run_metadata: 63810
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 |
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| 63810 | SRR14060980 | SRX10435564 | SRS8569035 | 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 | pubmed:33920039 | Torpor+radiation [18 24 M2 RAD] | GSM5208645 | tissue:Gastrointestinal tract | Torpor+radiation [18 24 M2 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 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 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; 100–200 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. | radiation cgy:32.64|temperature °c:18.5|melatonin µm:24 | GSM5208645 | GSM5208645: Torpor+radiation [18 24 M2 RAD]; Danio rerio; RNA Seq | GSM5208645 | 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; 100–200 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:GSM5208645 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP311962 | loader:fastq load.py | 18-24-M2-RAD_GTGAAA_S103_L008_R1_001.fastq.gz | fastq | 1589596300.0 | 31791926.0 | GSM5208645 r1 | 0:50 | A:343218732;C:412078303;G:480421414;T:353581599;N:296252 | 50 | 343218732 | 412078303 | 480421414 | 353581599 | 296252 | SRX10435564 | SRS8569035 | SRA1209926 | GEO | Hardiman Lab, Institute for Global Food Security, Queen's University Belfast | 1 | 0.61709 | 0.13219 | 0.8379 | 0.67633 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | United Kingdom | 2021-03-24 | Undetermined | Undetermined | Gut | Digestive System |