run_metadata: 74026

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
74026	SRR23340936	SRX19282967	SRS16684631	SRP420989	PRJNA931595	The effects of atorvastatin AVS and afidopyropen on developing zebrafish	GSE224522	Transcriptome Analysis	For RNA seq experiments 20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments: ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.				ERM H2	GSM7025525		tissue:larvae\|cell line:whole larvae\|treatment:Control\|geo loc name:missing\|collection date:missing	ERM H2	Raw data raw reads of FASTQ format were firstly processed through fastp. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count fpkm log2 fold change p value Supplementary files format and content: Afid vs ERM excel files containing read count fpkm log2 fold change p value	larvae		Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.		cell line:whole larvae\|treatment:Control	GSM7025525	GSM7025525: ERM H2; Danio rerio; RNA Seq	GSM7025525 r1	GSM7025525	1	Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP420989		loader:fastq load.py	ERM2_1.fq.gz ERM2_2.fq.gz	fastq fastq	8055333600.0	26851112.0	GSM7025525 r1	0:150 1:150	A:2174113541;C:1873627794;G:1868962308;T:2138528112;N:101845	150	150			2174113541	1873627794	1868962308	2138528112	101845	SRX19282967	SRS16684631	SRA1723725	University of Florida	University of Florida	2	0.95895	0.96097	0.11791	0.11772	0.68434	0.6832	0.4604	0.46478	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	nebnext	bulk	unknown	unknown		United States	2023-02-04	Larval	Larval	Cell Line	Cell Line