{"database": "metadata", "table": "run_metadata", "rows": [[49095, "SRR7697065", "SRX4555360", "SRS3672366", "SRP157997", "PRJNA486153", "Single cell analyses of Amyloid beta42 and Interleukin 4 on neural stem cell plasticity I", "GSE118577", "Transcriptome Analysis", "The neural stem cell NSC reservoir can be harnessed for stem cell based regenerative therapies. Zebrafish remarkably regenerate their brain by inducing NSC plasticity in a Amyloid \u00df 42 A\u00df42 induced experimental Alzheimer's disease AD model. Interleukin 4 IL 4 is also critical for AD induced NSC proliferation. However  the mechanisms of this response have remained unknown. Using single cell transcriptomics in the adult zebrafish brain  we identify distinct subtypes of NSCs and neurons and differentially regulated pathways and their gene ontologies and investigate how cell cell communication is altered through ligand receptor pairs in AD conditions. Our results propose the existence of heterogeneous and spatially organized stem cell populations that react distinctly to amyloid toxicity. This resource article provides an extensive database for the molecular basis of NSC plasticity in the AD model of the adult zebrafish brain. Further analyses of stem cell heterogeneity and neuro regenerative ability at single cell resolution could yield drug targets for mobilizing NSCs for endogenous neuro regeneration in humans. Overall design: Single cell analyses of zebrafish telencephalon by 10X Genomics", null, "pubmed:31018142;pubmed:34685728;pubmed:35681503", null, "amyloid beta 42", "GSM3333461", null, "tissue:Telencephalon|treatment:amyloid beta 42", "amyloid beta 42", "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 amyloid beta 42 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:amyloid beta 42", "GSM3333461", "GSM3333461: amyloid beta 42; Danio rerio; RNA Seq", "GSM3333461", 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:GSM3333461", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP157997", null, "dangling references:treat as unmapped", "AB42_possorted_genome_bam.bam", "10X Genomics bam file", 4538914104.0, 79630072.0, "GSM3333461 r1", "0:57", "A:1398743208;C:825411025;G:924551078;T:1388288174;N:1920619", 57, null, null, null, 1398743208, 825411025, 924551078, 1388288174, 1920619, "SRX4555360", "SRS3672366", "SRA759092", "GEO", "AG KIZIL, German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association", 1, 0.88003, null, 0.26711, null, 0.78336, null, 0.50584, 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": ["49095"], "units": {}, "query_ms": 10.15237200044794}