{"database": "metadata", "table": "run_metadata", "rows": [[42935, "SRR5833541", "SRX3010467", "SRS2360152", "SRP112616", "PRJNA394760", "Expression profiling of the retina of pde6c  a zebrafish model of retinal degeneration", "GSE101544", "Transcriptome Analysis", "Retinal degeneration often affects the whole retina even though the disease causing gene is specifically expressed in the light sensitive photoreceptors. These retinal defects can potentially be determined by gene expression profiling of the whole retina. In this study  we measured the gene expression profile of retinas microdissected from a zebrafish pde6cw59 pde6c mutant. Its retinas display not only photoreceptor degeneration but also issues in other cell types starting from 4 dpf dpf. To capture these initial changes  we subjected pde6c and wild type WT retinas at 5 dpf to RNA sequencing RNA Seq on the Illumina HiSeq 2000 platform. The sequencing analyses indicate that the RNA Seq dataset was of high quality. We also validated the RNA Seq results by Reverse Transcription Quantitative Polymerase Chain Reaction RT qPCR of seven phototransduction genes. We found that the fold changes of these genes measured by RT qPCR highly correlated to those measured by RNA Seq. Therefore  our RNA Seq dataset likely captures the molecular changes in the whole pde6c retina. This dataset will facilitate the characterization of the molecular defects in the pde6c retina at the initial stage of retinal degeneration Overall design: 3 samples of pde6c mutant and 3 samples of wild type animals are analyzed.", null, "pubmed:29231925", null, "wild type retina sample 1 WR1", "GSM2705944", null, "source name:retina|tissue:retina|genotype:wildtype|age:5 dpf", "wild type retina sample 1 WR1", "Generating genome index using STAR 2.5.3a using the Danio rerio.GRCz10.dna.toplevel.fa and Danio rerio.GRCz10.89.gtf from ensemble ftp Alignment using STAR 2.5.3a Read counting using featureCounts v1.5.2 Generating normalized expression measurements with cufflinks 2.2.1 Quantifying differential expression Genome build: Danio rerio.GRCz10.dna.toplevel.fa and Danio rerio.GRCz10.89.gtf from ensemble ftp For more analysis done  see https://gist.github.com/coralzhang/fc4e51609ff316486c1682feed6404a9/471afb15b7f7b230a38e4eedaadcf5f679412a07 Supplementary files format and content: text file with raw read counts or FPKM", "retina", null, "Total RNAs was extracted from the biological replicates by an optimized procedure that combined TRIzol Life Technologies  Grand Island  NY and RNeasy Micro kit Qiagen  Valencia  CA. The quality of the extracted total RNAs were evaluated by Bioanalyzer electrophoresis Agilent Technologies  Santa Clara  CA. Libraries were prepared according to Illumina's instructions.", null, "tissue:retina|genotype:wildtype|age:5 dpf", "GSM2705944", "GSM2705944: wild type retina sample 1 WR1; Danio rerio; RNA Seq", "GSM2705944", null, "1", "Total RNAs was extracted from the biological replicates by an optimized procedure that combined TRIzol Life Technologies  Grand Island  NY and RNeasy Micro kit Qiagen  Valencia  CA. The quality of the extracted total RNAs were evaluated by Bioanalyzer electrophoresis Agilent Technologies  Santa Clara  CA. Libraries were prepared according to Illumina's instructions.", "GEO Accession:GSM2705944", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP112616", null, null, "trim-WR1-R2.fastq.gz trim-WR1-R1.fastq.gz", "fastq fastq", 10078850313.0, 51108456.0, "GSM2705944 r1", "0:98.66 1:98.55", "A:2896366580;C:2023834885;G:2117794332;T:3040663699;N:190817", 98, 98, null, null, 2896366580, 2023834885, 2117794332, 3040663699, 190817, "SRX3010467", "SRS2360152", "SRA587806", "GEO", "Department of Statistics, University of Georgia", 2, 0.81956, 0.80495, 0.41661, 0.41171, 0.75773, 0.7599, 0.54429, 0.54605, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-07-17", "Larval", "Larval", "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": ["42935"], "units": {}, "query_ms": 9.200070002407301}