Search and Visualize Human RNA-Seq Gene Expression Data in NCBI’s GEO (Gene Expression Omnibus)

Are you interested in accessing consistently computed gene expression count matrices across thousands of experimental studies for half a million samples? Now you can! We are pleased to announce the availability of gene expression count matrices generated from all the human RNA-seq studies in GEO.  

Search 

You can find studies with RNA-seq counts by searching GEO Datasets with “rnaseq counts”[Filter].  

Visualize

We have integrated the RNA-seq count matrix with the GEO2R tool, allowing you to compare gene expression in two or more groups of samples on the GEO web site. GEO2R presents the results in a table of genes ordered by P-values. You can explore the data in an interactive graphical plot (Figure 1) that lets you identify differentially expressed genes and assess data set quality. 

Figure 1: Screenshot of GEO2R differential gene expression analysis results, including Volcano, Mean difference, Mean variance, UMAP, Venn, Boxplot, and Histogram plots.  

Download 

You can quickly download both raw and normalized RNA-seq count matrices by clicking the ‘Download Data’ link. You can use these files with common differential gene expression analysis and visualization tools for further examination.