{"database": "metadata", "table": "run_metadata", "rows": [[10231, "ERR6690609", "ERX6315378", "ERS7605274", "ERP131755", "PRJEB47482", "Transcriptional profiling of zebrafish embryos post 96 h exposure to two subsequent concentrations of 4 methyl 3 deoxy 1 9 12 trihydroxyestra 1 3 5107 tetraene 6 17 dione MDTETD and 12\u00df trihydroxy androsta 4 6 diene 3 17 dione THADD", "E-MTAB-10922", "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 sublethal concentrations of 4 methyl 3 deoxy 1 9 12 trihydroxyestra 1 3 5107 tetraene 6 17 dione MDTETD and 12\u00df trihydroxy androsta 4 6 diene 3 17 dione THADD. MDTETD and THADD both are degradation products of bile salts  which are steroid compounds from the digestive tracts of vertebrates  which enter the environment upon excretion  e.g. in manure.", "ENA FIRST PUBLIC:2021 10 11|ENA LAST UPDATE:2021 10 11", null, "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 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 350\u00b5l 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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2\u00b0C on a 12:12 h light/dark cycle. They were fed daily with TetraMin\u00ae 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\u00b0C 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. For the test solution preparation  first a high concentrated stock solution was prepared in water. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle. 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The test 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 \u201cgrowth protocol\u201d. 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\u00a9 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/\u00b5l 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\u00a9 Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit\u00a9 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\u00b0C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/\u00b5l total RNA at the sequencing facility \u201cNGS Services for Integrative Genomics\u201d at the University of G\u00f6ttingen 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.", "R1347", "SAMEA9926927", "Fraunhofer Attract Eco'n'OMICs Fraunhofer Institute for Molecular Biology and Applied Ecology IME", "ENA first public:2021 10 11|ENA last update:2021 10 11|External Id:SAMEA9926927|INSDC center alias:Fraunhofer Attract Eco'n'OMICs Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC center name:Fraunhofer Attract Eco'n'OMICs Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC first public:2021 10 11T16:25:38Z|INSDC last update:2021 10 11T16:25:38Z|INSDC status:public|Submitter Id:E MTAB 10922:R1347|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|individual:10|organism part:whole organism|sample name:E MTAB 10922:R1347|sex:mixed|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Transcriptional profiling of zebrafish embryos post 96 h exposure to 2 subsequent concentrations of 4 methyl 3 deoxy 1 9 12 trihydroxyestra 1 3 5107 tetraene 6 17 di1 MDTETD and 12\u03b2 trihydroxy androsta 4 6 diene 3 17 di1 THADD", "E MTAB 10922:R1347 s", "R1347 s", "Transcriptional profiling of zebrafish embryos post 96 h exposure to two subsequent concentrations of 4 methyl 3 deoxy 1 9 12 trihydroxyestra 1 3 5107 tetraene 6 17 dione MDTETD and 12\u03b2 trihydroxy androsta 4 6 diene 3 17 dione THADD", "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 350\u00b5l 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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2\u00b0C on a 12:12 h light/dark cycle. They were fed daily with TetraMin\u00ae 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\u00b0C 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.  For the test solution preparation  first a high concentrated stock solution was prepared in water. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle. 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The test 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 \u201cgrowth protocol\u201d.  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\u00a9 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/\u00b5l 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\u00a9 Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit\u00a9 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\u00b0C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/\u00b5l total RNA at the sequencing facility \u201cNGS Services for Integrative Genomics\u201d at the University of G\u00f6ttingen 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:4 methyl 3 deoxy 1 9 12 trihydroxyestra 1 3 5107 tetraene 6 17 di1|Experimental Factor: dose:1", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP131755", "Illumina HiSeq 4000 sequencing; Transcriptional profiling of zebrafish embryos post 96 h exposure to two subsequent concentrations of 4 methyl 3 deoxy 1 9 12 trihydroxyestra 1 3 5107 tetraene 6 17 dione MDTETD and 12\u03b2 trihydroxy androsta 4 6 diene 3 17 dione THADD", "ENA FIRST PUBLIC:2021 10 11|ENA LAST UPDATE:2021 10 11", "R1347.fastq.gz", "fastq", 2013684171.0, 39865705.0, "E MTAB 10922:R1347", "0:50.51 1:0", "A:513405372;C:495540575;G:469675681;T:534136644;N:925899", 50, 0, null, null, 513405372, 495540575, 469675681, 534136644, 925899, "ERX6315378", "ERS7605274", "ERA6149792", "Fraunhofer Attract Eco", "Fraunhofer Attract Eco", 1, 0.93259, null, 0.09724, null, 0.65269, null, 0.46848, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-10-11", "Larval", "Larval", "Whole Organism", "All anatomical structures"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["10231"], "units": {}, "query_ms": 12.609413010068238}