{"database": "metadata", "table": "run_metadata", "rows": [[42532, "SRR5687189", "SRX2921954", "SRS2287813", "SRP109268", "PRJNA390613", "Transcripts within Rod Photoreceptors of the Zebrafish Retina", "GSE100062", "Transcriptome Analysis", "Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish  an important animal model for vision science. Methods: Zebrafish rods  and non rod retinal cells of the XOPS:eGFP transgenic line  were separated by cell dissociation and fluorescence activated cell sorting FACS  followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas  and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01  597 transcripts were upregulated in rods vs. non rod retinal cells  and 1032 were downregulated. 13 324 total transcripts were detected in rods  including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas  and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish  which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods  4 GFP  FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.", null, "pubmed:29422031", null, "GFPpos1", "GSM2670720", null, "tissue:Zebrafish retinal rod photoreceptors|cell type:rod photoreceptors|genotype/variation:XOPS:eGFP|cell type:GFP+; FACS sorted rods", "GFPpos1", "Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation", "Zebrafish retinal rod photoreceptors", "Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37\u00b0C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 \u00b5L phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP  retinal cells were sorted using a FACSAria flow cytometer  using the 488 nm laser and FITC fluorescence filter  and the 70 \u00b5m nozzle. Some cells were collected for fluorescence microscopy  or for post sort FACS analysis. For RNA seq or qPCR  GFP+ and GFP  cells were collected separately in a final volume of 100 \u00b5L of the FACS sheath fluid  and RNA was immediately extracted.", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol  quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0  and experimental design was such that GFP+ cells  or GFP  cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample  and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN  and sequencing performed on an Illumina San Diego  CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample  and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating  monitored system water  housed and propagated according to The Zebrafish Book Westerfield.", "cell type:rod photoreceptors|genotype/variation:XOPS:eGFP|cell type:GFP+; FACS sorted rods", "GSM2670720", "GSM2670720: GFPpos1; Danio rerio; RNA Seq", "GSM2670720", null, "1", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol  quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0  and experimental design was such that GFP+ cells  or GFP  cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample  and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN  and sequencing performed on an Illumina San Diego  CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample  and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "GEO Accession:GSM2670720", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP109268", null, null, "GFPpositive1_TGACCA_L001_R1_001.fastq.gz GFPpositive1_TGACCA_L001_R2_001.fastq.gz", "fastq fastq", 2150958270.0, 3480515.0, "GSM2670720 r1", "0:309 1:309", "A:654306402;C:442036224;G:437971529;T:616642033;N:2082", 309, 309, null, null, 654306402, 442036224, 437971529, 616642033, 2082, "SRX2921954", "SRS2287813", "SRA574861", "GEO", "Biological Sciences, University of Idaho", 2, 0.65859, 0.66368, 0.295, 0.31011, 0.79324, 0.81454, 0.55325, 0.5597, 309, 309, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-06-15", "Undetermined", "Multi-stage", "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": ["42532"], "units": {}, "query_ms": 9.265700005926192}