run_metadata: 70435

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
70435	SRR19831102	SRX15874804	SRS13564510	SRP383398	PRJNA851939	Danio rerio breed:Wild type Transcriptome or Gene expression	PRJNA851939	Other	Evaluation of gene expression changes in zebrafish liver following a full life cycle exposure to metformin in order to evaluate the main pathways affected				CML	CML		strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:9 month\|dev stage:Adult\|sex:male\|tissue:Liver\|BioSampleModel:Model organism or animal									Ctrl male	Dre Ctrl male	Dre Ctrl male	Briefly one RNA pool of 5 livers n=1 from each treatment and sex with a minimum concentration of 40 ng/L were subjected to a quality control to determine RNA purity by measuring the ratio of absorbance at 260/280 nm on a NanoDrop Thermo Fisher Scientiphic USA; integrity and concentration were estimated using the Agilent 2100 BioAnalizer Agilent Technologies USA and integrity was further confirmed by 1 % agarose gel eletrophoresis. RNA samples with a RIN RNA integrity number above 6.3 passed the quality control and were used for library construction and further sequencing. post quality control proceedings RNA samples were then enriched using oligodT beads and rRNA was removed from total RNA using the Ribo Zero Kit Illumina USA. Subsequently sequencing libraries were prepared using Novogene NGS RNA Library Prep Set. Briefly Isolated mRNA was randomly fragmented by adding fragmentation buffer and cDNA synthesis was performed using mRNA template and random hexamer primers for the first strand post which a custom second strand synthesis buffer Illumina USA as well as dNTPs RNAse H and DNA polymerase I were added to start the second strand synthesis.. post end repair A tailing and sequencing adapter ligation were performed. In order to select cDNA fragments of approximately 250 300 bp samples were sonicated and magnetic beads were used to select the target fragment size post which UTP containing second strand were removed through enzyme digestion. cDNA library was then completed through size selection andPCR amplification. post cDNA library completion a preliminary quantification was performed using a Qubit 2.0 fluorometer Termo Fisher Scientific USA followed by Agilent 2100 Bioanalyzer to test insert size and lastly a Q PCR to quantify the library effective concentration precisely. Quantified libraries from each treatment and sex were then independently subjected to sequencing Illumina Novaseq 6000 paired end 2x150 generating an average of 35 million pair end reads for each sample.			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP383398			CML_1.fq.gz CML_2.fq.gz	fastq fastq	10198111200.0	33993704.0	CML 1.fq.gz	0:150 1:150	A:2734736413;C:2355820205;G:2381029396;T:2726450659;N:74527	150	150			2734736413	2355820205	2381029396	2726450659	74527	SRX15874804	SRS13564510	SRA1442579	CIIMAR - Interdisciplinary Centre of Marine and Environmental Research\|EDEC - Endocrine Disruptors and Emergent Contamina	CIIMAR - Interdisciplinary Centre of Marine and Environmental Research	2	0.94044	0.94085	0.06098	0.06137	0.71934	0.72129	0.52142	0.53876	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	ribozero	bulk	unknown	unknown		Portugal	2022-06-24	Adult	Adult	Liver	Liver and Biliary System