run_metadata: 59350

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59350	SRR11862829	SRX8413197	SRS6725508	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		pubmed:33462117		WT cartilage	GSM4575942		tissue:cartilage\|strain:Tgfli1a:EGFPy1; Tgsox10:DsRedel10\|genotype:WT\|age:21 dpf	WT 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		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.		strain:Tgfli1a:EGFPy1;Tgsox10:DsRedel10\|genotype:WT\|age:21 dpf	GSM4575942	GSM4575942: WT cartilage; Danio rerio; RNA Seq	GSM4575942		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:GSM4575942	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP265073			Nkx3-2-WT-4_S4_R1_001.fastq.gz Nkx3-2-WT-4_S4_R2_001.fastq.gz	fastq fastq	12792371587.0	86758219.0	GSM4575942 r4	0:27 1:120.45	A:3620447166;C:2712466949;G:3120686582;T:3299001093;N:39769797	27	120			3620447166	2712466949	3120686582	3299001093	39769797	SRX8413197	SRS6725508	SRA1080696	GEO	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	2	0.00534	0.94032	0.00143	0.13395	0.99159	0.87338	0.53475	0.45536	27	120	T	B	sc-like readlen	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2020-05-28	Larval	Larval	Bone or Cartilage	Skeletal Element