{"database": "metadata", "table": "run_metadata", "rows": [[41892, "SRR5320517", "SRX2619922", "SRS2029885", "SRP101558", "PRJNA378498", "Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development", "GSE95812", "Transcriptome Analysis", "Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development  how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes  with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes  which uncovered antagonistic functions of two Edn1 targets  follistatin a fsta and emx2  in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed  and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 /  2 replicates  jag1b /   jag1b+/+ control  hsp70I:Gal4; UAS:Edn1  hsp70I:Gal4; UAS:Nicd  and hsp70I:Gal4 control.", null, "pubmed:28705894", null, "WT hand2 sox10 2", "GSM2526396", null, "tissue:Pharyngeal arches|developmental stage:36 hpf|genotype:WT|treatment:N1", "WT hand2 sox10 2", "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 TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM 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. 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 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, "developmental stage:36 hpf|genotype:WT|treatment:N1", "GSM2526396", "GSM2526396: WT hand2 sox10 2; Danio rerio; RNA Seq", "GSM2526396", 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. 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 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:GSM2526396", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP101558", null, null, "GC-99_L000_R1_001.fastq.gz GC-99_L000_R2_001.fastq.gz", "fastq fastq", 5678291208.0, 37357179.0, "GSM2526396 r1", "0:76 1:76", "A:1598205402;C:1219592650;G:1242882414;T:1613938733;N:3672009", 76, 76, null, null, 1598205402, 1219592650, 1242882414, 1613938733, 3672009, "SRX2619922", "SRS2029885", "SRA543392", "GEO", "Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California", 2, 0.95476, 0.95009, 0.12808, 0.12848, 0.74602, 0.76008, 0.45997, 0.46118, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United States", "2017-03-08", "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": ["41892"], "units": {}, "query_ms": 13.208150994614698}