run_metadata: 34218

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
34218	SRR31539743	SRX26906743	SRS23386329	SRP548139	PRJNA1191617	Sox10 is required for systemic initiation of bone mineralization	GSE283071	Transcriptome Analysis	Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos		pubmed:39791977		Whole body 45 hpf sox10 mutant embryos biol rep 3	GSM8655448		source name:whole body\|tissue:whole body\|genotype:sox10 / \|time:45 hpf\|geo loc name:missing\|collection date:missing	Whole body 45 hpf sox10 mutant embryos biol rep 3	The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf	whole body		RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina’s TruSeq® stranded mRNA library preparation kit.		tissue:whole body\|genotype:sox10 / \|time:45 hpf	GSM8655448	GSM8655448: Whole body 45 hpf sox10 mutant embryos biol rep 3; Danio rerio; RNA Seq	GSM8655448 r1	GSM8655448	1	RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq® stranded mRNA library preparation kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP548139			45 hpf_mut 3_R1.fastq.gz 45 hpf_mut 3_R2.fastq.gz	fastq fastq	14338321572.0	47477886.0	GSM8655448 r1	0:151 1:151	A:3808719246;C:3382555065;G:3212075099;T:3933758367;N:1213795	151	151			3808719246	3382555065	3212075099	3933758367	1213795	SRX26906743	SRS23386329			Barske Lab, Human Genetics, Cincinnati Children's Hospital												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	bulk	bulk		United States	2024-11-27	Multi-stage	Multi-stage	Trunk	Surface Structure