ARCHS4: Massive Mining of Publicly Available RNA Sequencing Data

About this Class

Many cancer-related independent studies that employ bulk and single cell RNA-seq can be found in the Gene Expression Omnibus (GEO). While some studies provide aligned read files, these are processed non-uniformly. This shortcoming makes it difficult to query and integrate this data across studies and with additional external data.

To bridge the gap that currently exists between RNA-seq data generation and RNA-seq data processing and reuse, we developed the resource, All RNA-seq and ChIP-Seq Sample and Signature Search (ARCHS4).

ARCHS4 provides processed RNA-seq data from GEO to support retrospective data analyses and reuse by catering to users with different levels of computational expertise. Besides serving data from over one million samples uniformly aligned for download and API access, tools that utilizes ARCHS4 data provide gene function predictions from co-expression correlations, including ways to modulate the expression of long non-coding RNAs with small molecules, as well as ways to identify personalized novel immunotherapeutic targets for tumors profiled with RNA-seq. Importantly, using the ARCHS4 cost-effective infrastructure, we also provide a free FASTQ alignment service to the community.

In this workshop, we will present different ways to interact with the ARCHS4 resource, and related tools that utilize ARCHS4 data for systematic scientific discovery.

For questions about this training, contact Daoud Meerzaman or Mel Nisonger.