run_metadata: 29174

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
29174	SRR27237224	SRX22915658	SRS19883761	SRP478464	PRJNA1053781	Single cell gene expression profie of developing photoreceptor cells in larval zebrafish	GSE250379	Other	Molecular underpinnings of vertebrate retinal differentiation and maturation are poorly understood particularly for non mammalian species. We generated single cell transcriptome data from the larval zebrafish retina and characterized gene expression diversity among photoreceptor subtypes and their progenitors. Overall design: GFP positive differentiating photoreceptor cells and bipolar cells were collected from 4 dpf larval transgenic zebrafish Tgcrx:EGFPstl887 using fluorescence activated cell sorting.	parent bioproject:PRJNA1050288	pubmed:39531499		retina scRNA seq	GSM7978132		source name:retina\|tissue:retina\|genotype:Tgcrx:EGFPstl887\|developmental stage:4 dpf\|geo loc name:missing\|collection date:missing	retina scRNA seq	Read alignment and initial quality control were performed using Cell Ranger software version 7.0.0 10X Genomics. Assembly: GRCz11 Supplementary files format and content: Tab separated value file and matrix file	retina		Fifty heads were dissected from 4 dpf heterozygous Tgcrx:GFPstl887Tg larvae. Following dissection eyes were stored in ice cold Hanks’ Balanced Salt Solution HBSS until all eyes were harvested. Once the eyes were collected HBSS was removed and the eyes were incubated in 400 µl of calcium/magnesium free HBSS containing 0.4 mg papain Worthington Biochem for 15 min at 37°C. 800 µl of 10% fetal bovine serum FBS in Dulbecco's Modified Eagle Medium DMEM containing 5mM MgCl2 and 120 units DNaseI Roche were added to the mixture and incubated for 5 min at 37°C. Cells were then resuspended in 300 µl of sorting buffer 2.5 mM EDTA 25 mM HEPES 1% bovine serum albumin BSA in calcium/magnesium free HBSS. Cells were sorted on an Aria II FACS machine BD biosciences with gating based on forward scatter side scatter and GFP fluorescence and collected in 700 μl of D PBS without xxx+ and Mg2+ supplemented with 0.4 % BSA D PBS CMF in 1.5 ml microcentrifuge tubes. The collected cells were then centrifuged at 300×g for 5 min washed with D PBS CMF centrifuged and supernatant reduced to 80 µl. Cell density was quantified on a hemocytometer and 5000 cells were used for single cell library preparation. A library for single cell RNA seq was constructed with the Chromium v3 platform 10X Genomics Pleasanton CA according to the manufacturer protocol.		tissue:retina\|genotype:Tgcrx:EGFPstl887\|developmental stage:4 dpf	GSM7978132	GSM7978132: retina scRNA seq; Danio rerio; RNA Seq	GSM7978132 r1	GSM7978132	1	Fifty heads were dissected from 4 dpf heterozygous Tgcrx:GFPstl887Tg larvae. Following dissection eyes were stored in ice cold Hanks' Balanced Salt Solution HBSS until all eyes were harvested. Once the eyes were collected HBSS was removed and the eyes were incubated in 400 µl of calcium/magnesium free HBSS containing 0.4 mg papain Worthington Biochem for 15 min at 37°C. 800 µl of 10% fetal bovine serum FBS in Dulbecco's Modified Eagle Medium DMEM containing 5mM MgCl2 and 120 units DNaseI Roche were added to the mixture and incubated for 5 min at 37°C. Cells were then resuspended in 300 µl of sorting buffer 2.5 mM EDTA 25 mM HEPES 1% bovine serum albumin BSA in calcium/magnesium free HBSS. Cells were sorted on an Aria II FACS machine BD biosciences with gating based on forward scatter side scatter and GFP fluorescence and collected in 700 μl of D PBS without xxx+ and Mg2+ supplemented with 0.4 % BSA D PBS CMF in 1.5 ml microcentrifuge tubes. The collected cells were then centrifuged at 300×g for 5 min washed with D PBS CMF centrifuged and supernatant reduced to 80 µl. Cell density was quantified on a hemocytometer and 5000 cells were used for single cell library preparation. A library for single cell RNA seq was constructed with the Chromium v3 platform 10X Genomics Pleasanton CA according to the manufacturer protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP478464		loader:fastq load.py	crx.crx_S1_L003_R1_001.fastq.gz crx.crx_S1_L003_R2_001.fastq.gz	fastq fastq	45170138494.0	253764823.0	GSM7978132 r1	0:28 1:150	A:13826023801;C:9023674621;G:9590649474;T:12728940802;N:849796	28	150			13826023801	9023674621	9590649474	12728940802	849796	SRX22915658	SRS19883761	SRA1770358	Pathology and Immunology, Washington University School of Medicine	Pathology and Immunology, Washington University School of Medicine	2	0.0046	0.87155	0.00206	0.2263	0.99168	0.77784	0.30223	0.50112	28	150	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2023-12-17	Larval	Larval	Eye	Sensory System