PanXpresso - comprehensive collection of gene expression data across domains of life

Name: PanXpresso - comprehensive collection of gene expression data across domains of life
Published: 2026-08-29
License: http://creativecommons.org/licenses/by/4.0

Open this dataset in the live repository

Important usage condition: Use and redistribution are governed by CC BY 4.0. Review and comply with the license before using the data.

Persistent identifier: doi:10.60507/FK2/OBIGQH
Published version: 1.0
Publication date: 2026-08-29
License: CC BY 4.0

Description

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.

Creators

Natarajan, Shakunthala
Sterling, Claudia
Choudhary, Nancy
Khatun, Najnin
Brieske, Mia-Sophie
Busch, Hannah Elisa
Pucker, Boas

Keywords

gene expression, transcript abundance, plants, animals, fungi, archaea, bacteria

Files

Before downloading: Use and redistribution are governed by CC BY 4.0. Review and comply with the license before using the data.

File	Type	Bytes	Checksum
Daphnia_magna.tar.gz	application/gzip	182073954	MD5 87cebf7c78c7b9d1e61b2509ece908c5
Fragaria_ananassa.tar.gz	application/gzip	638655560	MD5 8a12693e718c23a9d199f7dd7ba80780
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Lonicera_japonica.tar.gz	application/gzip	60869891	MD5 926bb97180329aa04165e32a3e2e1bdb
Panicum_hallii.tar.gz	application/gzip	186380803	MD5 05588fc0ed5c1a11713a324f5bad44ba
Aegilops_speltoides.tar.gz	application/gzip	33363642	MD5 6cee71331f37f508229cae84e75d804c
Lentinula_edodes.tar.gz	application/gzip	74394019	MD5 5c32e732affa1752b4856ea739a60249
Capsicum_baccatum.tar.gz	application/gzip	53239897	MD5 5f782fbdf71fc34f88ddef0d61a64d30
Lupinus_angustifolius.tar.gz	application/gzip	60738538	MD5 99974656a3a8f63aa962a5f7bb9f9f40
Gynostemma_pentaphyllum.tar.gz	application/gzip	59677962	MD5 54d410b6b7e480bc165e4135d17ddb40
Wolffia_australiana.tar.gz	application/gzip	22335087	MD5 7feefba0cc974836d1d5f1dbe99b607b
Carya_illinoinensis.tar.gz	application/gzip	96463740	MD5 464d71fed45441c37529000b9ddfb5af
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Lactuca_saligna.tar.gz	application/gzip	83416337	MD5 9610dafe9e47710535c354fe4a20f5db
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Dionaea_muscipula.tar.gz	application/gzip	57609663	MD5 564aa0bc459c503ce3284688337a99d1
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Musa_balbisiana.tar.gz	application/gzip	63088772	MD5 110cd051126f51308ff10e3c745094af
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Actinidia_chinensis.tar.gz	application/gzip	257934764	MD5 b1b8f7c28aeee6b899994102e689ce92
Komagataella_phaffii.tar.gz	application/gzip	25422240	MD5 6f7b3a78ca0fa648a1193baab9ea7dff
Gallus_gallus.tar.gz	application/gzip	957307394	MD5 15b538afa501c44a846ccec649482b3b
Drosophila_simulans.tar.gz	application/gzip	85759788	MD5 d10a94d8e2331c18544413b367199a9d
Eucalyptus_grandis.tar.gz	application/gzip	140821429	MD5 9283c88db4b0cc159313bd1f3966ecc2
Oryza_brachyantha.tar.gz	application/gzip	35281681	MD5 fadeaeb1e24d476d1a4f3c35c77526ca
Zizania_latifolia.tar.gz	application/gzip	30611188	MD5 f6d14382bf904083f54a8a1d645c49c3
Xenopus_laevis.tar.gz	application/gzip	473263171	MD5 77b040b1f88a5e62fa8cfdce687d46dd
Gossypium_barbadense.tar.gz	application/gzip	742595290	MD5 d2244d712ad06e55c4da5a2f9840fcbe
Prunus_persica.tar.gz	application/gzip	485307486	MD5 2eac9051997cffb0d672df0fded5df60
Fagopyrum_esculentum.tar.gz	application/gzip	56684842	MD5 a1c21d82cda3700242e186b8beea92c2
Enterococcus_faecalis.tar.gz	application/gzip	4819991	MD5 7ac27b1a6e10396e5cb21e841d38c4ca
Euphorbia_peplus.tar.gz	application/gzip	36006477	MD5 4f4b369f04225dbe6c692afbf0639873
Equus_caballus.tar.gz	application/gzip	550922204	MD5 8cac59df2965e08433ec86bf0960351e
Salvia_miltiorrhiza.tar.gz	application/gzip	84338482	MD5 8e447984b14047e575a04bc4fe0eaf26
Panax_stipuleanatus.tar.gz	application/gzip	22649001	MD5 e0ee2b6e700a66455088cbdbabc65b0b
Sus_scrofa.tar.gz	application/gzip	1222661355	MD5 f7df730b7d54d9a21510e5c1baa781a0
Synechocystis_PCC_6803.tar.gz	application/gzip	6460853	MD5 a875d37dff6c58b2a446f1af77ed94a0
Musa_acuminata.tar.gz	application/gzip	115738420	MD5 85065a9748532cf41671b4d54e2ed2d3
Citrus_limon.tar.gz	application/gzip	144365316	MD5 a12533144888e0bf5ce3592796773b7a
Actinidia_valvata.tar.gz	application/gzip	50033798	MD5 8f24e16a7e9d2101900a23a417d3f014
Canna_indica.tar.gz	application/gzip	44212830	MD5 d45b25383ce52600a7cd31337166f1e0
Ricinus_communis.tar.gz	application/gzip	70845193	MD5 62a9e60e6d1196c048a76c9dba316661
Treponema_pallidum.tar.gz	application/gzip	865511	MD5 8a9a700bc8ae6873b1c2e165c526d630
Mus_musculus.tar.gz	application/gzip	1342091403	MD5 7f7ceaf51771dda4a9990362549536e9
Brassica_juncea.tar.gz	application/gzip	609021129	MD5 bd67a9a68c99f236f9d9a62cb5271f4f
Brassica_oleracea.tar.gz	application/gzip	424007298	MD5 c297b343ada0c1b5dcf248457add542b
Scutellaria_baicalensis.tar.gz	application/gzip	31691446	MD5 420370fae0683d57754c373b9696d2d8
Spinacia_oleracea.tar.gz	application/gzip	134005040	MD5 b15525fd8cf4c3cf6bacc19bf307450c
Quercus_lobata.tar.gz	application/gzip	58185002	MD5 57aa4c0140fb009dc7fcf5cbf016f348
Lactuca_sativa.tar.gz	application/gzip	567207845	MD5 75b5ccef5a7e7fb23c62ce95bd529590
Melaleuca_alternifolia.tar.gz	application/gzip	38259630	MD5 834b580892c3f32dbeaff48d2f2e5da5
Danio_rerio.tar.gz	application/gzip	716401519	MD5 d1fdff023af339e38ca50106d91f164b
Corchorus_capsularis.tar.gz	application/gzip	42170937	MD5 d7424f2a06a1170c5dc608b7bb457611
Elaeis_guineensis.tar.gz	application/gzip	137084230	MD5 0b624f5c49b871be5cc3f4678d58cc91
Gossypium_arboreum.tar.gz	application/gzip	214924182	MD5 d2b04742c6f42987baa3a8fd7c89c2c3
Hydrangea_macrophylla.tar.gz	application/gzip	92044574	MD5 860a11d1995b2d29281bbe9ca6c5618b
Simmondsia_chinensis.tar.gz	application/gzip	49611169	MD5 859f66990e6575859433b164429a03e2
Saccharomyces_cerevisiae.tar.gz	application/gzip	683254705	MD5 175ca85fbeaf3091fad25261c13d18db
Arabidopsis_suecica.tar.gz	application/gzip	94717504	MD5 f1994291e8bf8ae1e10a38112c6f7c02
Solanum_lycopersicum.tar.gz	application/gzip	2522765187	MD5 b4fb877fb57ba2bf63c97911a59bb91b
Elsholtzia_splendens.tar.gz	application/gzip	37120247	MD5 cf0e2a49a1f9450984b4b102945ce7dc
Chenopodium_album.tar.gz	application/gzip	101558723	MD5 fc31993860547c864f1d6d2862f83249
Drosophila_melanogaster.tar.gz	application/gzip	808363496	MD5 0dfdcda39a7cfded9e806877b2fc873c
Kalanchoe_laxiflora.tar.gz	application/gzip	80774730	MD5 9082c5d030e8e845ba6d9fb37ba28dde
Anisodus_tanguticus.tar.gz	application/gzip	60848014	MD5 27777b2ca5165c9a712f83352fa55940
Salix_purpurea.tar.gz	application/gzip	148417384	MD5 e537549a1ce27fc9b57c84ce9b667b86
Bonia_amplexicaulis.tar.gz	application/gzip	41505279	MD5 e0d91791e4cf1ee12fb230cba7353e93
Eruca_vesicaria.tar.gz	application/gzip	55646742	MD5 fec920ca0c2f14d5646e7b7113478bfd
Acinetobacter_baumannii.tar.gz	application/gzip	13610419	MD5 2887838c7b0836ba76a1a92ae72dab86
Persea_americana.tar.gz	application/gzip	143449500	MD5 67f31dd4de8d60ecb19cd8994aa2eab5
Nicandra_physalodes.tar.gz	application/gzip	38659581	MD5 275cf43df39a7ee01f00d94e87a58f1a
Ziziphus_jujuba.tar.gz	application/gzip	219258765	MD5 0aea701d3b12a31112d270d8e39e75aa
Brassica_carinata.tar.gz	application/gzip	173034870	MD5 c214d0de09433e9476a3082fc84b9787
Aristolochia_fimbriata.tar.gz	application/gzip	32953518	MD5 4691579d0d88c8660a48e61f82bd4ef6
Arctium_lappa.tar.gz	application/gzip	66510517	MD5 cd9701008c2b7e4df0b3de469f1d67a9
Momordica_charantia.tar.gz	application/gzip	84721830	MD5 d1590ef7b110c801dafb63d25d73997d
Aspergillus_niger.tar.gz	application/gzip	172930375	MD5 ac2524df7ae738cf86b81c3348babd2a
Prunus_armeniaca.tar.gz	application/gzip	90915912	MD5 9d49ccb698d707a344c4d442668eaca4
Rehmannia_glutinosa.tar.gz	application/gzip	75510559	MD5 1bea0122bbc65a77a75941bfaf8999e3
Caenorhabditis_elegans.tar.gz	application/gzip	855285061	MD5 415f06c92d1502b50b7edc0a2082cfeb
Methanosarcina_barkeri.tar.gz	application/gzip	2940506	MD5 f53e727481872c6b72398b50e9d633a0
Ceratopteris_richardii.tar.gz	application/gzip	148271748	MD5 83c67dc76514765c7d61a016675d71fb
Coffea_canephora.tar.gz	application/gzip	27853977	MD5 503766583255268e3142d115dcd1f36f
Arabidopsis_arenosa.tar.gz	application/gzip	82219094	MD5 6129ec1c56ebc9be513a93ef862a3deb
Citrus_unshiu.tar.gz	application/gzip	21530028	MD5 92d7aa1147fe87b431bd9545c5405ce0
Cocos_nucifera.tar.gz	application/gzip	69674142	MD5 15458b36d57e5d0857fd241caf9b7746
Prunus_cerasus.tar.gz	application/gzip	205764901	MD5 2d2e1d2079f0554aca08709908b33551
Cynara_cardunculus.tar.gz	application/gzip	51069198	MD5 f3ed7e027013c27d029271d6ab9a4fc9
Vigna_mungo.tar.gz	application/gzip	31956297	MD5 f4f101cac2b57c157e782358c0191483
Oncorhynchus_mykiss.tar.gz	application/gzip	520889073	MD5 acedcdfb5f2b770ddc75f1e121965acb
Saccharum_spontaneum.tar.gz	application/gzip	640126256	MD5 fe6f50904c99709ee99b65fc9e081399
Anas_platyrhynchos.tar.gz	application/gzip	315209978	MD5 db87f2b685cba81d1e65c0ac73ce561c
Ulmus_minor.tar.gz	application/gzip	164220912	MD5 93689b7734eab64ebb25ddfc63b1891b
Phoenix_dactylifera.tar.gz	application/gzip	82233238	MD5 3a4f92dbda7804cf13cfe0484dcc99f3
Amborella_trichopoda.tar.gz	application/gzip	73678784	MD5 3dba854ada301f52346b8fc3b82a5c7c
Jasminum_sambac.tar.gz	application/gzip	53696560	MD5 bd485b0ff6a28fff89fa68bece364898
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Nymphaea_colorata.tar.gz	application/gzip	33133892	MD5 37b0e50760a999b312b531e10a8cc91d
Brachypodium_sylvaticum.tar.gz	application/gzip	103505852	MD5 2ef70a0765050eb664b54f38e712e341
Portulaca_oleracea.tar.gz	application/gzip	128218433	MD5 6e95ede9a62b5c9d8ba24ef5aaba8d79
Actinidia_arguta.tar.gz	application/gzip	97470811	MD5 8fca5540299fcddf03f51bd320a6403d
Cercis_canadensis.tar.gz	application/gzip	40046978	MD5 be2031534ec453ce8f3c882b7be386bb
Candida_albicans.tar.gz	application/gzip	151147625	MD5 e98300609e3ced77fa4079a464661b4f
Cryptococcus_neoformans.tar.gz	application/gzip	117859386	MD5 afbe72cd621efc316680bf02cfcd7416
Eleusine_coracana.tar.gz	application/gzip	79022663	MD5 889b10c69f653cf21521060c6e6bf543
Salix_viminalis.tar.gz	application/gzip	47056664	MD5 ece4aea1bb6187ad628f586a6abb8538
Catharanthus_roseus.tar.gz	application/gzip	91565950	MD5 f764a0b8e996847a5c26a19cecbc1538
Schizosaccharomyces_pombe.tar.gz	application/gzip	112550478	MD5 8eb8d47e7cbee47bdbcff8197556110f
Methanococcus_maripaludis.tar.gz	application/gzip	1331906	MD5 eb44014d69596e6c46fdb59494a0044a
Aegilops_tauschii.tar.gz	application/gzip	153453682	MD5 e61d7eda07a8af52bb9ea625a182fa65
Ceratodon_purpureus.tar.gz	application/gzip	60468830	MD5 cd309366c97cc155efcdee8d3a72712a
Prunus_mume.tar.gz	application/gzip	78346905	MD5 8bd765d5136144ec77c15969f2899213
Fagopyrum_tataricum.tar.gz	application/gzip	166006913	MD5 5bc896f75fe7c6bee4ccefed055787b0
Malus_sylvestris.tar.gz	application/gzip	62170490	MD5 030b4eae28afc932ca24ce03610f083a
Tagetes_erecta.tar.gz	application/gzip	76228031	MD5 873706817f9e507f4f74f05aaed947d1
Fusarium_graminearum.tar.gz	application/gzip	137113358	MD5 6305c4d909d8666fd1dc1219ffb9bf97
Xanthoceras_sorbifolium.tar.gz	application/gzip	115546290	MD5 abe6590a13744466a15982d281bc9a08
Actinidia_eriantha.tar.gz	application/gzip	93554027	MD5 8bfd550f7d212ddd5f9d6e068154b0ed
Aspergillus_nidulans.tar.gz	application/gzip	55949221	MD5 d183cd2ba74cd3b412b5d9915d84296a
Atropa_belladonna.tar.gz	application/gzip	101278647	MD5 0e30fc4d8dc9997313b234b35e69e632
Arachis_hypogaea.tar.gz	application/gzip	1967965241	MD5 e53e44d745f6f9fdc69310a0dd50d47e
Lathyrus_oleraceus.tar.gz	application/gzip	331056653	MD5 94b425e139f5fa9d2c443c28ba760c00
Sporobolus_alterniflorus.tar.gz	application/gzip	63774476	MD5 a876a5a4ea149e0d75e75822c8b55493
Victoria_cruziana.tar.gz	application/gzip	21433046	MD5 f7206b21d98e99780854c9ff807d1b34
Beta_vulgaris.tar.gz	application/gzip	207611750	MD5 45dd4ef980dbc9c511b7fa7d89af0315
Sesbania_bispinosa.tar.gz	application/gzip	54402195	MD5 52b9e30e1dd629d09c22c6bba9584204
Pogostemon_cablin.tar.gz	application/gzip	155469513	MD5 7815fd1b6ba8b0dabd1dd9c31251e9f4
Fraxinus_pennsylvanica.tar.gz	application/gzip	27336212	MD5 2e22c7b835f00c68ba20927054c37656
Oryctolagus_cuniculus.tar.gz	application/gzip	357625058	MD5 a3965543d241cdded74de49d0daf64b5
Erigeron_canadensis.tar.gz	application/gzip	45300101	MD5 a135ab03e08a7f1852e8b6178bbb4080
Nicotiana_attenuata.tar.gz	application/gzip	181954959	MD5 bf441c38d4769790782118b23823e0e8
Mercurialis_annua.tar.gz	application/gzip	60384175	MD5 c0b4b55744f60bad2d0aeb4662e4ca63
Arabidopsis_thaliana_TAIR10.tar.gz	application/gzip	7206361816	MD5 20d2e16a61871c3a32316068aa01dd9b
Dendrobium_chrysotoxum.tar.gz	application/gzip	36431902	MD5 2092bd946596ef51d22052015fe85c4c
Prunus_campanulata.tar.gz	application/gzip	38958037	MD5 a9da3fc481ba344b105abf511f1c5498
Kandelia_obovata.tar.gz	application/gzip	59163075	MD5 87b0efbfd5e7472615c96a4d1a8e5616
Kalanchoe_fedtschenkoi.tar.gz	application/gzip	206800172	MD5 9ecbed0a98ef97dd9a8c2fcd3d7b7fac
Anacardium_occidentale.tar.gz	application/gzip	62469078	MD5 be2b4fb385ba718fcff88b6b57c5544b
Vicia_villosa.tar.gz	application/gzip	90602368	MD5 c736ed25f4e3a793f7fa62ce1618c740
Morella_rubra.tar.gz	application/gzip	70973409	MD5 1044bfc1adbeff1790dde56ae7db55e4
Puccinia_striiformis.tar.gz	application/gzip	124736089	MD5 3a8f176310546a833ca9c19bd20288b0
Trichoderma_reesei.tar.gz	application/gzip	54581263	MD5 cdb98364a528433cd24fa6c5d52c30d7
Yarrowia_lipolytica.tar.gz	application/gzip	44461470	MD5 edee03db1cbc1812d8a6fa47569d4cc6
Eragrostis_curvula.tar.gz	application/gzip	38229913	MD5 a4f86d4c850181131871490c5993eb63
Hordeum_marinum.tar.gz	application/gzip	50665969	MD5 02c32c5b470bdadbd128db9e9676cdea
Linum_trigynum.tar.gz	application/gzip	31687504	MD5 5727ea2d39e8db9d36b47078bf2f5488
Pharus_latifolius.tar.gz	application/gzip	31718831	MD5 3e6161175e820f37390f2d862f97c506
Vanilla_planifolia.tar.gz	application/gzip	51029198	MD5 f758ccae6d4cc504296c1c00c3035b21
Staphylococcus_epidermidis.tar.gz	application/gzip	3881065	MD5 2e015012e20c98a9831a5332747c6c35
Cichorium_intybus.tar.gz	application/gzip	92637252	MD5 0f08b37252a4e5b1f50f2dbe1e772384
Cucurbita_maxima.tar.gz	application/gzip	51804259	MD5 5d81f8a358377d053b055861a01f9e91
Pinellia_ternata.tar.gz	application/gzip	119419834	MD5 94cb8a33ca7abb0568cce3fd3196a764
Miscanthus_lutarioriparius.tar.gz	application/gzip	196906918	MD5 0b21092f856e34471802487bc44814b1
Lupinus_luteus.tar.gz	application/gzip	33557442	MD5 025d5df3f441446d642b8eae56c2c850
Hippophae_rhamnoides.tar.gz	application/gzip	59232434	MD5 85aa3c30016d5b0cafb77ce1643cc8fb
Methanocaldococcus_jannaschii.tar.gz	application/gzip	835938	MD5 bcf5b69406ce084b8451cf60fb8e916a
Gossypium_trilobum.tar.gz	application/gzip	36144061	MD5 8a470ed34f686dc330ec9bb56b6944c8
Artemisia_annua.tar.gz	application/gzip	145027801	MD5 429e5bce6d06a757944daf105bd8afa5
Aedes_aegypti.tar.gz	application/gzip	215055529	MD5 940be0878816e91787dc3407a1a90578
Cucumis_melo.tar.gz	application/gzip	179682617	MD5 a3d2919a1b8cc2b9b7845ef9cbe1fb5e
Eriocheir_sinensis.tar.gz	application/gzip	128434958	MD5 b1b4300fa02f5f4f7222a1a62957d01d
Pan_troglodytes.tar.gz	application/gzip	39986017	MD5 832057c94e1fc96c4a9c6bd00972ea6a
Vicia_faba.tar.gz	application/gzip	174775953	MD5 05cba99b80871b331dde58d08066fff5
Cannabis_sativa.tar.gz	application/gzip	212972125	MD5 0ff7b06dde8aff01feef0f411707043e
Dimocarpus_longan.tar.gz	application/gzip	101423072	MD5 f85a556c2d603ad85750320c0c931ac8
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Citation

Natarajan, Shakunthala; Sterling, Claudia; Choudhary, Nancy; Khatun, Najnin; Brieske, Mia-Sophie; Busch, Hannah Elisa; Pucker, Boas, 2026-08-29, PanXpresso - comprehensive collection of gene expression data across domains of life, doi:10.60507/FK2/OBIGQH, V1.0

Additional Dataverse fields

Id	822
Dataset Type	dataset
Internal Version Number	27
Latest Version Publishing State	RELEASED
Release Time	2026-08-29T05:04:43Z
Create Time	2026-08-27T09:50:39Z
Citation Date	2026-08-29
File Access Request	True

Export metadata

Static metadata exports available for this published dataset version:

Complete Dataverse metadata

Citation Metadata

Title title

PanXpresso - comprehensive collection of gene expression data across domains of life

Author author

Author Name
Natarajan, Shakunthala
Author Affiliation
University of Bonn
Author Identifier Scheme
ORCID
Author Identifier
Type Name
authorIdentifier
Multiple
False
Type Class
primitive
Value
https://orcid.org/0000-0002-4713-2380
Expandedvalue
Person Name
Natarajan, Shakunthala
@id
https://orcid.org/0000-0002-4713-2380
Scheme
ORCID
@type
https://schema.org/Person
Author Name
Sterling, Claudia
Author Affiliation
University of Bonn
Author Identifier Scheme
ORCID
Author Identifier
Type Name
authorIdentifier
Multiple
False
Type Class
primitive
Value
https://orcid.org/0009-0002-3078-4056
Expandedvalue
Person Name
Sterling, Claudia
@id
https://orcid.org/0009-0002-3078-4056
Scheme
ORCID
@type
https://schema.org/Person
Author Name
Choudhary, Nancy
Author Affiliation
University of Bonn
Author Identifier Scheme
ORCID
Author Identifier
Type Name
authorIdentifier
Multiple
False
Type Class
primitive
Value
https://orcid.org/0000-0002-2562-7905
Expandedvalue
Person Name
Choudhary, Nancy
@id
https://orcid.org/0000-0002-2562-7905
Scheme
ORCID
@type
https://schema.org/Person
Author Name
Khatun, Najnin
Author Affiliation
University of Bonn
Author Identifier Scheme
ORCID
Author Identifier
Type Name
authorIdentifier
Multiple
False
Type Class
primitive
Value
https://orcid.org/0009-0000-3003-3338
Expandedvalue
Person Name
Khatun, Najnin
@id
https://orcid.org/0009-0000-3003-3338
Scheme
ORCID
@type
https://schema.org/Person
Author Name
Brieske, Mia-Sophie
Author Affiliation
University of Bonn
Author Identifier Scheme
ORCID
Author Identifier
Type Name
authorIdentifier
Multiple
False
Type Class
primitive
Value
https://orcid.org/0009-0006-6581-9502
Expandedvalue
@id
https://orcid.org/0009-0006-6581-9502
Scheme
ORCID
@type
https://schema.org/Person
Author Name
Busch, Hannah Elisa
Author Affiliation
University of Bonn
Author Identifier Scheme
ORCID
Author Identifier
0009-0000-5300-680X
Author Name
Pucker, Boas
Author Affiliation
University of Bonn
Author Identifier Scheme
ORCID
Author Identifier
Type Name
authorIdentifier
Multiple
False
Type Class
primitive
Value
https://orcid.org/0000-0002-3321-7471
Expandedvalue
Person Name
Pucker, Boas
@id
https://orcid.org/0000-0002-3321-7471
Scheme
ORCID
@type
https://schema.org/Person

Dataset Contact datasetContact

Dataset Contact Name
Natarajan, Shakunthala
Dataset Contact Affiliation
University of Bonn
Dataset Contact Email
s64snata@uni-bonn.de
Dataset Contact Name
Pucker, Boas
Dataset Contact Affiliation
University of Bonn
Dataset Contact Email
pucker@uni-bonn.de

Ds Description dsDescription

Ds Description Value
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.
Ds Description Date
2026-08-27

Subject subject

Medicine, Health and Life Sciences

Free Keyword freeKeyword

Free Keyword Value
gene expression
Free Keyword Value
transcript abundance
Free Keyword Value
plants
Free Keyword Value
animals
Free Keyword Value
fungi
Free Keyword Value
archaea
Free Keyword Value
bacteria

Publication publication

Publication Relation Type
IsSupplementTo
Publication Citation
XpBrew and PanXpresso - automatic RNA-seq processing workflow and comprehensive collection of gene expression data (in preparation)
Publication IDType
doi
Publication IDNumber
10.64898/2026.08.27.747620
Publication URL
https://doi.org/10.64898/2026.08.27.747620

Notes Text notesText

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

Language language

English

Depositor depositor

Natarajan, Shakunthala

Date Of Deposit dateOfDeposit

2026-08-27

Date Of Collection dateOfCollection

Date Of Collection Start
2025-12-01
Date Of Collection End
2026-08-24

Kind Of Data kindOfData

Strucural annotation files, Gene expression data

Software software

Software Name
XpBrew
Software Version
v0.3

Data Sources dataSources

Please see the "Reference" information in SuppFile01_PanXpresso_DataSources-Reference-Taxonomy.tsv for details.

Software Metadata (CodeMeta v2.0)

Code Version codeVersion

0.3.0

Code Repository codeRepository

https://github.com/PuckerLab/XpBrew

Application Category applicationCategory

RNA-seq data processing workflow

Programming Language programmingLanguage

Python3

Operating System operatingSystem

Linux

Software Requirements Item softwareRequirementsItem

Software Requirements
kallisto, sratoolkit, pandas (v2.3.1 or greater), matplotlib (v3.10.5 or greater)

Software Help softwareHelp

https://github.com/PuckerLab/XpBrew

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