run_metadata: 33617

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
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.		pubmed:39345358;pubmed:40171762		cranial NCCs YM	GSM8464445		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’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˚C 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		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˚C 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		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP526857			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			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		United States	2024-08-16	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures