{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Guillaume Fourneaux"],"organism":["Ursus arctos"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14479"],"description":["Transcriptomic analysis of the brown bear (Ursus arctos) tissues during both active and inactive phases has unveiled significant differential gene expression, with thousands of genes exhibiting altered activity in all studied tissues (muscle, liver, adipose...). Nevertheless, transcriptional analyses of hibernating animal tissues are limited to organs that are important in metabolism. No information is available about the variations of gene expression in tissues that may have a lower impact on metabolism, like the skin, which is mainly a support tissue and a mechanical barrier against the external environment. That experiment brings information about the gene expression variations in the bear skin during hibernation."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Biopsies of the vastus lateralis muscle and skin tissue were collected from free-ranging brown bears (Ursus arctos), from Dalarna and Gävleborg counties, Sweden, in 2023. After collection, the samples were immediately frozen on dry ice until storage at -80°C. The same bears were captured during winter hibernation (in February) and during their active period (June). The study was approved by the Swedish Ethical Committee on Animal Experiment (applications Dnr C3/2016 and Dnr C18/2015), the Swedish Environmental Protection Agency (NV-0741-18), and the Swedish Board of Agriculture (Dnr 5.2.18–3060/17). All procedures complied with Swedish laws and regulations. Capture, anesthesia, and sampling were carried out according to an established biomedical protocol (Arnemo & Evans, 2017).","Nucleic Acid Extraction - before RNA extraction, samples were first crushed in a Precellys lysing kit for hard tissue. Total RNA from bear skin were extracted with the NucleoMag RNA kit from Macherey-Nagel (744350.1). Tissues were lysed in 350µL of reconstituted Lysis Buffer (45-60% guanidium thiocyanate) and transferred in 1,5mL Eppendorf tube. RNA from samples have been extracted with the robot KingFisher Duo Prime Purification System. The following information describes the detailed procedure automatically performed by the robot. 350µL of binding buffer (95-100% 2-propanol) and 28µL of NucleoMag B-Beads were added to the samples. Samples were mixed by shaking for 5mn at RT. The supernatant was removed and samples were dried for 5mn at RT. DNA was digested in 300µL of rDNase reaction buffer. Samples were mixed and incubated 15mn at RT. 350µL of binding buffer was added and mixed by shaking for 5mn at RT. The supernatant was removed and samples were washed with 600µL of washing buffer 1 (15-30% guanidium thiocyanate, 35-55% ethanol). The supernatant was removed and samples washed twice with 900µL of washing buffer 2 (75-90% ethanol). Samples were air dried 15mn at RT and eluted in 50µL of elution buffer. Samples were heated at 70°C for 5mn before dosing.","Sequencing - -Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail; -mRNA molecules were fragmented into small pieces; -The fragmented mRNA was synthesized into first strand cDNA using random primers; -The second strand cDNA was synthesized with dUTP instead of dTTP; -The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; -Digest the U-labeled second-strand template with Uracil-DNA-- Glycosylase (UDG) and perform PCR amplification; -Library quality control; -Library circularization; -The library was amplified to make DNA nanoball (DNB);  -Sequencing on DNBSEQ (DNBSEQ Technology) platform","Library Construction - -Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail; -mRNA molecules were fragmented into small pieces; -The fragmented mRNA was synthesized into first strand cDNA using random primers; -The second strand cDNA was synthesized with dUTP instead of dTTP; -The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; -Digest the U-labeled second-strand template with Uracil-DNA-- Glycosylase (UDG) and perform PCR amplification; -Library quality control; -Library circularization; -The library was amplified to make DNA nanoball (DNB);  -Sequencing on DNBSEQ (DNBSEQ Technology) platform"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - The statistical analyses were performed with R software, in its 4.3.0 version. DESeq2 R package (v1.42.0) was used to clean, normalize, and analyze the raw counts matrix. The DEGs gene list are based on a 0.05 threshold applied to the Bonferroni adjusted DESeq2 p-values. PCA analyses were then performed on the whole quantified transcriptome and for selected genes (DEGs) thanks to FactomineR and Factoextra packages (v2.9, v1.0.7) for QC purposes and main effects characterisations. These PCA analyses were performed on linearized data thanks to the edgeR and limma R packages (v4.0.9, v3.58.1), this linearization being performed through a log-cpm transformation."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["DNBSEQ-T7"],"study_type":["RNA-seq of coding RNA"],"species":["Ursus arctos"],"pubmed_title":["Hypermethylation of histone H3 in hibernating bear tissues"],"pubmed_authors":["Etienne Lefai","Guillaume Fourneaux1, Cécile Coudy-Gandilhon1, Charlène Pourpe1, Gwendal Cueff1, Manon Verdier2, Alina L. Evans3, Jon E. Swenson4, Christophe Tatout2, Aline Probst2, Fabrice Bertile5, Lydie Combaret1, Etienne Lefai1","Guillaume Fourneaux","Gwendal Cueff"],"additional_accession":[]},"is_claimable":false,"name":"RNASeq analysis of brown bear (Ursus arctos) skin tissue during active state and hibernation","description":"Transcriptomic analysis of the brown bear (Ursus arctos) tissues during both active and inactive phases has unveiled significant differential gene expression, with thousands of genes exhibiting altered activity in all studied tissues (muscle, liver, adipose...). Nevertheless, transcriptional analyses of hibernating animal tissues are limited to organs that are important in metabolism. No information is available about the variations of gene expression in tissues that may have a lower impact on metabolism, like the skin, which is mainly a support tissue and a mechanical barrier against the external environment. That experiment brings information about the gene expression variations in the bear skin during hibernation.","dates":{"release":"2025-09-05T00:00:00Z","modification":"2025-09-05T01:02:52.793Z","creation":"2024-09-26T15:50:21.162Z"},"accession":"E-MTAB-14479","cross_references":{"ENA":["ERP164531"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}