10.60507/FK2/OBIGQHNatarajan, ShakunthalaShakunthalaNatarajan0000-0002-4713-2380University of BonnSterling, ClaudiaClaudiaSterling0009-0002-3078-4056University of BonnChoudhary, NancyNancyChoudhary0000-0002-2562-7905University of BonnKhatun, NajninNajninKhatun0009-0000-3003-3338University of BonnBrieske, Mia-SophieMia-SophieBrieske0009-0006-6581-9502University of BonnBusch, Hannah ElisaHannah ElisaBusch0009-0000-5300-680XUniversity of BonnPucker, BoasBoasPucker0000-0002-3321-7471University of Bonnbonndata2026Medicine, Health and Life SciencesNatarajan, ShakunthalaUniversity of BonnPucker, BoasUniversity of Bonn2026-08-272026-08-292025-12-01/2026-08-24Strucural annotation files, Gene expression 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BY 4.0This is a comprehensive collection of gene expression count tables in transcripts per million (TPMs) encompassing species from five domains of life - plants, fungi, animals, bacteria and archaea. This data publication is referenced and discussed in detail in the manuscript - “XpBrew and PanXpresso - automatic RNA-seq processing workflow and comprehensive collection of gene expression data”. This dataset contains the annotation files, and expression files bundled as a tarball per species. It also includes a detailed supplementary file that provides information on the data sources and quality of the datasets used in the study, along with a detailed taxonomic classification of the different species covered in the current collection.XpBrew, v0.3Coding (.cds.fasta), peptide (.pep.fasta), and count table (.tpms.tsv) are the three main files available in every species tarball. For some species, primary isoform retained coding (.repr.cds.fasta), peptide (.repr.pep.fasta) and count table (.repr.tpms.tsv), files have also been included. README.txt has all the details on the investigators, and the list of files/ folders along with the methods SuppFile01_PanXpresso_DataSources-Reference-Taxonomy.tsv has the data sources and references for the datasets processed in this study