{"database": "metadata", "table": "run_metadata", "rows": [[72482, "SRR22577930", "SRX18540943", "SRS16005328", "SRP412040", "PRJNA910181", "Transcriptomic data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos", "GSE220546", "Transcriptome Analysis", "Heat alters biology from molecular to ecological levels  but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here  we provide a comprehensive picture of the molecular signatures of this process  by integrating multiomic and phenotypic data. In individual zebrafish embryos  repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow down in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulphur containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response  extracellular signalling  glycosaminoglycan/keratan sulphate  and lipid metabolism. Consequently  non heat exposed receivers exposed to stress metabolites only experienced accelerated catch up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most  mediated by apelin signalling. Our results prove the concept of indirect heat induced stress propagation towards naive receivers  inducing phenotypes comparable to those resulting from direct heat exposure  but utilising distinct molecular pathways. Group exposing a non laboratory zebrafish line  we independently confirm that the glycosaminoglycan biosynthesis related gene chs1  and the mucus glycoprotein gene prg4a  functionally connected to the candidate stress metabolite classes sugars and phosphocholine  are differentially expressed in receivers. This hints at the production of Schreckstoff like cues in receivers  leading to further stress propagation within groups  which may have ecological and animal welfare implications for aquatic populations in a changing climate. Overall design: Zebrafish embryos were exposed for 24 hours to thermal stress TS and stress metabolites SM released by heat stressed zebrafish embryos  in a two way factorial design TSxSM  yielding four experimental treatments: fresh medium at 27\u00b0C control C  fresh medium with thermal stress TS  medium containing stress metabolites at 27\u00b0C SM  and medium containing stress metabolites with thermal stress TS+SM. Each treatment contains n = 3 biological replicates  each representing the pooled gene expression from 20 individual embryos.", null, "pubmed:37228511", null, "SM2  sample RNA10", "GSM6806697", null, "source name:1 dpf whole body embryos|tissue:1 dpf whole body embryos|genotype:Wild type Line: AB|time:1 dpf group:SM|treatment:Stress Metabolites at 27C", "SM2  sample RNA10", "The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1. Reads were filtered and trimmed using fastp v0.23.1  to remove low quality reads  polyG  polyX  and Illumina adapter sequences. Default parameters were used along with   dup calc accuracy 3   trim poly g   trim poly x Reads were aligned to the zebrafish reference genome using STAR v2.6.1 Reads were counted by gene using STAR v2.6.1   runMode alignReads   quantMode TranscriptomeSAM GeneCounts   outSAMtype BAM SortedByCoordinate   outSAMunmapped None   outSAMattributes Standard Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2. Assembly: primary genome assembly GRCz11.104 http://ftp.ensembl.org/pub/release 104/fasta/danio rerio/dna/Danio rerio.GRCz11.dna sm.primary assembly.fa.gz and http://ftp.ensembl.org/pub/release 104/gtf/danio rerio/Danio rerio.GRCz11.104.gtf.gz Supplementary files format and content: The files with \" ReadsPerGenes.fastp.noD.tab\" name extensions are read counts per gene obtained from STAR  which were used in DESeq2 for differential expression analysis.", "1 dpf whole body embryos", "Two temperature protocols were used  either i a control constant temperature of 27\u00b0C  or ii  thermal stress protocol consisting of repeated heat stress with temperature fluctuations  between 27  29  32  29  and 27\u00b0C  with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium fresh medium free of metabolites or stress medium with stress metabolites  SM and incubated with their temperature protocols for 24 hours  from 11 am once they reached the stage of 2 3.3 hpf to 11 am on the next day. At 1 dpf  i.e. post 24 hours of experimental treatment  embryos were sampled by pools of 20 per condition  and snap frozen at  80\u00b0C before total RNA extraction.", "Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations  and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.", "Zebrafish eggs were sanitised with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish wild type AB maintained at 27\u00b0C  with 14:10 light:dark cycles.  Embryos were incubated in individual 0.2 mL PCR tubes one embryo per tube containing 200 \u03bcL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol.", "tissue:1 dpf whole body embryos|genotype:Wild type Line: AB|time:1 dpf group:SM|treatment:Stress Metabolites at 27C", "GSM6806697", "GSM6806697: SM2  sample RNA10; Danio rerio; RNA Seq", "GSM6806697 r1", "GSM6806697", "1", "Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations  and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP412040", null, "loader:fastq load.py", "211020_A00291_0393_AHM5V2DRXY_1_12030WK0008L01_1.fastq.gz 211020_A00291_0393_AHM5V2DRXY_1_12030WK0008L01_2.fastq.gz", "fastq fastq", 2826043300.0, 28260433.0, "GSM6806697 r1", "0:50 1:50", "A:759619748;C:653720748;G:665257649;T:747369546;N:75609", 50, 50, null, null, 759619748, 653720748, 665257649, 747369546, 75609, "SRX18540943", "SRS16005328", "SRA1555908", "Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull", "Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull", 2, 0.95699, 0.9614, 0.09422, 0.09721, 0.73079, 0.73241, 0.48945, 0.49521, 50, 50, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2022-12-08", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"]], "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": ["72482"], "units": {}, "query_ms": 14.272323998739012}