• Please evaluate this workshop

Support

• Contact HSLS MolBio for consultations