{"database": "metadata", "table": "run_metadata", "rows": [[60461, "SRR12287397", "SRX8790730", "SRS7059122", "SRP273065", "PRJNA647840", "Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish", "GSE154895", "Transcriptome Analysis", "We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.", null, "pubmed:33634099", null, "36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 2", "GSM4681957", null, "source name:36hpf zebrafish eyes|treatment:DMSO control|age:36hpf|tissue:eyes", "36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 2", "Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681", "36hpf zebrafish eyes", null, "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", null, "treatment:DMSO control|age:36hpf|tissue:eyes", "GSM4681957", "GSM4681957: 36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 2; Danio rerio; RNA Seq", "GSM4681957", null, "1", "Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads", "GEO Accession:GSM4681957", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP273065", null, null, "DMSO_2.fq", "fastq", 710470350.0, 14209407.0, "GSM4681957 r1", "0:50", "A:180578463;C:165554366;G:164357951;T:199952943;N:26627", 50, null, null, null, 180578463, 165554366, 164357951, 199952943, 26627, "SRX8790730", "SRS7059122", "SRA1102335", "GEO", "Clark, Ophthalmology and Visual Sciences, Washington University", 1, 0.92993, null, 0.12326, null, 0.73316, null, 0.50795, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2020-07-22", "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": ["60461"], "units": {}, "query_ms": 11.501068000143277}