run_metadata: 70439

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
70439	SRR19846953	SRX15890622	SRS13579726	SRP383494	PRJNA852585	Control of cranial ectomesenchyme fate by Nr2f nuclear receptors	GSE206903	Transcriptome Analysis	Certain cranial neural crest cells are uniquely endowed with the ability to make skeletal cell types otherwise only derived from mesoderm. As these cells migrate into the pharyngeal arches they downregulate neural crest specifier genes and upregulate so called ectomesenchyme genes characteristic of skeletal progenitors. While both external and cell autonomous factors have been proposed as triggers of this transition the details remain obscure. Here we report the Nr2f nuclear receptors as novel intrinsic activators of the ectomesenchyme program: zebrafish nr2f5 and nr2f2; nr2f5 mutants show a marked delay in upregulation of ectomesenchyme genes such as dlx2a prrx1a/b sox9a twist1a and fli1a and in downregulation of the non ectomesenchyme specifier sox10. Depending on genotype mutants partially or fully recover likely via functional redundancy with other Nr2f genes. Loss of sox10 fully rescued skeletal development in nr2f5 single but not nr2f2; nr2f5 double mutants while the ectomesenchyme defect persisted in both. Sox10 perdurance thus antagonizes the recovery rather than causing the initial aberration. Unraveling the mechanics of Nr2f function will help solve the enduring puzzle of how cranial neural crest acquire skeletal potency. Overall design: Bulk RNA seq was performed on FACS purified zebrafish neural crest cells expressing sox10:DsRed from 20 hpf nr2f2[unknown]; nr2f5[mutant] embryos 2 replicates: n = 88 & 35 and wild type control embryos 2 replicates: n = 110 & 120.		pubmed:36367707		sox10:DsRed+ neural crest cells from 20 hpf nr2f2;nr2f5 mutant embryos biol rep 1	GSM6266709		tissue:sox10:DsRed+ neural crest cells\|cell type:sox10:DsRed+ neural crest cells\|genotype:nr2f2[unk]; nr2f5[mut]\|developmental stage:20 hpf	sox10:DsRed+ neural crest cells from 20 hpf nr2f2;nr2f5 mutant embryos biol rep 1	Illumina control software was used for base calling. Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: TPM Barske2022.txt: Tab delimited text file includes TPM values for each transcript.	sox10:DsRed+ neural crest cells		Total RNA was extracted from sorted cells using the RNeasy Micro kit Qiagen. The purified RNA samples were tested for quality and quantity on a BioAnalyzer and then reverse transcribed into cDNA using the SMARTer kit. cDNA amplification was adjusted based on the RNA input and the size and amount of cDNA was measured by BioAnalyzer. Sonication was performed on an S2 ultrasonicator. DNA libraries were created with the Kapa Hyper Prep kit and NextFlex adapters assessed by Bioanalyzer and quantified using the Kapa Library Quantification kit.		cell type:sox10:DsRed+ neural crest cells\|genotype:nr2f2[unk]; nr2f5[mut]\|developmental stage:20 hpf	GSM6266709	GSM6266709: sox10:DsRed+ neural crest cells from 20 hpf nr2f2;nr2f5 mutant embryos biol rep 1; Danio rerio; RNA Seq	GSM6266709 r1	GSM6266709	1	Total RNA was extracted from sorted cells using the RNeasy Micro kit Qiagen. The purified RNA samples were tested for quality and quantity on a BioAnalyzer and then reverse transcribed into cDNA using the SMARTer kit. cDNA amplification was adjusted based on the RNA input and the size and amount of cDNA was measured by BioAnalyzer. Sonication was performed on an S2 ultrasonicator. DNA libraries were created with the Kapa Hyper Prep kit and NextFlex adapters assessed by Bioanalyzer and quantified using the Kapa Library Quantification kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP383494		loader:fastq load.py	sox10DsRed-MUT1-S1-R1.fastq.gz sox10DsRed-MUT1-S1_R2_001.fastq.gz	fastq fastq	4812271816.0	31659683.0	GSM6266709 r1	0:76 1:76	A:1327161695;C:1091694077;G:1133722041;T:1259497189;N:196814	76	76			1327161695	1091694077	1133722041	1259497189	196814	SRX15890622	SRS13579726			Human Genetics, Cincinnati Children's Hospital Medical Center	2	0.90398	0.90573	0.03493	0.0351	0.76928	0.77429	0.46651	0.46743	76	76	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	bulk	bulk		United States	2022-06-24	Segmentation	Embryo	Brain	Nervous System