{"database": "metadata", "table": "run_metadata", "rows": [[59345, "SRR11862832", "SRX8413198", "SRS6725509", "SRP265073", "PRJNA635584", "Single cell analysis of juvenile Nkx3.2 mutant zebrafish craniofacial skeleton", "GSE151354", "Transcriptome Analysis", "The specification and maintenance of distinct zones of chondrocytes within growth plates and joints ensures proper skeletal development through maturity. Rare mutations in the transcription factor NKX3.2 underlie Spondylo megaepiphyseal metaphyseal dysplasia SMMD  which is characterized by skeletal defects including scoliosis  large epiphyses  wide growth plates  and supernumerary joints in the distal limbs. Embryonic knockdown of nkx3.2 function in zebrafish had revealed a requirement in jaw joint specification  yet embryonic lethality of nkx3.2 knockdown zebrafish and mouse Nkx3.2 mutants had precluded an analysis of post embryonic functions. Here we report adult viable nkx3.2 zebrafish mutants that display ectopic cartilage overgrowth in place of a missing jaw joint  as well as severe dysmorphologies of the facial skeleton  skullcap  and spine. We also isolate rare viable nkx3.2 knockdown animals that lack the jaw joint but fail to display ectopic cartilage growth and scoliosis  indicating post embryonic roles for Nkx3.2 beyond jaw joint specification. Consistently  we observe nkx3.2 expression in the subarticular zone of the adult jaw joint and in pre hypertrophic growth plate chondrocytes. Single cell RNA sequencing reveals an upregulation of stress induced pathways in mutants  including the prostaglandin D2 synthase ptgdsb.1 and the mTOR regulator sestrin1  which we confirm by in situ RNA analysis of the defective jaw joint region. Our data reveal a zebrafish model for the joint and spine defects of SMMD and point to post embryonic roles for Nkx3.2 in buffering the stress response and dampening proliferation in joint adjacent chondrocytes. Overall design: Single cell RNA sequencing of FACS isolated cartilages fli:GFP/sox10:DsRed+ from wildtype and nkx3.2 mutants", null, "pubmed:33462117", null, "nkx3.2 mutant cartilage", "GSM4575943", null, "tissue:cartilage|strain:Tgfli1a:EGFPy1; Tgsox10:DsRedel10|genotype:nkx3.2 el802/el802|age:22 dpf", "nkx3.2 mutant cartilage", "Reads were aligned to z11 genome using Cell Ranger 3. Genome build: z11 Supplementary files format and content: barcode  gene and matrix files from Cell Ranger alignment and trimming", "cartilage", null, "Cells were dissociated from 21dpf zebrafish and FACS sorted for fli1a:eGFP;sox10:DsRed double positive live cells. Single cells were processed through the 10X chromium controller Barcoded cDNA libraries were generated using 10X Genomics standard scRNAseq protocol using three prime Gene Expression v2 Library kit.", null, "strain:Tgfli1a:EGFPy1;Tgsox10:DsRedel10|genotype:nkx3.2 el802/el802|age:22 dpf", "GSM4575943", "GSM4575943: nkx3.2 mutant cartilage; Danio rerio; RNA Seq", "GSM4575943", null, "1", "Cells were dissociated from 21dpf zebrafish and FACS sorted for fli1a:eGFP;sox10:DsRed double positive live cells. Single cells were processed through the 10X chromium controller Barcoded cDNA libraries were generated using 10X Genomics standard scRNAseq protocol using three prime Gene Expression v2 Library kit.", "GEO Accession:GSM4575943", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP265073", null, null, "Nkx3-2-MUT-3_S7_R1_001.fastq.gz Nkx3-2-MUT-3_S7_R2_001.fastq.gz", "fastq fastq", 10287717159.0, 69768062.0, "GSM4575943 r3", "0:27 1:120.46", "A:2893541462;C:2211093397;G:2523388252;T:2627515640;N:32178408", 27, 120, null, null, 2893541462, 2211093397, 2523388252, 2627515640, 32178408, "SRX8413198", "SRS6725509", "SRA1080696", "GEO", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00413, 0.94417, 0.00109, 0.11868, 0.99338, 0.87274, 0.57301, 0.47692, 27, 121, "T", "B", "sc-like readlen", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-05-28", "Larval", "Larval", "Bone or Cartilage", "Skeletal Element"]], "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": ["59345"], "units": {}, "query_ms": 7.644950004760176}