run_metadata: 42527

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
42527	SRR5687194	SRX2921959	SRS2287818	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.		pubmed:29422031		GFPneg2	GSM2670725		tissue:Zebrafish retinal cells not rods\|cell type:non rod retinal cells\|genotype/variation:XOPS:eGFP\|cell type:GFP ; FACS sorted non rods from retina	GFPneg2	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 cells not rods	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°C. 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 µL 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 µm 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 µL of the FACS sheath fluid and RNA was immediately extracted.	RNA was extracted from tissue samples using the NucleoSpin® RNA kit Macherey Nagel using the manufacturer’s 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’s 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® 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:non rod retinal cells\|genotype/variation:XOPS:eGFP\|cell type:GFP ; FACS sorted non rods from retina	GSM2670725	GSM2670725: GFPneg2; Danio rerio; RNA Seq	GSM2670725		1	RNA was extracted from tissue samples using the NucleoSpin® RNA kit Macherey Nagel using the manufacturer’s 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’s 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® 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:GSM2670725	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina MiSeq		SRP109268			GFPnegaitive2_CAGATC_L001_R1_001.fastq.gz GFPnegaitive2_CAGATC_L001_R2_001.fastq.gz	fastq fastq	1718976888.0	2781516.0	GSM2670725 r1	0:309 1:309	A:529099301;C:352155163;G:350456178;T:487264195;N:2051	309	309			529099301	352155163	350456178	487264195	2051	SRX2921959	SRS2287818	SRA574861	GEO	Biological Sciences, University of Idaho	2	0.71906	0.72599	0.20211	0.20881	0.77761	0.79289	0.65883	0.66469	309	309	B	B	biological fallback assumption	illumina	miseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		United States	2017-06-15	Undetermined	Multi-stage	Eye	Sensory System