{"database": "metadata", "table": "run_metadata", "rows": [[31850, "SRR28735528", "SRX24301507", "SRS21065426", "SRP502615", "PRJNA1101945", "Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [RNA seq]", "GSE264309", "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: AB and double knockout for stim2   stim2a;stim2b /  zebrafish 5dpf larvae were used to isolate the total RNA from their eyes. The experimental setup involved 3 replicates per each condition stim2 KO vs control consisting of 35 eyes per repetition.", "parent bioproject:PRJNA1101942", "pubmed:39424970", null, "stim2KO  repllicate 2  RNASeq", "GSM8215877", null, "source name:eye|tissue:eye|genotype:stim2a;stim2b / |age:5 dpf|geo loc name:missing|collection date:missing", "stim2KO  repllicate 2  RNASeq", "Raw RNA seq data were converted to FASTQ format with bcl2fastq2 v2.17  Illumina  and FastQC v0.11.4 was used to assess the quality of each sequencing run. We then utilized the SQuIRE pipeline45 for subsequent steps. STAR version 2.5.3a  StringTie version 1.3.3b  and DESeq2 version 1.16.149 were used within the SQuIRE pipeline for read alignment  transcript assembly  and quantification for each replicate  and differential gene expression analysis  respectively. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated files with raw reads for each sample", "eye", null, "Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260  280  and 230 nm  and Bioanalyzer Nano RNA chip Agilent  USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research  Irvine  CA  USA according to the manufacturer\u2019s recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.", null, "tissue:eye|genotype:stim2a;stim2b / |age:5 dpf", "GSM8215877", "GSM8215877: stim2KO  repllicate 2  RNASeq; Danio rerio; RNA Seq", "GSM8215877 r1", "GSM8215877", "1", "Total RNA was isolated for RNA seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260  280  and 230 nm  and Bioanalyzer Nano RNA chip Agilent  USA analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit ZYMO Research  Irvine  CA  USA according to the manufacturer's recommendations. Library construction was conducted using stranded Illumina TruSeq protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP502615", null, "loader:fastq load.py", "mut_rep_2_R1_001.fastq.gz mut_rep_2_R2_001.fastq.gz", "fastq fastq", 5641008570.0, 27925785.0, "GSM8215877 r1", "0:101 1:101", "A:1421655053;C:1399106135;G:1439454285;T:1380731092;N:62005", 101, 101, null, null, 1421655053, 1399106135, 1439454285, 1380731092, 62005, "SRX24301507", "SRS21065426", "SRA1848589", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", "Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS", 2, 0.95794, 0.9601, 0.05457, 0.05365, 0.70942, 0.71151, 0.42408, 0.42666, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Poland", "2024-04-18", "Larval", "Larval", "Eye", "Sensory System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["31850"], "units": {}, "query_ms": 9.411655999429058}