run_metadata: 31860

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
31860	SRR28735568	SRX24301541	SRS21065460	SRP502616	PRJNA1101946	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]	GSE264310	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b / ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates 30 larvae per each sample and Tg control 2 replicates 30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.	parent bioproject:PRJNA1101942	pubmed:39424970		stim2KO repllicate 1 scRNASeq	GSM8215881		source name:head\|tissue:head\|cell type:neuronal\|genotype:stim2a;stim2b / ; TgHuC:GCaMP5G\|age:5 dpf larvae\|geo loc name:missing\|collection date:missing	stim2KO repllicate 1 scRNASeq	Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR for each sample with the following parameters: soloType CB UMI Simple soloCBwhitelist 3M february 2018.txt [from Cell Ranger] soloUMIlen 12 soloCBmatchWLtype 1MM multi Nbase pseudocounts soloUMIfiltering MultiGeneUMI CR soloUMIdedup 1MM CR soloCellFilter EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files	head		5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit’s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer’s protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual’s guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA tailing adapter ligation and 12 cycle indexing PCR – was performed.		tissue:head\|cell type:neuronal\|genotype:stim2a;stim2b / ; TgHuC:GCaMP5G\|age:5 dpf larvae	GSM8215881	GSM8215881: stim2KO repllicate 1 scRNASeq; Danio rerio; RNA Seq	GSM8215881 r1	GSM8215881	1	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer's protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA tailing adapter ligation and 12 cycle indexing PCR – was performed.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550		SRP502616			RIS_F63_0005_P24_V12_S2_R2_001.fastq.gz RIS_F63_0005_P24_V12_S2_R1_001.fastq.gz	fastq fastq	17678874240.0	138116205.0	GSM8215881 r2	0:28 1:100	A:5142406165;C:3696946044;G:3986515668;T:4852338487;N:667876	28	100			5142406165	3696946044	3986515668	4852338487	667876	SRX24301541	SRS21065460	SRA1848620	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.01372	0.87988	0.00546	0.35939	0.99082	0.78042	0.23783	0.55977	28	100	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		Poland	2024-04-18	Larval	Larval	Head	Nervous System