{"database": "metadata", "table": "run_metadata", "rows": [[70437, "SRR19846951", "SRX15890624", "SRS13579728", "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.", null, "pubmed:36367707", null, "sox10:DsRed+ neural crest cells from 20 hpf wild type embryos   biol rep 1", "GSM6266711", null, "tissue:sox10:DsRed+ neural crest cells|cell type:sox10:DsRed+ neural crest cells|genotype:wild type|developmental stage:20 hpf", "sox10:DsRed+ neural crest cells from 20 hpf wild type 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", null, "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.", null, "cell type:sox10:DsRed+ neural crest cells|genotype:wild type|developmental stage:20 hpf", "GSM6266711", "GSM6266711: sox10:DsRed+ neural crest cells from 20 hpf wild type embryos   biol rep 1; Danio rerio; RNA Seq", "GSM6266711 r1", "GSM6266711", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP383494", null, "loader:fastq load.py", "sox10DsRed-CON1-S5-R1.fastq.gz sox10DsRed-CON1-S5-R2.fastq.gz", "fastq fastq", 4875797328.0, 32077614.0, "GSM6266711 r1", "0:76 1:76", "A:1340486054;C:1109815504;G:1153492417;T:1271807986;N:195367", 76, 76, null, null, 1340486054, 1109815504, 1153492417, 1271807986, 195367, "SRX15890624", "SRS13579728", null, null, "Human Genetics, Cincinnati Children's Hospital Medical Center", 2, 0.92525, 0.92846, 0.04508, 0.04513, 0.75789, 0.76217, 0.47713, 0.47624, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "United States", "2022-06-24", "Segmentation", "Embryo", "Brain", "Nervous System"]], "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": ["70437"], "units": {}, "query_ms": 11.55829499475658}