{"database": "metadata", "table": "run_metadata", "rows": [[39800, "SRR2145843", "SRX1133833", "SRS1023799", "SRP062048", "PRJNA291981", "Yap and Taz regulate retinal pigment epithelial cell fate", "GSE71681", "Transcriptome Analysis", "The optic vesicle comprises a pool of bi potential progenitor cells from  which the retinal pigment epithelium RPE and neural retina fates  segregate during ocular morphogenesis. Several transcription factors and signaling pathways have been shown to be important for RPE  maintenance and differentiation  but an understanding of the initial  fate specification and determination of this ocular cell type is lacking.  We show that Yap/Taz Tead activity is necessary and sufficient for  optic vesicle progenitors to adopt RPE identity in zebrafish. A Teadresponsive  transgene is expressed within the domain of the optic cup  from which RPE arises  and Yap immunoreactivity localizes to the  nuclei of prospective RPE cells. yap yap1 mutants lack a subset of  RPE cells and/or exhibit coloboma. Loss of RPE in yap mutants is  exacerbated in combination with taz wwtr1 mutant alleles such that   when Yap and Taz are both absent  optic vesicle progenitor cells  completely lose their ability to form RPE. The mechanism of Yap dependent  RPE cell type determination is reliant on both nuclear  localization of Yap and interaction with a Tead co factor. In contrast to  loss of Yap and Taz  overexpression of either protein within optic  vesicle progenitors leads to ectopic pigmentation in a dosagedependent  manner. Overall  this study identifies Yap and Taz as key  early regulators of RPE genesis and provides a mechanistic  framework for understanding the congenital ocular defects of  Sveinsson\u2019s chorioretinal atrophy and congenital retinal coloboma. Overall design: 60 pooled eyes from 36 hpf wild type or vsx2:Gal4/dsRed:14xUAS:YapS87A embryos were pooled for one sample.  Three wild type and three vsx2:Gal4/dsRed:14xUAS:YapS87A pools were analyzed for RNA.", null, "pubmed:26209646", null, "WT rep1", "GSM1844487", null, "source name:whole eye|developmental stage:36 hpf|tissue:whole eye|genotype:vsx2:Gal4 sibling control", "WT rep1", "RNA quality was determined using an Agilent BioAnalyzer.  50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University  Nashville  TN. Sequencing results were analyzed by VANGARD Vanderbilt University  Nashville  TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66. 30M reads per sample Genome build: Danio rerio EnsEMBL release 66. Supplementary files format and content: tab delimited txt include fkpm for each sample.", "whole eye", null, "Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al.  2012 except that RNA was eluted in a 50\u03bcl final volume. RNA quality was determined using an Agilent BioAnalyzer.  50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University  Nashville  TN. Sequencing results were analyzed by VANGARD Vanderbilt University  Nashville  TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66.", null, "developmental stage:36 hpf|tissue:whole eye|genotype:vsx2:Gal4 sibling control", "GSM1844487", "GSM1844487: WT rep1; Danio rerio; RNA Seq", "GSM1844487", null, "1", "Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al.  2012 except that RNA was eluted in a 50\u03bcl final volume. RNA quality was determined using an Agilent BioAnalyzer.  50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University  Nashville  TN. Sequencing results were analyzed by VANGARD Vanderbilt University  Nashville  TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66.", "GEO Accession:GSM1844487", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP062048", null, null, "WT_1_sequence.txt.gz", "fastq", 1666445961.0, 32675411.0, "GSM1844487 r1", "0:51", "A:421437796;C:380026405;G:379400332;T:465027467;N:20553961", 51, null, null, null, 421437796, 380026405, 379400332, 465027467, 20553961, "SRX1133833", "SRS1023799", "SRA282186", "GEO", "Medical College of Wisconsin", 1, 0.91935, null, 0.0764, null, 0.73083, null, 0.47263, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-08-05", "Pharyngula", "Embryo", "Eye", "Sensory 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": ["39800"], "units": {}, "query_ms": 11.645175000012387}