run_metadata: 67976

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
67976	SRR17547554	SRX13717013	SRS11594777	SRP354402	PRJNA796216	Stress resilience is established during development and is regulated by complement factors	GSE193433	Transcriptome Analysis	Individuals in a population respond differently to stressful situations. While resilient individuals recover efficiently others are susceptible to the same stressors. Most existing information regarding the factors regulating stress resilience in vertebrates is from specific areas of the brain from adult rodents or humans. In order to study resilience during development we established a new paradigm to identify resilience in zebrafish larvae. Using this assay we identified resilient and susceptible subsets of zebrafish larvae at 6 dpf and performed gene expression analysis on whole larvae. Overall design: Total RNA from resilient and susceptible groups was extracted either at basal conditions or 30 minutes following a 5 minute stress. 5 biological replicates 1 larva per sample were subjected to next generation sequencing.		pubmed:36640352		Susceptible stressed 4 [Sus stress 9]	GSM5800168		tissue:Susceptible larva\|source type:Whole larva\|strain:AB\|archetype:Susceptible\|age:7 dpf	Susceptible stressed 4 [Sus stress 9]	Reads were trimmed using cutadapt DOI: 10.14806/ej.17.1.200 parameters: a ADAPTER1 A ADAPTER2 a “A{10}” a “T{10}” –times 2 q 20 m 25. Reads were mapped to genome /shareDB/genomes/Danio rerio/UCSC/danRer11/Star index/ using STAR DOI: 10.1093/bioinformatics/bts635 v2.4.2a parameters: –alignEndsType EndToEnd –outFilterMismatchNoverLmax 0.05 –twopassMode Basic. Counting was done using STAR. Normalization of the counts and differential expression analysis was performed using DESeq2 DOI: 10.1186/s13059 014 0550 8 Genome build: danRer11 Supplementary files format and content: Raw counts normalized measurements fold change post Deseq2	Susceptible larva	Zebrafish larvae were differentiated into resilient and susceptible groups at 6 dpf. They were let to rest for a day and at 7 dpf single larvae were collected in Trizol either at basal conditions or 30 minutes following a stressful event.	RNA was extracted by the basic Trizol chloroform phase separation method precipitated with isopropanol washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols	Wildtype zebrafish larvae were grown in uncrowded densities till 6 dpf	source type:Whole larva\|strain:AB\|archetype:Susceptible\|age:7 dpf	GSM5800168	GSM5800168: Susceptible stressed 4 [Sus stress 9]; Danio rerio; RNA Seq	GSM5800168 r1	GSM5800168	1	RNA was extracted by the basic Trizol chloroform phase separation method precipitated with isopropanol washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP354402			Sus_stress_9_S20_L002_R1_001.fastq.gz	fastq	493766280.0	5878170.0	GSM5800168 r2	0:84 1:0	A:128477502;C:115522900;G:119992333;T:129772804;N:741	84	0			128477502	115522900	119992333	129772804	741	SRX13717013	SRS11594777	SRA1355607	Molecular Cell Biology, Weizmann Institute of Science	Molecular Cell Biology, Weizmann Institute of Science	1	0.9505		0.09356		0.66523		0.48634		84		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		Israel	2022-01-11	Larval	Larval	Undetermined	Undetermined