ARCHS⁴ Chrome Extension

What is ARCHS⁴?

All RNA-seq and CHIP-Seq Signature Search Space (ARCHS⁴) is a browser extension that adds content to the landing pages of RNA-seq datasets available on the Gene Expression Omnibus (GEO). The extension adds links to download files that contain the aligned reads mapped to genes with counts, as well as a heatmap visualization summary of the expression data from the processed samples using Clustergrammer.

What functions does the ARCHS⁴ Chrome extension add to GEO pages?

The ARCHS⁴ extension enriches GSE landing pages on GEO in two ways:

1. By adding a link to an updated Series Matrix File, containing the gene counts generated from the matching raw sequencing files available on the SRA database.
2. By adding an interactive heatmap visualization of the expression top 1000 most variable genes, generated using Clustergrammer.

Where is the extension active?

The ARCHS⁴ extension is currently active on the landing pages of GEO Series (GSE) containing data from human (Homo sapiens) and mouse (Mus musculus) samples generated by high-throughput RNA-sequencing. The extension can be tested on this landing page: GSE77197.

How were the raw sequencing files processed?

Available FASTQ files were downloaded from the SRA database and aligned against the Ensembl references using Kallisto (GRCh38.cdna.all for human data, GRCm38.cdna.all for mouse data). Sample profiles were built by adding all gene counts from corresponding SRA level gene counts.