Transcriptomics Overview

This page catalogs all publicly available Transcriptomics datasets in the Hibernomics Database. Currently, 40 species have transcriptomics data, comprising 43 datasets from peer-reviewed publications. Each card below provides accession numbers, sequencing platforms, and links to original publications.

40
Species with Data
Out of 59 hibernating species
43
Total Datasets
Curated from literature
31
SRA Available
With public archive accessions
9
Literature Only
DOI-linked publications

Species with Transcriptomics Data

RNA
Available

A. davidianus | Andrias davidianus

Amphibia > Caudata > Cryptobranchidae

Illumina HiSeq 2500

AccessionSRP099564
PlatformIllumina HiSeq 2500
Publication10.1016/j.gdata.2017.07.008
Dataset 2PRJNA1332065
Platform 2Illumina (RNA-seq, skin, light-driven color)
2017-07-01 Browse SRA
RNA
Literature

A. sinensis | Andrias sinensis

Reptilia > Crocodilia > Alligatoridae

Illumina RNA-Seq

PlatformIllumina RNA-Seq
Publication10.3390/life12111787
2022-01-01 View Paper
RNA
Literature

B. gargarizans | Bufo gargarizans

Amphibia > Anura > Bufonidae

Illumina HiSeq 2500

PlatformIllumina HiSeq 2500
Publication10.3389/fevo.2022.924248
Dataset 2PRJNA506999
Platform 2Illumina HiSeq X10 (3 skin sites)
Dataset 3PRJNA1269961
2022-07-14 View Paper
RNA
Literature

C. anna | Calypte anna

Aves > Apodiformes > Trochilidae

Illumina HiSeq

PlatformIllumina HiSeq
Publication10.1016/j.cell.2019.05.037
2019-06-20 View Paper
RNA
Available

C. medius | Cheirogaleus medius

Mammalia > Primates > Cheirogaleidae

Illumina HiSeq 2000 (WAT, captive)

AccessionSRP049327
PlatformIllumina HiSeq 2000 (WAT, captive)
Publication10.1093/gbe/evw163
Dataset 2PRJNA400868
Platform 2Illumina HiSeq 2500 (WAT, wild C. crossleyi)
2016-08-01 Browse SRA
RNA
Available

C. partellus | Chilo partellus

Insecta > Lepidoptera > Crambidae

Illumina (transcriptome, digestive protease response)

AccessionPRJNA1046474
PlatformIllumina (transcriptome, digestive protease response)
Publication10.1002/arch.70096
2023-01-01 Browse SRA
RNA
Available

C. septempunctata | Coccinella septempunctata

Insecta > Coleoptera > Coccinellidae

Illumina HiSeq 2000

AccessionPRJNA547368
PlatformIllumina HiSeq 2000
Publication10.1371/journal.pone.0236249
Dataset 2PRJNA1158213
Platform 2BGISEQ-500
2020-08-17 Browse SRA
RNA
Available

D. nitedula | Dryomys nitedula

Mammalia > Rodentia > Gliridae

Illumina (hypothalamus RNA-seq, active vs. hibernation)

AccessionGSE207494
PlatformIllumina (hypothalamus RNA-seq, active vs. hibernation)
Publication10.1002/2211-5463.13731
2024-01-01 Browse SRA
RNA
Available

E. carinata | Eremias carinata

Reptilia > Squamata > Colubridae

Illumina

AccessionCNP0004039
PlatformIllumina
Publication10.1038/s42003-023-04598-0
2023-01-01 Browse SRA
RNA
Literature

E. europaeus | Erinaceus europaeus

Mammalia > Eulipotyphla > Erinaceidae

Illumina NovaSeq

PlatformIllumina NovaSeq
Publication10.1242/jeb.167890
2019-04-12 View Paper
RNA
Available

E. fuscus | Eptesicus fuscus

Mammalia > Chiroptera > Vespertilionidae

Illumina GAIIx (venom gland transcriptome)

AccessionSRP027593
PlatformIllumina GAIIx (venom gland transcriptome)
2012-01-01 Browse SRA
RNA
Available

E. multiocellata | Eremias multiocellata

Reptilia > Squamata > Lacertidae

Illumina (RNA-seq)

AccessionPRJCA001024
PlatformIllumina (RNA-seq)
Publication10.1073/pnas.1816086116
Platform 2RNA-seq (liver, Leishmania infection)
2019-02-11 Browse SRA
RNA
Available

E. quercinus | Eliomys quercinus

Mammalia > Rodentia > Gliridae

Illumina (hypothalamus RNA-seq, active vs. hibernation)

AccessionGSE207494
PlatformIllumina (hypothalamus RNA-seq, active vs. hibernation)
Publication10.1002/2211-5463.13731
2024-01-01 Browse SRA
RNA
Available

F. multistriata | Fejervarya multistriata

Amphibia > Anura > Dicroglossidae

BGISEQ-500 (light-driven skin color)

AccessionCNR0950002
PlatformBGISEQ-500 (light-driven skin color)
Publication10.1016/j.celrep.2024.114693
Platform 2RNA-seq + Metabolomics (tail resorption)
2024-01-01 Browse SRA
RNA
Available

G. brevicaudus | Glirulus brevicaudus

Reptilia > Squamata > Viperidae

Illumina HiSeq X Ten

AccessionPRJNA1267255
PlatformIllumina HiSeq X Ten
Publication10.1038/s41598-026-40454-1
2026-03-06 Browse SRA
RNA
Available

H. aspersa | Helix aspersa

Gastropoda > Stylommatophora > Helicidae

Ion Torrent PGM

AccessionSRR5273244
PlatformIon Torrent PGM
Publication10.1007/s11033-017-4232-4
Dataset 2SRX10567815
Platform 2BGISEQ-500
2017-09-01 Browse SRA
RNA
Available

I. tridecemlineatus | Ictidomys tridecemlineatus

Mammalia > Rodentia > Sciuridae

454/Roche (deep transcriptome, multiple tissues)

AccessionSRR352220
Platform454/Roche (deep transcriptome, multiple tissues)
Publication10.1371/journal.pone.0027021
2011-07-20 Browse SRA
RNA
Available

L. sylvaticus | L. sylvaticus

Amphibia > Anura > Hylidae

Illumina HiSeq 2500 (ventral skin, Bd exposure)

AccessionPRJNA392411
PlatformIllumina HiSeq 2500 (ventral skin, Bd exposure)
Publication10.1098/rsos.170910
Dataset 2PRJNA1162529
Platform 2Next-generation sequencing (liver miRNA, anoxia)
2018-02-21 Browse SRA
RNA
Available

M. auratus | Mesocricetus auratus

Mammalia > Rodentia > Cricetidae

Illumina NovaSeq 6000 (lung, COVID-19)

AccessionPRJNA952603
PlatformIllumina NovaSeq 6000 (lung, COVID-19)
Publication10.1126/scitranslmed.abq1533
Dataset 2PRJNA646705
Platform 2HiSeq X Ten (single-cell, multiple organs)
2023-08-09 Browse SRA
RNA
Available

M. himalayana | Marmota himalayana

Mammalia > Rodentia > Sciuridae

Affymetrix (hibernating liver transcriptome)

AccessionGSE2024
PlatformAffymetrix (hibernating liver transcriptome)
2004-12-03 Browse SRA
RNA
Literature

M. monax | Marmota monax

Mammalia > Rodentia > Sciuridae

Illumina RNA-Seq (liver + spleen, comparative transcriptome)

PlatformIllumina RNA-Seq (liver + spleen, comparative transcriptome)
Publication10.1371/journal.pone.0165875
2016-11-01 View Paper
RNA
Available

M. murinus | Microcebus murinus

Mammalia > Primates > Cheirogaleidae

Illumina (total RNA-seq, liver)

AccessionSRX270644
PlatformIllumina (total RNA-seq, liver)
Publication10.1016/j.gene.2018.08.014
Platform 2small RNA-Seq (muscle, torpor)
2018-11-01 Browse SRA
RNA
Available

M. reevesii | Mauremys reevesii

Reptilia > Testudines > Geoemydidae

Illumina HiSeq 2500

AccessionSRP153785
PlatformIllumina HiSeq 2500
Publication10.7717/peerj.6557
Dataset 2SRP310345
Platform 2Illumina HiSeq 4000
2019-03-08 Browse SRA
RNA
Available

N. parkeri | Nanorana parkeri

Amphibia > Anura > Ranidae

Illumina HiSeq 2500

AccessionPRJCA010139
PlatformIllumina HiSeq 2500
Publication10.1016/j.cbpa.2022.111336
2022-01-01 Browse SRA
RNA
Available

N. pygmaeus | Nycticebus pygmaeus

Mammalia > Primates > Lorisidae

Illumina HiSeq 2000 (8 tissues)

AccessionCRA003461
PlatformIllumina HiSeq 2000 (8 tissues)
Publication10.1073/pnas.2123030119
2022-09-13 Browse SRA
RNA
Available

P. mucosus | Ptyas mucosus

Reptilia > Squamata > Colubridae

BGISEQ-500 (8 tissues)

AccessionPRJNA955401
PlatformBGISEQ-500 (8 tissues)
Publication10.5334/cogs120
2022-12-09 Browse SRA
RNA
Available

P. nigromaculatus | Pelophylax nigromaculatus

Amphibia > Anura > Ranidae

Illumina HiSeq 2500

AccessionGEGI01000000
PlatformIllumina HiSeq 2500
Publication10.1186/s12864-018-4735-7
Platform 2Transcriptome (liver, 6PPD/6PPD-Q)
2018-01-01 Browse SRA
RNA
Available

R. dybowskii | Rana dybowskii

Amphibia > Anura > Ranidae

Illumina (skin, Aeromonas infection)

AccessionPRJNA1152028
PlatformIllumina (skin, Aeromonas infection)
Publication10.1016/j.aquaculture.2024.740736
Platform 2RNA-seq (testis vs ovary, reproduction)
2024-01-01 Browse SRA
RNA
Available

R. ferrumequinum | Rhinolophus ferrumequinum

Mammalia > Chiroptera > Rhinolophidae

Illumina HiSeq X Ten (gut)

AccessionPRJNA638701
PlatformIllumina HiSeq X Ten (gut)
Publication10.1186/s12983-020-00366-w
Dataset 2PRJNA515764
Platform 2Illumina HiSeq 2500 (cochlea)
2020-01-01 Browse SRA
RNA
Available

S. beecheyi | Spermophilus beecheyi

Mammalia > Rodentia > Sciuridae

Illumina NovaSeq 6000 (13 tissues)

AccessionPRJNA804109
PlatformIllumina NovaSeq 6000 (13 tissues)
Publication10.1002/jez.b.23145
2022-05-24 Browse SRA
RNA
Available

S. dauricus | Spermophilus dauricus

Mammalia > Rodentia > Sciuridae

BGISEQ-500

AccessionCRA005977
PlatformBGISEQ-500
Publication10.1016/j.cbpa.2022.111336
Platform 2RNA-seq + Metabolomics (heart)
2022-11-15 Browse SRA
RNA
Available

S. lateralis | Spermophilus lateralis

Mammalia > Rodentia > Sciuridae

Affymetrix (hibernating liver transcriptome)

AccessionGSE2024
PlatformAffymetrix (hibernating liver transcriptome)
2004-12-03 Browse SRA
RNA
Available

T. aculeatus | Tachyglossus aculeatus

Mammalia > Monotremata > Tachyglossidae

Illumina GAIIx (venom gland transcriptome)

AccessionSRP027593
PlatformIllumina GAIIx (venom gland transcriptome)
2012-01-01 Browse SRA
RNA
Literature

T. carolina | Terrapene carolina

Reptilia > Testudines > Emydidae

Illumina RNA-Seq (liver + spleen, comparative transcriptome)

PlatformIllumina RNA-Seq (liver + spleen, comparative transcriptome)
Publication10.1371/journal.pone.0165875
2016-11-01 View Paper
RNA
Literature

T. hermanni | Testudo hermanni

Reptilia > Testudines > Testudinidae

Illumina RNA-Seq

PlatformIllumina RNA-Seq
Publication10.3390/life12111787
2022-01-01 View Paper
RNA
Available

T. sibiricus | Tamias sibiricus

Mammalia > Rodentia > Sciuridae

Illumina NovaSeq 6000

AccessionPRJNA1101579
PlatformIllumina NovaSeq 6000
Publication10.1016/j.celrep.2024.114693
Dataset 2SRR19961278
Platform 2Illumina Hiseq X10 (transcriptome)
2024-01-01 Browse SRA
RNA
Literature

U. americanus | Ursus americanus

Mammalia > Carnivora > Ursidae

Illumina NovaSeq

PlatformIllumina NovaSeq
Publication10.1016/j.celrep.2021.109234
2021-06-15 View Paper
RNA
Available

U. arctos | Ursus arctos

Mammalia > Carnivora > Ursidae

PacBio Iso-Seq + Illumina

AccessionPRJNA1194020
PlatformPacBio Iso-Seq + Illumina
Publication10.1016/j.celrep.2022.111215
Dataset 2PRJNA835146
Platform 2Illumina HiSeq 2500 (13 tissues)
2022-01-01 Browse SRA
RNA
Available

U. maritimus | Ursus maritimus

Mammalia > Carnivora > Ursidae

Illumina + ONT (Long-read)

AccessionPRJNA514749
PlatformIllumina + ONT (Long-read)
Publication10.3389/fgene.2019.00643
2019-06-26 Browse SRA
RNA
Literature

U. parryii | Urocitellus parryii

Mammalia > Rodentia > Sciuridae

Illumina NovaSeq

PlatformIllumina NovaSeq
Publication10.1242/jeb.245678
Platform 2qPCR (miRNA profiling)
2022-09-20 View Paper

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58 species
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40 species
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11 species
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19 species
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