run_metadata: 59866

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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
59866	SRR12054789	SRX8583208	SRS6874825	SRP268010	PRJNA640615	Molecular classification of zebrafish retinal ganglion cells links genes to behavior	GSE152842	Transcriptome Analysis	Retinal ganglion cells RGCs form an array of feature detectors which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single cell transcriptomics we systematically classified RGCs in adult and larval zebrafish thereby identifying marker genes for >30 stable and several transient cell types cell type specific markers and their maturational changes. We used this catalog to engineer transgenic driverreporter lines enabling experimental genetic access to specific RGC types. Strikingly expression of a few transcription factors often predicts dendrite morphological features in particular and axonal projections to specific tectal layers and extratectal targets. Moreover iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally chemogenetic ablation of eomesa+ RGCs which comprise three melanopsin expressing types with a specific projections to thalamus pretectum and one deep tectal layerpattern selectively impaired a visual behavior phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset 200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell.		pubmed:33357413		Adult Zebrafish 6	GSM4627218		source name:Zebrafish retina 4 mpf 6 mpf\|tissue:retina	Adult Zebrafish 6	Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0 10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10 release 82 using “cellranger count” with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10 release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples	Zebrafish retina 4 mpf 6 mpf	All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed.	Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3’ v2 platform 10X Genomics Pleasanton CA	Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s solution 17 mM NaCl 2 mM KCl 0.12 mM MgSO4 1.8 mM CaNO32 1.5 mM HEPES.	tissue:retina	GSM4627218	GSM4627218: Adult Zebrafish 6; Danio rerio; RNA Seq	GSM4627218		1	Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics Pleasanton CA	GEO Accession:GSM4627218	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP268010		assembly:GRCz10\|intentional duplicate	ZebrafishRGC6.bam	10X Genomics bam file	11333584262.0	115648819.0	GSM4627218 r1	0:98	A:3357618948;C:2223130462;G:2352697999;T:3398318533;N:1818320	98				3357618948	2223130462	2352697999	3398318533	1818320	SRX8583208	SRS6874825	SRA1089100	GEO	Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley	1	0.87718		0.26282		0.7838		0.50701		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2020-06-19	Multi-stage	Multi-stage	Eye	Sensory System