{"database": "metadata", "table": "run_metadata", "rows": [[55541, "SRR10550579", "SRX7232580", "SRS5733210", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv FLX Str whole 6", "GSM4196113", null, "source name:Lrv FLX Str whole|genotype/variation:SR4G transgenic|stress status:Str|drug status:FLX|tissue:larvae head", "Lrv FLX Str whole 6", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv FLX Str whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Str|drug status:FLX|tissue:larvae head", "GSM4196113", "GSM4196113: Lrv FLX Str whole 6; Danio rerio; RNA Seq", "GSM4196113", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196113", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_FLX_Str_6_S55_R1_001.trimmed.fastq.gz", "fastq", 1667637008.0, 22201140.0, "GSM4196113 r1", "0:75.11 1:0", "A:438989346;C:397147842;G:367576938;T:463905385;N:17497", 75, 0, null, null, 438989346, 397147842, 367576938, 463905385, 17497, "SRX7232580", "SRS5733210", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.94774, null, 0.13955, null, 0.69842, null, 0.47883, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous 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": ["55541"], "units": {}, "query_ms": 7.665968994842842}