run_metadata: 76698

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
76698	SRR25253555	SRX20999594	SRS18272867	SRP449239	PRJNA994180	Evolution of neuronal cell classes and types in the vertebrate retina [Zebrafish]	GSE237214	Transcriptome Analysis	The basic plan of the retina is conserved across vertebrates yet species differ profoundly in their visual needs Baden et al. 2020. One might expect that retinal cell types evolved to accommodate these varied needs but this has not been systematically studied. Here we generated and integrated single cell transcriptomic atlases of the retina from 17 species: humans two non human primates four rodents three ungulates opossum ferret tree shrew a teleost fish a bird a reptile and a lamprey. Molecular conservation of the six retinal cell classes photoreceptors horizontal cells bipolar cells amacrine cells retinal ganglion cells [RGCs] and Müller glia is striking with transcriptomic differences across species correlated with evolutionary distance. Major subclasses are also conserved whereas variation among types within classes or subclasses is more pronounced. However an integrative analysis revealed that numerous types are shared across species based on conserved gene expression programs that likely trace back to the common ancestor of jawed vertebrates. The degree of variation among types increases from the outer retina photoreceptors to the inner retina RGCs suggesting that evolution acts preferentially to shape the retinal output. Finally we identified mammalian orthologs of midget RGCs which comprise >80% of RGCs in the human retina subserve high acuity vision and were believed to be primate specific Berson 2008; in contrast the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved thereby facilitating high visual acuity and increased cortical processing of visual information. Overall design: Single cell RNA seq was performed on cells isolated from fresh retina. Fluorescence activated cell sorting was used to collect Calcein blueCB positive live cells. For some collections CB+ cells were further seprated using CD90/THY1 and/or CD73 expression as an strategy to enrich for RGCs and/or to deplete phototreceptors respectively Please note that he enrichment strategy was not effective for some species/samples. Approximately 8000 cells were recovered from each sample and each cell was sequenced to a depth of 40000 reads.	parent bioproject:PRJNA994164	pubmed:38092908		Zebrafish BC1	GSM7596935		source name:Retina\|tissue:Retina\|cell type:Retinal neurons\|geo loc name:missing\|collection date:missing	Zebrafish BC1	We used cellranger v7.0 10X Genomics to align the sc and snRNA seq datasets following manufacturer’s instructions. For each species sequencing reads were demultiplexed into distinct samples and the .fastq.gz files corresponding to each sample were aligned to reference transcriptomes to obtain binary alignment map .bam files. Assembly: Zv82 Supplementary files format and content: To include both exonic and intronic reads in the quantification of gene expression for each sample regardless of cellular or nuclear origin we applied velocyto to the corresponding .bam files. This generated two separate gene expression matrices GEMs; genes x cells for each sample corresponding to “spliced” and “unspliced” reads. The two GEMs were summed element by element to obtain “total” GEM for each sample. Supplementary files format and content: GEMs from different sample runs were combined column wise concatenated to yield a full species’ GEM.	Retina	None	Retinas were dissected in Ames solution Sigma Aldrich; equilibrated with 95% O2/5% CO2 for all use immediately following enucleation. They were dissociated in papain followed by FACS sorting. Cells were stained for either THY1/CD90 to enrich for RGCs or for CD73 to deplete photoreceptors. Single cell libraries were generated using the Chromium 3’ V3 platform 10X Genomics Pleasanton CA according to the manufacturer’s protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full length cDNA; this was followed by amplification enzymatic fragmentation and 5’ adaptor and sample index attachment to yield the final libraries. Single cell RNA sequecning 10X Genomics		tissue:Retina\|cell type:Retinal neurons	GSM7596935	GSM7596935: Zebrafish BC1; Danio rerio; RNA Seq	GSM7596935 r1	GSM7596935	1	Retinas were dissected in Ames solution Sigma Aldrich; equilibrated with 95% O2/5% CO2 for all use immediately following enucleation. They were dissociated in papain followed by FACS sorting. Cells were stained for either THY1/CD90 to enrich for RGCs or for CD73 to deplete photoreceptors. Single cell libraries were generated using the Chromium three prime V3 platform 10X Genomics Pleasanton CA according to the manufacturer's protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full length cDNA; this was followed by amplification enzymatic fragmentation and five prime adaptor and sample index attachment to yield the final libraries. Single cell RNA sequecning 10X Genomics		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP449239		intentional duplicate	ZfishBC1.bam	10X Genomics bam file	6529192180.0	66624410.0	GSM7596935 r1	0:98	A:1937703976;C:1274004687;G:1327972080;T:1988461414;N:1050023	98				1937703976	1274004687	1327972080	1988461414	1050023	SRX20999594	SRS18272867	SRA1672086	Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley	Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley	1	0.84848		0.27131		0.81233		0.48186		98		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2023-07-12	Undetermined	Undetermined	Eye	Sensory System