run_metadata: 39795
This data as json
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 39795 | SRR2145848 | SRX1133838 | SRS1023794 | 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’s 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. | pubmed:26209646 | YapS87A rep3 | GSM1844492 | source name:whole eye|developmental stage:36 hpf|tissue:whole eye|genotype:vsx2:Gal4/dsRed:14xUAS:YapS87A | YapS87A rep3 | 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 | 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 50μl 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. | developmental stage:36 hpf|tissue:whole eye|genotype:vsx2:Gal4/dsRed:14xUAS:YapS87A | GSM1844492 | GSM1844492: YapS87A rep3; Danio rerio; RNA Seq | GSM1844492 | 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 50μl 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:GSM1844492 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP062048 | YapS87A_3_sequence.txt.gz | fastq | 1680502581.0 | 32951031.0 | GSM1844492 r1 | 0:51 | A:431882743;C:376993099;G:378520286;T:464147117;N:28959336 | 51 | 431882743 | 376993099 | 378520286 | 464147117 | 28959336 | SRX1133838 | SRS1023794 | SRA282186 | GEO | Medical College of Wisconsin | 1 | 0.9063 | 0.08492 | 0.73279 | 0.45445 | 51 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United States | 2015-08-05 | Pharyngula | Embryo | Eye | Sensory System |