{"database": "metadata", "table": "run_metadata", "rows": [[33617, "SRR30274406", "SRX25735496", "SRS22375280", "SRP526857", "PRJNA1148965", "The Gq/11 family of G alpha subunits is necessary and sufficient for lower jaw development", "GSE275013", "Transcriptome Analysis", "Development of the vertebrate jaw apparatus depends on highly conserved signaling pathways. Patterning of the lower jaw is driven by Endothelin receptor type A Ednra and secreted ligand Endothelin 1 Edn1. The Ednra signaling pathway establishes the identity of lower jaw progenitors by regulating expression of numerous patterning genes  but the intracellular signaling mechanisms linking receptor activation to gene regulation remains poorly understood. As a first step towards addressing this question  we examined the function of the Gq/11 family of Ga subunits in zebrafish using pharmacological and genetic ablation of Gq/11 activity and transgenic induction of a constitutively active Gq protein in edn1 /  embryos. Loss of Gq/11 activity fully recapitulated the edn1 /  phenotype  with genes encoding for G11 being most essential. Furthermore  inducing Gq activity in edn1 /  embryos not only restored Ednra dependent jaw structures and gene expression signatures but also caused homeosis of the upper jaw structures into a lower jaw like structure. These results indicate that Gq/11 is necessary and sufficient to mediate the lower jaw patterning mechanism for Ednra. Overall design: Zebrafish embryos were first treated with YM 254890 or DMSO control between 16   36 hpf. Then  cranial neural crest cells NCCs labeled with two transgenes  sox10:mRFP and fli1a:EGFP  were isolated at 36 hpf by fluorescence activated cell sorting FACS. Isolated cranial NCCs were then analyzed by scRNA seq.", null, "pubmed:39345358;pubmed:40171762", null, "cranial NCCs  YM", "GSM8464445", null, "source name:Facial mesenchyme|tissue:Facial mesenchyme|age:36 hpf|cell type:Cranial neural crest cells|genotype:Tgsox10:mRFP;Tgfli1a:EGFP|treatment:YM|geo loc name:missing|collection date:missing", "cranial NCCs  YM", "Sequence reads were  converted to count matrices with Cell Ranger v5.0.1 10X Genomics. Subsequent analyses of count matrices were performed with Seurat version 4.3.0 in R studio. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Facial mesenchyme", "Dechorionated zebrafish embryos were treated with 100uM YM 254890 or 10%v/v DMSO vehicle control from 16 hpf 36 hpf", "Cranial neural crest cells were isolated from zebrafish embryos using a fli1a:EGFP and sox10:mRFP double labeling technique as described in Barske et al.  2016; Askary et al.  2017; Mitchell et al.  2021 with some modifications. In brief  140 double positive embryos were dechorionated at 14 hpf with 2 mg/ml Pronase Roche  cat. 10165921001  then 70 embryos were treated with 100 uM YM 254890 Adipogen  cat. AG CN2 0509 M001 or DMSO control from 16 hpf 36 hpf. At 36 hpf  10 embryos from each condition were set aside for skeletal preparations at 6 dpf. For the remaining embryos  the heads were severed  pooled  and deyolked by gentle pipetting in Ca2+ free Ringer\u2019s solution 116 mM NaCl  2.9 mM KCl  5 mM HEPES  pH 7.0. The embryos were then dissociated into single cells with mechanical agitation and enzymatic digestion for 15 minutes at 4\u02daC with cold activated protease from Bacillus licheniformis Sigma Aldrich  cat. P5380 in dissociation buffer 10 mg/ml Bacillus licheniformis protease  125 U/ml DNAse  2.5 mM EDTA  PBS  followed by enzyme neutralization with stop solution 30% fetal bovine serum  0.8 mM CaCl2  in PBS. Cells were then centrifuged 400xg  resuspended in cell suspension buffer [1% fetal bovine serum  0.8 mM CaCl2  Leibovitz\u2019s L 15 Medium Gibco  cat. 21083 027]  filtered through a 70 uM strainer PluriSelect  cat. 43 10040 40  centrifuged 400xg again and resuspended in sorting buffer 1% fetal bovine serum  1 mM EDTA  25 mM HEPES. EGFP and mRFP double positive cells were then purified with fluorescence activated cell sorting using MoFlo XDP100 Beckman Coulter. A total of 72 000 and 86 000 double positive cells were purified for DMSO and YM treated samples  respectively. Cells were once again centrifuged 400xg and resuspended in cell suspension buffer. post confirming cell viability with trypan blue Gibco  cat. 15250 061  8000 cells for each condition were submitted to the Genomics and Microarray Core CU AMC for single cell RNA sequencing. Library was prepared according to manufacturer's protocol three prime NextGEM V3.1  10X Genomics", null, "tissue:Facial mesenchyme|age:36 hpf|cell type:Cranial neural crest cells|genotype:Tgsox10:mRFP;Tgfli1a:EGFP|treatment:YM", "GSM8464445", "GSM8464445: cranial NCCs  YM; Danio rerio; RNA Seq", "GSM8464445 r1", "GSM8464445", "1", "Cranial neural crest cells were isolated from zebrafish embryos using a fli1a:EGFP and sox10:mRFP double labeling technique as described in Barske et al.  2016; Askary et al.  2017; Mitchell et al.  2021 with some modifications. In brief  140 double positive embryos were dechorionated at 14 hpf with 2 mg/ml Pronase Roche  cat. 10165921001  then 70 embryos were treated with 100 uM YM 254890 Adipogen  cat. AG CN2 0509 M001 or DMSO control from 16 hpf 36 hpf. At 36 hpf  10 embryos from each condition were set aside for skeletal preparations at 6 dpf. For the remaining embryos  the heads were severed  pooled  and deyolked by gentle pipetting in Ca2+ free Ringer's solution 116 mM NaCl  2.9 mM KCl  5 mM HEPES  pH 7.0. The embryos were then dissociated into single cells with mechanical agitation and enzymatic digestion for 15 minutes at 4\u02daC with cold activated protease from Bacillus licheniformis Sigma Aldrich  cat. P5380 in dissociation buffer 10 mg/ml Bacillus licheniformis protease  125 U/ml DNAse  2.5 mM EDTA  PBS  followed by enzyme neutralization with stop solution 30% fetal bovine serum  0.8 mM CaCl2  in PBS. Cells were then centrifuged 400xg  resuspended in cell suspension buffer [1% fetal bovine serum  0.8 mM CaCl2  Leibovitz's L 15 Medium Gibco  cat. 21083 027]  filtered through a 70 uM strainer PluriSelect  cat. 43 10040 40  centrifuged 400xg again and resuspended in sorting buffer 1% fetal bovine serum  1 mM EDTA  25 mM HEPES. EGFP and mRFP double positive cells were then purified with fluorescence activated cell sorting using MoFlo XDP100 Beckman Coulter. A total of 72 000 and 86 000 double positive cells were purified for DMSO and YM treated samples  respectively. Cells were once again centrifuged 400xg and resuspended in cell suspension buffer. post confirming cell viability with trypan blue Gibco  cat. 15250 061  8000 cells for each condition were submitted to the Genomics and Microarray Core CU AMC for single cell RNA sequencing. Library was prepared according to manufacturer's protocol three prime NextGEM V3.1  10X Genomics", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP526857", null, null, "YM-treated_S9_L001_R2_001.fastq.gz YM-treated_S9_L001_R1_001.fastq.gz", "fastq fastq", 133560759038.0, 442254169.0, "GSM8464445 r1", "0:151 1:151", "A:49523643076;C:22144256343;G:30982866215;T:30893839980;N:16153424", 151, 151, null, null, 49523643076, 22144256343, 30982866215, 30893839980, 16153424, "SRX25735496", "SRS22375280", "SRA1949431", "David Clouthier, Craniofacial Biology, University of Colorado Anschutz Medical Campus", "David Clouthier, Craniofacial Biology, University of Colorado Anschutz Medical Campus", 2, 0.00156, 0.3917, 0.00133, 0.06002, 0.99997, 0.9529, 0.0, 0.52259, 151, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-16", "Pharyngula", "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": ["33617"], "units": {}, "query_ms": 11.017440001523937}