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HSLS MolBio Workshops

Information & resources for hands-on bioinformatics classes.

Objective

This is 2 part workshop and 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 EngineBioJupies, GREINiDEP R shiny app (RNA-Seq), and Geo2R (Microarray). 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 BioJupies, iDEP R shiny app, or Geo2R 

  • 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.

Workshop Materials

PowerPoints

Lecture Videos

  • Part 1 -  covers how to search gene expression data in GEO and analyze it using Correlation Engine 
  • Part 2  covers how to analyze the gene expression data using Biojupies, GREIN, iDEP,  and Geo2R and also how to submit data to NCBI GEO.

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)

  • BioJupies

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]

GSE152075: raw_counts_upload_ready

GSE152075: Metadata (.csv)

Preanalyzed Results:

 GSE101788; AI-10-49 vs. DMSO

GSE52778: Albuterol and Dexamethasone treatment vs. untreated (practice exercise)

GSE152075: DEG Sars_cov-2 positive vs. negative 

  • GREIN

GSE147507: Transcriptional response to SARS-CoV-2 infection (software demonstration)

Preanalyzed Results:

GSE147507:DEG_NHBE_cells _ SARS-Cov-2 vs mock 

GSE147507: DEG_Calu3_SARS-Cov-2 vs. Mock

  • 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)

Preanalyzed Results:

GSE152075: DEG Sars-Cov-2 Pos vs Neg

  • 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)

ChIP-Seq

GEO data submission

 

Databases & Tools

Feedback & Support

Support