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Part 1: Document Description
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Citation |
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Title: |
PanXpresso - comprehensive collection of gene expression data across domains of life |
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Identification Number: |
doi:10.60507/FK2/OBIGQH |
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Distributor: |
bonndata |
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Date of Distribution: |
2026-08-29 |
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Version: |
1 |
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Bibliographic Citation: |
Natarajan, Shakunthala; Sterling, Claudia; Choudhary, Nancy; Khatun, Najnin; Brieske, Mia-Sophie; Busch, Hannah Elisa; Pucker, Boas, 2026, "PanXpresso - comprehensive collection of gene expression data across domains of life", https://doi.org/10.60507/FK2/OBIGQH, bonndata, V1 |
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Citation |
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Title: |
PanXpresso - comprehensive collection of gene expression data across domains of life |
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Identification Number: |
doi:10.60507/FK2/OBIGQH |
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Authoring Entity: |
Natarajan, Shakunthala (University of Bonn) |
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Sterling, Claudia (University of Bonn) |
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Choudhary, Nancy (University of Bonn) |
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Khatun, Najnin (University of Bonn) |
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Brieske, Mia-Sophie (University of Bonn) |
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Busch, Hannah Elisa (University of Bonn) |
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Pucker, Boas (University of Bonn) |
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Software used in Production: |
XpBrew |
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Distributor: |
bonndata |
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Access Authority: |
Natarajan, Shakunthala |
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Access Authority: |
Pucker, Boas |
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Depositor: |
Natarajan, Shakunthala |
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Date of Deposit: |
2026-08-27 |
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Holdings Information: |
https://doi.org/10.60507/FK2/OBIGQH |
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Study Scope |
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Keywords: |
Medicine, Health and Life Sciences |
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Abstract: |
This 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. |
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Date of Collection: |
2025-12-01-2026-08-24 |
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Kind of Data: |
Strucural annotation files, Gene expression data |
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Notes: |
Coding (.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 |
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Methodology and Processing |
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Sources Statement |
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Data Sources: |
Please see the "Reference" information in SuppFile01_PanXpresso_DataSources-Reference-Taxonomy.tsv for details. |
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Data Access |
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Notes: |
<a href="http://creativecommons.org/licenses/by/4.0">CC BY 4.0</a> |
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Other Study Description Materials |
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Related Publications |
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Citation |
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Title: |
XpBrew and PanXpresso - automatic RNA-seq processing workflow and comprehensive collection of gene expression data (in preparation) |
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Identification Number: |
10.64898/2026.08.27.747620 |
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Bibliographic Citation: |
XpBrew and PanXpresso - automatic RNA-seq processing workflow and comprehensive collection of gene expression data (in preparation) |
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Acer_saccharum.tar.gz |
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Acinetobacter_baumannii.tar.gz |
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Actinidia_arguta.tar.gz |
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Actinidia_chinensis.tar.gz |
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Actinidia_deliciosa.tar.gz |
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Actinidia_eriantha.tar.gz |
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Actinidia_valvata.tar.gz |
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Adiantum_capillus_veneris.tar.gz |
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Aedes_aegypti.tar.gz |
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Aegilops_speltoides.tar.gz |
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Aegilops_tauschii.tar.gz |
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Alnus_glutinosa.tar.gz |
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Amaranthus_hypochondriacus.tar.gz |
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Amaranthus_tricolor.tar.gz |
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Amborella_trichopoda.tar.gz |
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Ambrosia_artemisiifolia.tar.gz |
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Anacardium_occidentale.tar.gz |
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Ananas_comosus.tar.gz |
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Anas_platyrhynchos.tar.gz |
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Andrographis_paniculata.tar.gz |
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Androsace_vitaliana.tar.gz |
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Anisodus_acutangulus.tar.gz |
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Anisodus_tanguticus.tar.gz |
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Apis_mellifera.tar.gz |
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Apium_graveolens.tar.gz |
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Apostasia_shenzhenica.tar.gz |
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Arabidopsis_arenosa.tar.gz |
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Arabidopsis_halleri.tar.gz |
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Arabidopsis_lyrata.tar.gz |
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Arabidopsis_suecica.tar.gz |
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Arabidopsis_thaliana_TAIR10.tar.gz |
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Arabidopsis_thaliana_TAIR12.tar.gz |
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Arachis_duranensis.tar.gz |
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Arachis_hypogaea.tar.gz |
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Arachis_ipaensis.tar.gz |
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Arachis_stenosperma.tar.gz |
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Arctium_lappa.tar.gz |
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Argentina_anserina.tar.gz |
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Aristolochia_fimbriata.tar.gz |
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Artemisia_annua.tar.gz |
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Asparagus_officinalis.tar.gz |
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Aspergillus_flavus.tar.gz |
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Aspergillus_fumigatus.tar.gz |
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Aspergillus_nidulans.tar.gz |
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Aspergillus_niger.tar.gz |
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Atropa_belladonna.tar.gz |
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Bacillus_subtilis.tar.gz |
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Bacteroides_thetaiotaomicron.tar.gz |
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Beauveria_bassiana.tar.gz |
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Benincasa_hispida.tar.gz |
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Beta_vulgaris.tar.gz |
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Betula_platyphylla.tar.gz |
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Bombyx_mori.tar.gz |
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Bonia_amplexicaulis.tar.gz |
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Botrytis_cinerea.tar.gz |
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Brachypodium_distachyon.tar.gz |
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Brachypodium_sylvaticum.tar.gz |
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Brassica_carinata.tar.gz |
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Brassica_juncea.tar.gz |
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Brassica_napus.tar.gz |
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Brassica_oleracea.tar.gz |
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Brassica_rapa.tar.gz |
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Brugmansia_arborea.tar.gz |
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Caenorhabditis_elegans.tar.gz |
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Cajanus_cajan.tar.gz |
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Candida_albicans.tar.gz |
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Candida_auris.tar.gz |
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Cannabis_sativa.tar.gz |
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Canna_indica.tar.gz |
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Capra_hircus.tar.gz |
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Capsella_grandiflora.tar.gz |
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Capsella_rubella.tar.gz |
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Capsicum_annuum.tar.gz |
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Capsicum_baccatum.tar.gz |
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Capsicum_chinense.tar.gz |
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Capsicum_frutescens.tar.gz |
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Cardamine_hirsuta.tar.gz |
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Carica_papaya.tar.gz |
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Carya_illinoinensis.tar.gz |
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Castanea_dentata.tar.gz |
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Castanea_mollissima.tar.gz |
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Catharanthus_roseus.tar.gz |
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Ceratodon_purpureus.tar.gz |
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Ceratopteris_richardii.tar.gz |
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Cercis_canadensis.tar.gz |
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Chenopodium_album.tar.gz |
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Chenopodium_quinoa.tar.gz |
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Chlamydomonas_reinhardtii.tar.gz |
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Cicer_arietinum.tar.gz |
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Cichorium_intybus.tar.gz |
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Cinnamomum_kanehirae.tar.gz |
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Citrullus_colocynthis.tar.gz |
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Citrullus_lanatus.tar.gz |
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Citrus_clementina.tar.gz |
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Citrus_limon.tar.gz |
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Citrus_trifoliata.tar.gz |
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Citrus_unshiu.tar.gz |
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Clostridioides_difficile.tar.gz |
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Cocos_nucifera.tar.gz |
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Coffea_arabica.tar.gz |
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Coffea_canephora.tar.gz |
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Coix_lacryma_jobi.tar.gz |
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Colocasia_esculenta.tar.gz |
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Columba_livia.tar.gz |
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Coptis_chinensis.tar.gz |
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Corchorus_capsularis.tar.gz |
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Corchorus_olitorius.tar.gz |
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Cornus_florida.tar.gz |
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Cryptococcus_neoformans.tar.gz |
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Cryptomeria_japonica.tar.gz |
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Cucumis_melo.tar.gz |
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Cucumis_sativus.tar.gz |
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Cucurbita_maxima.tar.gz |
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Cucurbita_moschata.tar.gz |
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Cucurbita_pepo.tar.gz |
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Cyclocarya_paliurus.tar.gz |
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Cymbidium_ensifolium.tar.gz |
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Cynara_cardunculus.tar.gz |
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Danio_rerio.tar.gz |
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Daphnia_magna.tar.gz |
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Datura_stramonium.tar.gz |
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Datura_wrightii.tar.gz |
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Daucus_carota.tar.gz |
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Dendrobium_catenatum.tar.gz |
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Dendrobium_chrysotoxum.tar.gz |
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Dendrobium_nobile.tar.gz |
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Dimocarpus_longan.tar.gz |
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Dionaea_muscipula.tar.gz |
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Dorcoceras_hygrometricum.tar.gz |
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Drosophila_melanogaster.tar.gz |
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Drosophila_simulans.tar.gz |
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Durio_zibethinus.tar.gz |
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Elaeis_guineensis.tar.gz |
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Eleusine_coracana.tar.gz |
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Elsholtzia_splendens.tar.gz |
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Enterococcus_faecalis.tar.gz |
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Equus_caballus.tar.gz |
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Eragrostis_curvula.tar.gz |
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Erigeron_canadensis.tar.gz |
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Eriocheir_sinensis.tar.gz |
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Eruca_vesicaria.tar.gz |
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Erythranthe_guttata.tar.gz |
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Escherichia_coli.tar.gz |
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Eucalyptus_globulus.tar.gz |
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Eucalyptus_grandis.tar.gz |
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Eucommia_ulmoides.tar.gz |
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Euphorbia_peplus.tar.gz |
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Euryale_ferox.tar.gz |
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Eutrema_salsugineum.tar.gz |
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Fagopyrum_esculentum.tar.gz |
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Fagopyrum_tataricum.tar.gz |
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Fagus_sylvatica.tar.gz |
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Fragaria_ananassa.tar.gz |
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Fragaria_vesca.tar.gz |
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Fraxinus_americana.tar.gz |
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Fraxinus_pennsylvanica.tar.gz |
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Fusarium_graminearum.tar.gz |
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Fusarium_oxysporum.tar.gz |
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Gallus_gallus.tar.gz |
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Gastrodia_elata.tar.gz |
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Glycine_max.tar.gz |
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Glycine_soja.tar.gz |
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Gossypium_arboreum.tar.gz |
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Gossypium_australe.tar.gz |
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Gossypium_barbadense.tar.gz |
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Gossypium_hirsutum.tar.gz |
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Gossypium_raimondii.tar.gz |
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Gossypium_trilobum.tar.gz |
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Gynostemma_pentaphyllum.tar.gz |
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Haloferax_volcanii.tar.gz |
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Helianthus_annuus.tar.gz |
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Hibiscus_cannabinus.tar.gz |
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Hippophae_rhamnoides.tar.gz |
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Hordeum_erectifolium.tar.gz |
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Hordeum_marinum.tar.gz |
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Humulus_lupulus.tar.gz |
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Hydrangea_macrophylla.tar.gz |
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Isatis_tinctoria.tar.gz |
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Jasminum_sambac.tar.gz |
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Joinvillea_ascendens.tar.gz |
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Juglans_mandshurica.tar.gz |
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Juglans_regia.tar.gz |
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Juglans_sigillata.tar.gz |
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Kalanchoe_fedtschenkoi.tar.gz |
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Kalanchoe_laxiflora.tar.gz |
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Kandelia_obovata.tar.gz |
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Victoria_cruziana.tar.gz |
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Notes: |
application/gzip |
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Vigna_angularis.tar.gz |
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Notes: |
application/gzip |
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Label: |
Vigna_mungo.tar.gz |
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Notes: |
application/gzip |
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Label: |
Vigna_radiata.tar.gz |
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Notes: |
application/gzip |
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Label: |
Vigna_umbellata.tar.gz |
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Notes: |
application/gzip |
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Label: |
Vigna_unguiculata.tar.gz |
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Notes: |
application/gzip |
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Label: |
Vitis_amurensis.tar.gz |
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Notes: |
application/gzip |
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Label: |
Vitis_riparia.tar.gz |
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Notes: |
application/gzip |
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Label: |
Vitis_rotundifolia.tar.gz |
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Notes: |
application/gzip |
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Label: |
Vitis_vinifera.tar.gz |
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Notes: |
application/gzip |
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Withania_somnifera.tar.gz |
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Notes: |
application/gzip |
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Label: |
Wolffia_australiana.tar.gz |
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Notes: |
application/gzip |
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Xanthoceras_sorbifolium.tar.gz |
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Notes: |
application/gzip |
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Xenopus_laevis.tar.gz |
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Notes: |
application/gzip |
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Yarrowia_lipolytica.tar.gz |
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Notes: |
application/gzip |
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Label: |
Zea_mays.tar.gz |
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Notes: |
application/gzip |
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Zingiber_officinale.tar.gz |
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Notes: |
application/gzip |
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Zizania_latifolia.tar.gz |
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Notes: |
application/gzip |
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Ziziphus_jujuba.tar.gz |
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Notes: |
application/gzip |
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Zostera_marina.tar.gz |
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Notes: |
application/gzip |