run_metadata: 9887

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
9887	ERR4140030	ERX4107343	ERS4556106	ERP121678	PRJEB38271	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups	E-MTAB-9056	Transcriptome Analysis	The aim of this sequencing experiment was to screen for ecotoxicogenomic fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. Triiodothyronine T3 CAS: 6893 02 3 was tested as a model substance for thyroidal inducing activity. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to two different sub lethal concentrations of T3 for xxx hours under semi static conditions. Each test comprised of a low exposure LE high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.	ENA FIRST PUBLIC:2020 09 30\|ENA LAST UPDATE:2020 05 12		Protocols: For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 hpf again overall survival hatch rates morphological malformations and physiological changes were recorded before RNA and protein extraction. T3 3 three prime 5 Triiodo L thyronine CAS number 6893 02 3 95% purity was purchased from Merck KGgA Darmstadt Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample about 40 50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope 15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals 6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals 6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel 740933.250 according to the manufacturer's protocol. RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent G2939BA using RNApico© chips Agilent 5067 1513. Samples were stored at 80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.	R167	SAMEA6828483	Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany	ENA FIRST PUBLIC:2020 07 31T04:03:57Z\|ENA LAST UPDATE:2020 05 12T15:52:19Z\|External Id:SAMEA6828483\|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology Applied Ecology and Bioresources Division Schmallenberg Germany Institute of Ecology Evolution and Diversity Goethe University Frankfurt Frankfurt am Main Germany\|INSDC first public:2020 07 31T04:03:57Z\|INSDC last update:2020 05 12T15:52:19Z\|INSDC status:public\|Submitter Id:E MTAB 9056:R167\|age:96\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval day 4\|genotype:wild type genotype\|growth condition:high exposure\|individual:pool of 10 fish\|organism part:whole organism\|sample name:E MTAB 9056:R167\|scientific name:Danio rerio\|sex:mixed\|strain:AB									Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyro9 T3 below acute toxicity levels against untreated control groups	E MTAB 9056:R167 s	R167 s	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups	For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 hpf again overall survival hatch rates morphological malformations and physiological changes were recorded before RNA and protein extraction. T3 3 three prime 5 Triiodo L thyronine CAS number 6893 02 3 95% purity was purchased from Merck KGgA Darmstadt Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample about 40 50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope 15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals 6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals 6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel 740933.250 according to the manufacturer's protocol. RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent G2939BA using RNApico© chips Agilent 5067 1513. Samples were stored at 80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.	Experimental Factor: compound:3 3 prime 5 triiodo L thyro9\|Experimental Factor: dose:0.000327	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 4000		ERP121678	Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups	ENA FIRST PUBLIC:2020 09 30\|ENA LAST UPDATE:2020 05 13	R167_sr.fastq.gz	fastq	1422756236.0	28174340.0	E MTAB 9056:R167	0:50.50 1:0	A:366380887;C:345824655;G:330108682;T:379312527;N:1129485	50	0			366380887	345824655	330108682	379312527	1129485	ERX4107343	ERS4556106	ERA2597448	Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany\|European Nucleotide Archive	Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany\|European Nucleotide Archive	1	0.93724		0.10506		0.65001		0.47599		51		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown		Germany	2020-05-12	Larval	Larval	Whole Organism	All anatomical structures