{"database": "metadata", "table": "run_metadata", "rows": [[49096, "SRR7698982", "SRX4557276", "SRS3674267", "SRP158038", "PRJNA486182", "Single cell analyses of Amyloid beta42 and Interleukin 4 on neural stem cell plasticity IV", "GSE118599", "Other", "Neural stem cells NSCs constitute the reservoir for new cells and might be harnessed for stem cell based regenerative therapies. Zebrafish has remarkable ability to regenerate its brain by inducing NSC plasticity upon Alzheimer's pathology. We recently identified that NSCs enhance their proliferation and neurogenic outcome in an Amyloid beta42 based A\u00df42 experimental Alzheimer's disease model in zebrafish brain and Interleukin 4 IL4 is a critical molecule for inducing NSC proliferation in AD conditions. However  the mechanisms by which A\u00df42 and IL4 affect NSCs remained unknown. Using single cell transcriptomics  we determined distinct subtypes of NSCs and neurons in adult zebrafish brain  identified differentially expressed genes post A\u00df42 and IL4 treatments  analyzed the gene ontology and pathways that are affected by A\u00df42 and IL4  and investigated how cell cell communication is altered through secreted molecules and their receptors. Our results constitute the most extensive resource in the Alzheimer's disease model of adult zebrafish brain  are likely to provide unique insights into how A\u00df42/IL4 affects NSC plasticity and yield in novel drug targets for mobilizing neural stem cells for endogenous neuro regeneration. Overall design: Single cell analyses of zebrafish telencephalon by 10X Genomics", null, "pubmed:31905199", null, "serotonin", "GSM3334111", null, "tissue:Telencephalon|treatment:serotonin", "serotonin", "The fastq files were aligned to zebrafish transcript Ensembl Version 91by using STAR. The BAM files were as input for Cell Ranger 10X genmoics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Genome build: danRer10 Supplementary files format and content: tab delimited file  with gene names in rows and cell names and counts in columns.", "Telencephalon", "Fish were injected serotonin by CVMI.", "Cells from telencephalon wre dissocuated and her4.1:GFP positve ande negative cells were sorted firstly and then mixed with equal number. The library preparation was performed by 10X Genomics as per manufactur protocol", "Fish were kept at 28 \u00b0C water system with 14/10 hours light/dark cycles", "treatment:serotonin", "GSM3334111", "GSM3334111: serotonin; Danio rerio; RNA Seq", "GSM3334111", null, "1", "Cells from telencephalon wre dissocuated and her4.1:GFP positve ande negative cells were sorted firstly and then mixed with equal number. The library preparation was performed by 10X Genomics as per manufactur protocol", "GEO Accession:GSM3334111", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP158038", null, "dangling references:treat as unmapped", "SRT_possorted_genome_bam.bam", "10X Genomics bam file", 6880682724.0, 120713732.0, "GSM3334111 r1", "0:57", "A:2102623379;C:1264130463;G:1410616586;T:2100393658;N:2918638", 57, null, null, null, 2102623379, 1264130463, 1410616586, 2100393658, 2918638, "SRX4557276", "SRS3674267", "SRA759542", "GEO", "AG KIZIL, German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association", 1, 0.87735, null, 0.27987, null, 0.78346, null, 0.49332, null, 57, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2018-08-15", "Undetermined", "Adult", "Brain", "Nervous 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": ["49096"], "units": {}, "query_ms": 11.64992899975914}