{"database": "metadata", "table": "run_metadata", "rows": [[68598, "SRR18049402", "SRX14201672", "SRS12022091", "SRP360102", "PRJNA807540", "Nrf2 dictates the neuronal survival and differentiation of embryonic zebrafish harboring compromised tRNA synthetase", "GSE196846", "Transcriptome Analysis", "tRNA synthetase deficiency leads to unfolded protein responses in neuronal disorders; however  its function in embryonic neurogenesis remains unclear. This study identified an aars1cq71/cq71 mutant zebrafish allele that showed increased neuronal apoptosis and compromised neurogenesis. aars1 transcripts were highly expressed in primary neural progenitor cells  and their aberration resulted in protein overloading and activated Perk. nfe2l2b  a paralog of mammalian Nfe2l2  which encodes Nrf2  is a pivotal executor of Perk signaling that regulates neuronal phenotypes in aars1cq71/cq71 mutants. Interference of nfe2l2b in nfe2l2b?1/?1 mutants did not affect global larval development. However  aars1cq71/cq71;nfe2l2b?1/?1 mutant embryos exhibited increased neuronal cell survival and neurogenesis compared with their aars1cq71/cq71 siblings. nfe2l2b was harnessed by Perk at two levels. Its transcript was regulated by Chop  an implementer of Perk. It was also phosphorylated by Perk. Both pathways synergistically assured the nuclear functions of nfe2l2b to control cell survival by targeting p53. Our study extends the understanding of tRNA synthetase in neurogenesis and implies that Nrf2 is a cue to mitigate neurodegenerative pathogenesis. Overall design: Single cell analyses of zebrafish midbrain by 10X Genomics", null, "pubmed:35929539", null, "midbrain aars1ENU / ", "GSM5903027", null, "source name:midbrain|developmental stage:2 dpf|tissue:midbrain|genotype:aars1ENU /  mutant", "midbrain aars1ENU / ", "The scRNA seq data were aligned to the zebrafish reference genome Danio rerio  GRCz11 by cellranger 5.0.0. The resulting matrix was inputted into Seurat v3 for quality control  filtration  dimensionality reduction  clustering analysis and differential expressed genes analysis Genome build: GRCz11 Supplementary files format and content: Cell Ranger output files barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz", "midbrain", null, "The 10x RNA seq libraries were constructed using Chromium single cell gene expression platform and Chromium Chromium Single Cell three prime Reagent v3 Kits according to the manufacture's protocol.", null, "developmental stage:2 dpf|tissue:midbrain|genotype:aars1ENU /  mutant", "GSM5903027", "GSM5903027: midbrain aars1ENU / ; Danio rerio; RNA Seq", "GSM5903027 r1", "GSM5903027", "1", "The 10x RNA seq libraries were constructed using Chromium single cell gene expression platform and Chromium Chromium Single Cell three prime Reagent v3 Kits according to the manufacture's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP360102", null, null, "R21001156-MUT-MUT-1_combined_R1.fastq.gz R21001156-MUT-MUT-1_combined_R2.fastq.gz", "fastq fastq", 27575933400.0, 91919778.0, "GSM5903027 r1", "0:150 1:150", "A:11721973614;C:4814188024;G:4730547766;T:6308524645;N:699351", 150, 150, null, null, 11721973614, 4814188024, 4730547766, 6308524645, 699351, "SRX14201672", "SRS12022091", "SRA1374754", "Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University", "Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University", 2, 0.0, 0.91413, 0.0, 0.20444, 1.0, 0.78555, null, 0.54347, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-02-16", "Hatching", "Embryo", "Brain", "Nervous System"]], "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": ["68598"], "units": {}, "query_ms": 13.492935999693145}