{"database": "metadata", "table": "run_metadata", "rows": [[42955, "SRR5855386", "SRX3024625", "SRS2373890", "SRP113259", "PRJNA395253", "Nr2f transcription factors promote the identity \u00a0of the vertebrate upper jaw", "GSE101719", "Transcriptome Analysis", "The jaws are complementary in form and function but develop asymmetrically  as the lower but not upper jaw bone forms around a prominent cartilage template. How such differences in skeletal composition are patterned is unclear. Here  we identify four Nuclear receptor 2f genes  nr2f1a  nr2f1b  nr2f2  and nr2f5  as enriched in zebrafish upper jaw precursors. Whereas loss of Nr2f genes results in expansion of upper jaw cartilage to resemble that of the lower jaw  Nr2f5 misexpression inhibits lower jaw cartilage formation. Genome wide analyses show that Nr2f genes prevent expansion of lower jaw associated gene expression into the upper jaw territory. Further  restriction of Nr2f expression by Endothelin1 signaling is critical for lower jaw development  as reducing Nr2f dosage fully restores lower jaw development in edn1 mutants. We propose that Nr2f genes drive jaw asymmetry by limiting early cartilage differentiation in the upper jaw to preserve more precursors for later osteogenesis. Overall design: Zebrafish pharyngeal arch cells expressing both fli1a:GFP and sox10:DsRed were isolated by FACS from 36 hpf nr2f2; nr2f5 double mutant embryos 2 replicates: n = 37 & 84; 18 858 & 30 655 cells  sox10:Gal4+ embryos n = 69; 86 517 cells  sox10:Gal4; UAS:Nr2f5 embryos n = 84; 56 866 cells.", null, "pubmed:29358039", null, "sox10:Gal4; UAS:Nr2f5  fli1a:GFP+ sox10:DsRed+", "GSM2713940", null, "tissue:pharyngeal arch cells|Stage:36 hpf|genotype/variation:sox10:Gal4; UAS:Nr2f5|identification:fin biopsies taken at 24 hpf genotyped for Gal4 and the UAS allele", "sox10:Gal4; UAS:Nr2f5  fli1a:GFP+ sox10:DsRed+", "Raw sequencing data in Fastq format were imported into Partek Flow\u00ae for alignment and quantification. In pre alignment QC  the reads from all samples were generally of high quality  with the average quality score for each sample exceeding 33. The reads were then trimmed at both ends based on the Phred quality score  with a minimum end quality level of 20 and a minimum acceptable read length of 25. Trimmed reads were aligned to the Danio rerio GRCz10 genome assembly Emsembl v80 using the TopHat 2 algorithm. Aligned reads were quantified with the Partek E/M algorithm using default parameters to generate TPM values. Genome build: GRCz10 Supplementary files format and content: The csv text files have the TPM values for each gene in each sample.", "pharyngeal arch cells", null, "GFP/DsRed double positive cells populations were collected into RLT lysis buffer Qiagen  and total RNA was immediately extracted using the RNeasy Micro kit Qiagen according to the manufacturer\u2019s instructions. The purified RNA was evaluated for quality and quantity  on a BioAnalyzer Pico RNA chip Agilent  Santa Clara  CA and then reverse transcribed into cDNA using the SMARTer kit Clontech  Mountain View  CA. cDNA amplification was adjusted based on the RNA input quantity  and the size and amount of generated cDNA was measured by BioAnalyzer. The samples were sonicated on a S2 ultrasonicator Covaris  Woburn  MA according to Clontech\u2019s recommendations. DNA libraries were assembled using the Kapa Hyper prep kit Kapa Biosystems  Wilmington  MA with NextFlex adapters Bioo Scientific  Austin  TX. Libraries were assessed by Bioanalyzer and quantified using qPCR Kapa Library Quantification kit. Sequencing was performed on a NextSeq 500 75 bp paired end reads Illumina  San Diego  CA. Library construction and sequencing were performed at the USC Molecular Genomics Core at the USC Norris Comprehensive Cancer Center.", "Embryos were maintained at 28.5 degrees C until 27 hpf  and then transferred to 22 degrees C to slow their development. Embryos were dissociated and sorted once they achieved morphological criteria corresponding to the standard 36 hpf stage", "Stage:36 hpf|genotype/variation:sox10:Gal4; UAS:Nr2f5|identification:fin biopsies taken at 24 hpf genotyped for Gal4 and the UAS allele", "GSM2713940", "GSM2713940: sox10:Gal4; UAS:Nr2f5  fli1a:GFP+ sox10:DsRed+; Danio rerio; RNA Seq", "GSM2713940", null, "1", "GFP/DsRed double positive cells populations were collected into RLT lysis buffer Qiagen  and total RNA was immediately extracted using the RNeasy Micro kit Qiagen according to the manufacturer\u2019s instructions. The purified RNA was evaluated for quality and quantity  on a BioAnalyzer Pico RNA chip Agilent  Santa Clara  CA and then reverse transcribed into cDNA using the SMARTer kit Clontech  Mountain View  CA. cDNA amplification was adjusted based on the RNA input quantity  and the size and amount of generated cDNA was measured by BioAnalyzer. The samples were sonicated on a S2 ultrasonicator Covaris  Woburn  MA according to Clontech\u2019s recommendations. DNA libraries were assembled using the Kapa Hyper prep kit Kapa Biosystems  Wilmington  MA with NextFlex adapters Bioo Scientific  Austin  TX. Libraries were assessed by Bioanalyzer and quantified using qPCR Kapa Library Quantification kit. Sequencing was performed on a NextSeq 500 75 bp paired end reads Illumina  San Diego  CA. Library construction and sequencing were performed at the USC Molecular Genomics Core at the USC Norris Comprehensive Cancer Center.", "GEO Accession:GSM2713940", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP113259", null, null, "sox10Gal4UASNr2f5_GC103_S4_R1_001.fastq.gz sox10Gal4UASNr2f5_GC103_S4_R2_001.fastq.gz", "fastq fastq", 1876943424.0, 12348312.0, "GSM2713940 r1", "0:76 1:76", "A:277876402;C:637297214;G:668302099;T:293137389;N:330320", 76, 76, null, null, 277876402, 637297214, 668302099, 293137389, 330320, "SRX3024625", "SRS2373890", "SRA589735", "GEO", "Crump Lab, Stem Cell Biology and Regenerative Medicine, University of Southern California", 2, 0.95473, 0.94996, 0.08065, 0.07608, 0.84177, 0.85127, 0.82239, 0.8689, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United States", "2017-07-20", "Pharyngula", "Embryo", "Pharyngeal Arch", "Multi-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": ["42955"], "units": {}, "query_ms": 11.097210997832008}