run_metadata: 55548

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
55548	SRR10550572	SRX7232573	SRS5733204	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FLX exposure in both environmental and therapeutic concentrations on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish.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				Lrv FLX Bsal whole 4	GSM4196106		source name:Lrv FLX Bsal whole\|genotype/variation:SR4G transgenic\|stress status:Bsal\|drug status:FLX\|tissue:larvae head	Lrv FLX Bsal whole 4	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 Bsal 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’s protocol using 250ng of starting material.		genotype/variation:SR4G transgenic\|stress status:Bsal\|drug status:FLX\|tissue:larvae head	GSM4196106	GSM4196106: Lrv FLX Bsal whole 4; Danio rerio; RNA Seq	GSM4196106		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:GSM4196106	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP233586			Lrv_FLX_Bsal_4_S69_R1_001.trimmed.fastq.gz	fastq	1802344612.0	23981363.0	GSM4196106 r1	0:75.16 1:0	A:455847939;C:444174899;G:406307504;T:495995239;N:19031	75	0			455847939	444174899	406307504	495995239	19031	SRX7232573	SRS5733204	SRA1003923	GEO	Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada	1	0.9537		0.13958		0.6929		0.4996		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown		Canada	2019-11-27	Multi-stage	Multi-stage	Head	Nervous System