{"database": "metadata", "table": "run_metadata", "rows": [[63813, "SRR14060977", "SRX10435561", "SRS8569033", "SRP311962", "PRJNA716978", "Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model", "GSE169522", "Transcriptome Analysis", "We hypothesised that induction of a torpor like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis  a torpor like state was induced in zebrafish using melatonin treatment and cold temperature  and radiation exposure was administered twice over the course of 10 days. The protective effects of induced torpor were assessed via RNA sequencing of mRNA extracted from the GIT.  A systems level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation  torpor  and torpor+radiation groups. The results revealed that melatonin and cold temperature successfully induced a torpor like state in zebrafish as shown by decreased metabolism and activity levels. Low dose radiation caused DNA damage and oxidative stress triggering a stress response  including steroidal signalling and changes to metabolism  damage to the central nervous system and cell cycle arrest. This stress response was attenuated in the torpor+radiation group by an increase in biosynthesis  proliferation  cell survival signals and expression of genes involved in protection against the adverse effects of radiation  particularly in neurons  suggesting a radioprotective effect conferred by a torpor state. This proof of concept model provides compelling initial evidence for utilizing an induced torpor like state as a potential countermeasure for radiation exposure. Overall design: Transcriptomic analysis of zebrafish GIT assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, "pubmed:33920039", null, "Torpor+radiation [18 24 F1 RAD]", "GSM5208642", null, "tissue:Gastrointestinal tract", "Torpor+radiation [18 24 F1 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 Genome build: zebrafish genome GRCz11 Supplementary files format and content: HTSeq counts  DESeq output", "Gastrointestinal tract", "A melatonin group 28.5  melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M 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 GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer\u2019s protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", null, "radiation cgy:32.64|temperature \u00b0c:18.5|melatonin \u00b5m:24", "GSM5208642", "GSM5208642: Torpor+radiation [18 24 F1 RAD]; Danio rerio; RNA Seq", "GSM5208642", null, "1", "Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit Qiagen  Hilden  Germany. To prepare mRNA Seq libraries the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  USA was utilized; 100\u2013200 ng of total input GIT RNA was used in accordance with the manufacturer's protocol. High through put sequencing was performed at the University of North Carolina Chapel Hill High Throughput Sequencing Facility  Chapel Hill  NC and the Queens University Belfast  Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of 25 million reads.", "GEO Accession:GSM5208642", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP311962", null, "loader:fastq load.py", "18-24-F1-RAD_GTGGCC_S100_L008_R1_001.fastq.gz", "fastq", 2369508350.0, 47390167.0, "GSM5208642 r1", "0:50", "A:509515197;C:623307582;G:694019366;T:542224292;N:441913", 50, null, null, null, 509515197, 623307582, 694019366, 542224292, 441913, "SRX10435561", "SRS8569033", "SRA1209926", "GEO", "Hardiman Lab, Institute for Global Food Security, Queen's University Belfast", 1, 0.62827, null, 0.14038, null, 0.828, null, 0.66975, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2021-03-24", "Undetermined", "Undetermined", "Gut", "Digestive System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["63813"], "units": {}, "query_ms": 8.05710100394208}