run_metadata: 72665
This data as json
| rowid | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | run.attributes | run.filename | run.semantic_name | run.total_bases | run.total_spots | run.alias | run.read_lengths | run.base_counts | run.r1_length | run.r2_length | run.r3_length | run.r4_length | run.Acount | run.Ccount | run.Gcount | run.Tcount | run.Ncount | run.experiment | run.pool_member | submission.accession | submission.srasource | submission.bioprojectsource | seqdetective.n_mates | seqdetective.mapping_rate.mate1 | seqdetective.mapping_rate.mate2 | seqdetective.nofeature_rate.mate1 | seqdetective.nofeature_rate.mate2 | seqdetective.sparsity.mate1 | seqdetective.sparsity.mate2 | seqdetective.pos_strand_rate.mate1 | seqdetective.pos_strand_rate.mate2 | seqdetective.readlen.mate1 | seqdetective.readlen.mate2 | seqdetective.judgement.mate1 | seqdetective.judgement.mate2 | seqdetective.judgement.reason | platform_family | instrument_generation | read_bias | selection_class | prep_kit | sc_or_bulk | tech_class | technology | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 72665 | SRR23048174 | SRX19001702 | SRS16421809 | SRP416971 | PRJNA922874 | Transcriptome Profiling Reveals Enhanced Mitochondrial Activity as a Cold Adaptive Strategy to Hypothermia in Zebrafish Muscle | GSE222614 | Transcriptome Analysis | The utilisation of synthetic torpor for interplanetary travel once seemed farfetched. However mounting evidence points to torpor induced protective benefits from the main hazards of space travel namely exposure to radiation and microgravity. To determine the radio protective effects of an induced torpor like state we exploited the ectothermic nature of the Danio rerio zebrafish in reducing their body temperatures to replicate the hypothermic states seen during natural torpor. We also administered melatonin as a sedative to reduce physical activity. Zebrafish were then exposed to low dose radiation 0.3Gy to simulate radiation exposure on long term space missions. Transcriptomic analysis found that radiation exposure led to an upregulation of inflammatory and immune signatures and a differentiation and regeneration phenotype driven by STAT3 and MYOD1 transcription factors. In addition DNA repair processes were downregulated in the muscle two days' post irradiation. The effects of hypothermia led to an increase in mitochondrial translation including genes involved in oxidative phosphorylation and a downregulation of ex tracellular matrix and developmental genes. Upon radiation exposure increases in endoplasmic reticulum stress genes were observed in a torpor+radiation group with downregulation of im mune related and ECM genes. Exposing hypothermic zebrafish to radiation also resulted in a downregulation of ECM and developmental genes however immune/inflammatory related pathways were downregulated in contrast to that observed in the radiation only group. A cross species comparison was performed with the muscle of hibernating Ursus arctos horribilis brown bear to define shared mechanisms of cold tolerance. Shared responses show an upregula tion of protein translation and metabolism of amino acids as well as a hypoxia response with the shared downregulation of glycolysis ECM and developmental genes. Overall design: Transcriptomic analysis of zebrafish muscle assessing the protective effects of induced torpor on the harmful effects of low dose radiation | 18 M2 24 Rad | GSM6927788 | source name:Muscle|tissue:Muscle|condition:Torpor+radiation|geo loc name:missing|collection date:missing | 18 M2 24 Rad | Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Assembly: zebrafish genome GRCz11 | Muscle | A melatonin group 28.5 melatonin received melatonin daily for 10 days at a concentration of 24 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM melatonin. A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol. | Total mRNA was extracted from liver tissue of the zebrafish using Qiagen’s miRNeasy Mini kit Qiagen Hilden Germany. To prepare mRNA seq kit poly A capture KAPA RNA hyperIllumina San Diego CA USA; was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer’s protocol. High through put RNA sequencing RNAseq was performed at the Queens University Belfast Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded PE50 strategy. | tissue:Muscle|condition:Torpor+radiation|radiation cgy:32.64|temperature c:18.5|melatonin um:24 | GSM6927788 | GSM6927788: 18 M2 24 Rad; Danio rerio; RNA Seq | GSM6927788 r1 | GSM6927788 | 1 | Total mRNA was extracted from liver tissue of the zebrafish using Qiagen's miRNeasy Mini kit Qiagen Hilden Germany. To prepare mRNA seq kit poly A capture KAPA RNA hyperIllumina San Diego CA USA; was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer's protocol. High through put RNA sequencing RNAseq was performed at the Queens University Belfast Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded PE50 strategy. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 2000 | SRP416971 | loader:fastq load.py | PN0320_008_S8_L001_R1_001.fastq.gz PN0320_008_S8_L001_R2_001.fastq.gz | fastq fastq | 2030494635.0 | 20112784.0 | GSM6927788 r1 | 0:50.44 1:50.51 | A:537958829;C:467846795;G:473301503;T:551248281;N:139227 | 50 | 50 | 537958829 | 467846795 | 473301503 | 551248281 | 139227 | SRX19001702 | SRS16421809 | SRA1572773 | Queens university Belfast | Queens university Belfast | 2 | 0.96799 | 0.96544 | 0.05168 | 0.05576 | 0.82617 | 0.82739 | 0.60829 | 0.60078 | 51 | 51 | B | B | biological fallback assumption | illumina | nextseq_v2 | unknown | poly_a | unknown | bulk | unknown | unknown | United Kingdom | 2023-01-11 | Undetermined | Undetermined | Muscle | Muscular System |