run_metadata: 10076

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
10076	ERR4910327	ERX4777150	ERS5435097	ERP125509	PRJEB41694	mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups	E-MTAB-9853	Transcriptome Analysis	The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of the heavily used organophosphate insecticide Chlorpyrifos CAS 2921 88 2. The Insecticide Resistance Action Committee IRAC classified Chlorpyrifos post its mode of action MoA in the target organism as an acetylcholinesterase AChE inhibitor Group 1B. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects based on similarly altered transcriptomic and proteomic profiles. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE 0.75 mg/L high exposure HE 3 mg/L 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 data normalization and differential gene expression analysis with DESeq2.	ENA FIRST PUBLIC:2021 10 15\|ENA LAST UPDATE:2021 10 15		Protocols: Catalogue no. 2921 88 2. 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 collected 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 then 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. Chlorpyrifos CAS 2921 88 2 PESTANAL® analytical standard was purchased from Merck KGgA Darmstadt Germany. For the test solution preparation first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. 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 45 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 >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent G2939BA using the Agilent RNA 6000 Nano Kit© Agilent 5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. 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. Libraries were validated using a Fragment Analyzer system Agilent Santa Clara USA before sequencing.	R836	SAMEA7678115	Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany	ENA first public:2021 10 15\|ENA last update:2021 10 15\|External Id:SAMEA7678115\|INSDC center alias:Fraunhofer Attract Eco'n'OMICs Fraunhofer Institute for Molecular Biology and Applied Ecology Schmallenberg Germany Evolutionary Ecology and Environmental Toxicology Faculty Biological Sciences Goethe University Frankfurt Frankfurt Germany\|INSDC center name:Fraunhofer Attract Eco'n'OMICs Fraunhofer Institute for Molecular Biology and Applied Ecology Schmallenberg Germany Evolutionary Ecology and Environmental Toxicology Faculty Biological Sciences Goethe University Frankfurt Frankfurt Germany\|INSDC first public:2021 10 15T00:15:29Z\|INSDC last update:2021 10 15T00:15:29Z\|INSDC status:public\|Submitter Id:E MTAB 9853:R836\|age:96\|batch:T2\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval day 4\|extraction date:09.12.2019\|genotype:wild type genotype\|organism part:whole organism\|rin:9 8\|sample name:E MTAB 9853:R836\|sex:mixed\|strain:AB									Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups	E MTAB 9853:R836 s	R836 s	mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups	Catalogue no. 2921 88 2. 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 collected 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 then 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. Chlorpyrifos CAS 2921 88 2 PESTANAL® analytical standard was purchased from Merck KGgA Darmstadt Germany. For the test solution preparation first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. 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 45 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 >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent G2939BA using the Agilent RNA 6000 Nano Kit© Agilent 5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. 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. Libraries were validated using a Fragment Analyzer system Agilent Santa Clara USA before sequencing.	Experimental Factor: compound:chlorpyrifos\|Experimental Factor: dose:0.00075\|Experimental Factor: growth condition:low exposure	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 4000		ERP125509	Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups	ENA FIRST PUBLIC:2021 10 15\|ENA LAST UPDATE:2021 10 15	R836.fastq.gz	fastq	1816994468.0	35959155.0	E MTAB 9853:R836	0:50.53 1:0	A:465931946;C:444466278;G:425419784;T:479276121;N:1900339	50	0			465931946	444466278	425419784	479276121	1900339	ERX4777150	ERS5435097	ERA3184347	Fraunhofer Attract Eco	Fraunhofer Attract Eco	1	0.92973		0.10412		0.66425		0.4798		51		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown		Germany	2021-10-15	Larval	Larval	Whole Organism	All anatomical structures