This page explains how to start RNA-Seq data analysis using Gene Count data obtained from GEO (Gene Expression Omnibus).
RNA-Seq datasets deposited in GEO often include Gene Count tables provided as Supplementary Files.
Even when Supplementary Files are not available, GEO may provide Gene Count data calculated using standardized processing pipelines.
In such cases, the data can be downloaded from:
https://www.ncbi.nlm.nih.gov/geo/download/?acc=[GSE_accession_number]
Supplementary Files have the advantage of being consistent with the results reported in the original publication.
However, since FASTQ processing methods vary between studies, they are not always suitable for integrative analysis across different series.
In contrast, GEO-calculated Gene Count data are generated using standardized protocols, making them more suitable for reanalysis and integration across multiple datasets.
In either case, once a Gene Count table is available, you can start RNA-Seq data analysis immediately without performing FASTQ preprocessing.
In this video, we demonstrate the following two approaches:
- Using Supplementary Files
- Using GEO-calculated Gene Count data
We show how to obtain these Gene Count tables from GEO and import them into Subio Platform.
For detailed instructions on importing experimental parameters, please refer to the following page:
→ How to Import Experimental Parameters
Next Step
For a complete guide to RNA-Seq data analysis, please see the full tutorial here.
After completing the data import in this video, you can follow it to proceed with the downstream analysis.