Massive mining of publicly available RNA-seq data from human and mouse

Abstract

RNA sequencing (RNA-seq) is the leading technology for genome-wide transcript quantification. However, publicly available RNA-seq data is currently provided mostly in raw form, a significant barrier for global and integrative retrospective analyses. ARCHS4 is a web resource that makes the majority of published RNA-seq data from human and mouse available at the gene and transcript levels. For developing ARCHS4, available FASTQ files from RNA-seq experiments from the Gene Expression Omnibus (GEO) were aligned using a cloud-based infrastructure. In total 187,946 samples are accessible through ARCHS4 with 103,083 mouse and 84,863 human. Additionally, the ARCHS4 web interface provides intuitive exploration of the processed data through querying tools, interactive visualization, and gene pages that provide average expression across cell lines and tissues, top co-expressed genes for each gene, and predicted biological functions and protein–protein interactions for each gene based on prior knowledge combined with co-expression.

Targeting the Recently Deorphanized Receptor GPR83 for the Treatment of Immunological, Neuroendocrine and Neuropsychiatric Disorders

“…However, according to various online databases (ARCHS and BioGPS), which compile data from various RNA-seq and microarray studies, GPR83 is also expressed in a variety of immune cells including B cells, granulocytes, and neutrophils. 65,66 …”

Novel approaches leading towards peptide GPCR de‐orphanisation

“…Nonetheless, 34 orphan receptors have proposed endogenous ligands ( yellow boxes ), whereas the majority do not ( black boxes ). Gene expression data reveals abundant and ubiquitous tissue expression for many orphan receptors (Lachmann et al, ; green ring , darker shading denotes higher abundance ). Aggregated disease associations for orphan receptors from OpenTargets (Carvalho‐Silva et al, ) highlight the clinical relevance and therapeutic potential across disease areas ( purple ring , darker shading denotes stronger association ).…”

The long non‐coding RNA LINC 00941 and SPRR 5 are novel regulators of human epidermal homeostasis

“…Analysis of LINC00941 regulated genes per [20] (GSE59827) and Bao et al [21] (GSE67382) keratinocytes were downloaded from the Gene Expression Omnibus (GEO) database [40] and uploaded into UCSC [41] to visualize the peak location with respect to SPRR5. Furthermore, the prediction of upstream transcription factors for SPRR5 was done with the ARCHS 4 tool from the Ma'ayan Lab [42]. Inverse regulation of SPRR5 and LINC00941 was tested using publicly available RNA-Seq datasets from squamous cell carcinoma (GSE84293), basal cell carcinoma (GSE58375; both Smoothened inhibitor-sensitive and Smoothened inhibitor-resistant cancer types) and psoriasis (GSE83645) by mapping the reads to hg38 with Bowtie2 (version 2.3.3.1; for GSE83645) [43] or STAR (version 2.5.2b) [28] in either paired or single-stranded mode, depending on the nature of the RNA-Seq data with default settings (except for GSE58375, which was done with -outFilterScoreMinOverLread 0,-outFilterMatchNminOverLread 0, and -outFilterMatchNmin 0).…”