run_metadata: 72752

This data as json

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
72752	SRR23110584	SRX19061955	SRS16477630	SRP418118	PRJNA925134	BMP dependent cellular dynamics during cranial suture establishment in zebrafish	GSE223147	Transcriptome Analysis	Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics in vivo expression validation photoconversion based lineage tracing and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish a model for the coronal synostosis of Saethre Chotzen Syndrome reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture misregulated bone formation and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics		pubmed:39138165		9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg	GSM6940302		source name:calvaria\|cell type:various\|tissue:calvaria\|age:juvenile 9 11 mm\|strain:tubingen\|geo loc name:missing\|collection date:missing	9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg	Data analysis was performed with Seurat version 4.1.1 and datasets were filtered by nFeature RNA > 200 nFeature RNA < 2500 and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial “Integration and Label Transfer” from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files and rds files	calvaria		We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer’s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer’s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.	The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771.	cell type:various\|tissue:calvaria\|age:juvenile 9 11 mm\|strain:tubingen	GSM6940302	GSM6940302: 9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg; Danio rerio; RNA Seq	GSM6940302 r1	GSM6940302	1	We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM CaCl2 Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP418118			9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-1_S1_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-1_S1_L001_R2_001.fastq.gz	fastq fastq	11012858533.0	74696398.0	GSM6940302 r1	0:27 1:120.43	A:3253931864;C:2230032555;G:2516883171;T:3003935990;N:8074953	27	120			3253931864	2230032555	2516883171	3003935990	8074953	SRX19061955	SRS16477630	SRA1576283	Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles	Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles	2	0.00603	0.89151	0.00212	0.18091	0.98849	0.79634	0.5277	0.52269	27	120	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2023-01-18	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures