run_metadata: 70016

This data as json

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70016	SRR19264398	SRX15324786	SRS13053402	SRP375841	PRJNA839281	Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene	GSE203258	Transcriptome Analysis	Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish				RNA Retene 0.512 µM Replicate 2	GSM6165387		tissue:Whole zebrafish larvae\|timepoint:48 hpf 0.512 µM\|FISH strain:Tropical 5D	RNA Retene 0.512 µM Replicate 2	Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11	Whole zebrafish larvae	Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM	48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.	Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.	timepoint:48 hpf 0.512 µM\|FISH strain:Tropical 5D	GSM6165387	GSM6165387: RNA Retene 0.512 µM Replicate 2; Danio rerio; RNA Seq	GSM6165387 r1	GSM6165387	1	48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400		SRP375841			Ret10_2.fq Ret10_1.fq	fastq fastq	4542900600.0	45429006.0	GSM6165387 r1	0:100 1:100	A:1189304147;C:1055343156;G:1099652770;T:1198600527;N:0	100	100			1189304147	1055343156	1099652770	1198600527	0	SRX15324786	SRS13053402	SRA1422455	Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University	Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University	1	0.93819		0.07628		0.712		0.4832		100		B		usable mapping rate	bgi	bgi	3prime	poly_a	unknown	bulk	unknown	unknown		United States	2022-05-18	Multi-stage	Multi-stage	Whole Organism	All anatomical structures