{"database": "metadata", "table": "run_metadata", "rows": [[53284, "SRR11869570", "SRX8419560", "SRS6731104", "SRP216221", "PRJNA556409", "RNA seq of mondoa zebrafish mutants", "GSE134778", "Transcriptome Analysis", "The glucose sensing Mondo pathway regulates expression of metabolic genes in mammals. Here  we have revealed an unexpected role of this pathway in vertebrate embryonic development. We characterized Mondo pathway function in the zebrafish and showed that knock down of mondoa impaired the early morphogenetic movement of epib in zebrafish embryos. Expression of nsdhl   an enzyme of cholesterol and pregnenolone synthesis  was strongly reduced in these embryos. Loss of Nsdhl function likewise impaired epib and led to microtubule cytoskeleton defects in the embryo  similar to MondoA loss of function. both epib and microtubule cytoskeleton defects were partially restored by pregnenolone treatment. Gene disruption of mondoa perturbed epib with only partial penetrance  likely due to compensatory changes in the expression of cholesterol/steroid metabolism genes. Collectively  our results show a novel role for MondoA in the regulation of early vertebrate development  connecting glucose  cholesterol and steroid hormone metabolism with early embryonic cell movements. Overall design: RNA seq  in mondoa zebrafish mutants", "parent bioproject:PRJNA603464", "pubmed:32969791", null, "mondoa s 1", "GSM4577397", null, "source name:total RNA|tissue:embryo|genotype:MZmondoA mutant allel: ka405  ZFIN ID: ZDB ALT 180628 2|phenotype:affected epib|Stage:5 hpf", "mondoa s 1", "Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14. Sequences were aligned to the full reference genome index build with Ensembl annotation to improve accuracy on splices junctions using STAR 2.4.0i A custom Perl script was used to quantify uniquely mapped reads. For each Ensembl gene  all exons of the respective annotated protein coding transcripts were considered. Genome build: zv10 Supplementary files format and content: counts exon.txt  exonic counts for each indicated gene and  sample", "total RNA", null, "Embryos were sampled in liquid nitrogen and stored at  80\u00b0C until further processing. RNA was extracted with TRIzol Life Technologies following the manufacturer\u2019s instructions with minor modifications: 30 larvae were sampled in a volume of 1.5 ml TRIzol reagent. Samples were kept at least overnight at  80\u00b0C. In order to disrupt the cell membranes  the samples were passed four times through a syringe with a diameter of 0.45 mm. Total RNA Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat kit and TruSeq RNA Single Indexes kits A and B Illumina  San Diego  CA  according to manufacturer's instructions. Briefly  cytoplasmic and mitochondrial ribosomal RNA rRNA was removed using biotinylated  target specific oligos combined with Ribo Zero rRNA removal beads. Following purification  the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase  Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the three prime ends of the blunt DNA fragments using a Klenow fragment three prime to five primeexo minus enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification 30 sec at 98oC; [10 sec at 98oC  30 sec at 60oC  30 sec at 72oC] x 12 cycles; 5 min at 72oC. Surplus PCR primers were further removed by purification using AMPure XP beads Beckman Coulter  Villepinte  France and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.", null, "tissue:embryo|genotype:MZmondoA mutant allel: ka405  ZFIN ID: ZDB ALT 180628 2|phenotype:affected epib|Stage:5 hpf", "GSM4577397", "GSM4577397: D mondoa s 1; Danio rerio; RNA Seq", "GSM4577397", null, "1", "Embryos were sampled in liquid nitrogen and stored at  80\u00b0C until further processing. RNA was extracted with TRIzol Life Technologies following the manufacturer's instructions with minor modifications: 30 larvae were sampled in a volume of 1.5 ml TRIzol reagent. Samples were kept at least overnight at  80\u00b0C. In order to disrupt the cell membranes  the samples were passed four times through a syringe with a diameter of 0.45 mm. Total RNA Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat kit and TruSeq RNA Single Indexes kits A and B Illumina  San Diego  CA  according to manufacturer's instructions. Briefly  cytoplasmic and mitochondrial ribosomal RNA rRNA was removed using biotinylated  target specific oligos combined with Ribo Zero rRNA removal beads. Following purification  the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase  Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the three prime ends of the blunt DNA fragments using a Klenow fragment three prime to five primeexo minus enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification 30 sec at 98oC; [10 sec at 98oC  30 sec at 60oC  30 sec at 72oC] x 12 cycles; 5 min at 72oC. Surplus PCR primers were further removed by purification using AMPure XP beads Beckman Coulter  Villepinte  France and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.", "GEO Accession:GSM4577397", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP216221", null, null, "VRGN23_S2.R1.fastq VRGN23_S2.R2.fastq", "fastq fastq", 6872302500.0, 68723025.0, "GSM4577397 r1", "0:50 1:50", "A:1873323778;C:1557060731;G:1546029001;T:1894832528;N:1056462", 50, 50, null, null, 1873323778, 1557060731, 1546029001, 1894832528, 1056462, "SRX8419560", "SRS6731104", "SRA925866", "GEO", "Naef Lab, SV, EPFL", 2, 0.89976, 0.90345, 0.27147, 0.27139, 0.74957, 0.76187, 0.50583, 0.51168, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "3prime", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "Switzerland", "2020-05-28", "Blastula", "Embryo", "Embryo Imprecise", "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": ["53284"], "units": {}, "query_ms": 9.192601995891891}