{"database": "metadata", "table": "run_metadata", "rows": [[39924, "SRR2392491", "SRX1240720", "SRS1067359", "SRP063659", "PRJNA295533", "Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face", "GSE72985", "Transcriptome Analysis", "Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear  yet the cellular mechanisms by which this occurs have remained unclear. Here  we show that Endothelin1 Edn1 signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest derived cells begin skeletal differentiation. In wild types  initial Jagged Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral intermediate zones of the pharyngeal arches. Reduced Jagged Notch signaling results in an expansion of pre cartilage condensations in the upper face  with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further  by studying new mutants for zebrafish prrx1a and prrx1b  we find that Prrx1 genes function in parallel to Jagged Notch signaling to restrict the formation of dorsal barx1+ pre cartilage condensations. Consistently  combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together  our work suggests that Edn1 works through parallel inhibition of Jagged Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face. Overall design: We performed RNAseq on FACS sorted neural crest derived pharyngeal arch cells fli1a:GFP; sox10:DsRed double positive from wild type embryos at 3 different stages 20  28  and 36 hpf and embryos with altered levels of Edn1 and Notch signaling edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants  dibenzazepine treated embryos  and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat shocked UAS:Edn1+ and hsp70I:Gal4+ transgenics and jag1b+/+ controls.", null, "pubmed:27058748", null, "hspEdn1 36hpf DP", "GSM1876259", null, "source name:Pharyngeal arches|tissue:Pharyngeal arches|developmental stage:embryo|age:36 hpf|genotype:hspGal4 ; UASEdn1|treatment:Heat shocked", "hspEdn1 36hpf DP", "Raw sequencing data in Fastq format was imported into the Partek Flow\u00ae interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality  with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values. Genome build: GRCz10 Supplementary files format and content: csv text files include RPKM values for each gene in each sample", "Pharyngeal arches", null, "GFP/DsRed double positive  double negative  and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer\u2019s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products  Wilmington  DE  USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent  Santa Clara  CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech  Mountain View  CA  according to the manufacturer\u2019s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris  Woburn  MA according to Clontech\u2019s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems  Wilmington  MA and NextFlex adapters Bioo Scientific  Austin  TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina  San Diego  CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.", null, "tissue:Pharyngeal arches|developmental stage:embryo|age:36 hpf|genotype:hspGal4 ; UASEdn1|treatment:Heat shocked", "GSM1876259", "GSM1876259: hspEdn1 36hpf DP; Danio rerio; RNA Seq", "GSM1876259", null, "1", "GFP/DsRed double positive  double negative  and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer\u2019s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products  Wilmington  DE  USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent  Santa Clara  CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech  Mountain View  CA  according to the manufacturer\u2019s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris  Woburn  MA according to Clontech\u2019s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems  Wilmington  MA and NextFlex adapters Bioo Scientific  Austin  TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina  San Diego  CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.", "GEO Accession:GSM1876259", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP063659", null, null, "GC-63_L000_R1_001.fastq.gz GC-63_L000_R2_001.fastq.gz", "fastq fastq", 8241464016.0, 54220158.0, "GSM1876259 r1", "0:76 1:76", "A:2338801834;C:1581411340;G:1652427014;T:2666281574;N:2542254", 76, 76, null, null, 2338801834, 1581411340, 1652427014, 2666281574, 2542254, "SRX1240720", "SRS1067359", "SRA297650", "GEO", "Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California", 2, 0.88843, 0.85822, 0.15095, 0.14812, 0.75978, 0.7751, 0.49125, 0.48482, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United States", "2015-09-14", "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": ["39924"], "units": {}, "query_ms": 7.543274001363898}