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| Status |
Public on May 02, 2023 |
| Title |
Liver, sh931 (RNA-seq) |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mesocricetus auratus |
| Characteristics |
tissue: Liver
sample id: sh931
hibernation stage: torpor late
hibernation stage abbr: TL
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| Treatment protocol |
All hibernating animals were kept in darkness until euthanization. Arousal was induced at > 3 days of torpor by gentle handling. The animal's activity pattern accurately identified torpor bouts of hamsters, as evidenced by mouth temperature (Tm) at euthanization, being 9.0±0.9°C and 35.0±2.1°C for TL and AE, respectively, whereas SE animals had a Tm of 35.7±0.5°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Liver was flushed with physiological salt solution, removed and snap-frozen in liquid nitrogen and stored at −80 °C.
Total RNA was extracted from liver tissue samples of three animals per hibernation phase using Nucleospin (Machery Nagel, Düren, Germany). Concentrations were measured using Nanodrop and processed for RNA sequencing (RNAseq) by NXTGNT (www.nxtgnt.com). RNA quality was checked using a Bioanalyzer RNA 6000 nano chip assay and Ribogreen assay (Invitrogen, Carlsbad, CA, USA). 437ng RNA per sample was used for further analysis. cDNA libraries were prepared for sequencing using Truseq stranded mRNA library prep (Illumina, San Diego, CA. USA) according to protocol. Sequencing was performed on a NextSeq500 High output flow cell, generating single-end 75bp reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Mapping and quantification of RNA-seq reads was done with STAR aligner (v.2.7.0f) against MesAur 1.0 genome reference (gene annotation from Ensembl release 96)
Count data for all samples obtained by alignment with STAR.
Assembly: MesAur1.0
Supplementary files format and content: Count data
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| Submission date |
Mar 30, 2022 |
| Last update date |
May 02, 2023 |
| Contact name |
Jeroen Galle |
| Organization name |
Ghent University
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| Department |
Dept. Of Mathematical Modelling, Statistics and Bioinformatics
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| Lab |
Biobix, Lab of Bioinformatics and Computational Genomics
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| Street address |
Coupure Links 653
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| City |
Ghent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
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| Platform ID |
GPL24490 |
| Series (2) |
| GSE199814 |
Liver transcriptomic and methylomic analyses identify transcriptional MAPK regulation in facultative hibernation of Syrian hamster [RNA-Seq] |
| GSE199817 |
Liver transcriptomic and methylomic analyses identify transcriptional MAPK regulation in facultative hibernation of Syrian hamster |
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| Relations |
| BioSample |
SAMN27112555 |
| SRA |
SRX14677356 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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