run_metadata: 49096
This data as json
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| 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 Aß42 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 Aß42 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 Aß42 and IL4 treatments analyzed the gene ontology and pathways that are affected by Aß42 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 Aß42/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 | pubmed:31905199 | serotonin | GSM3334111 | 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 °C water system with 14/10 hours light/dark cycles | treatment:serotonin | GSM3334111 | GSM3334111: serotonin; Danio rerio; RNA Seq | GSM3334111 | 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 | SRP158038 | 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 | 2102623379 | 1264130463 | 1410616586 | 2100393658 | 2918638 | SRX4557276 | SRS3674267 | SRA759542 | GEO | AG KIZIL, German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association | 1 | 0.87735 | 0.27987 | 0.78346 | 0.49332 | 57 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2018-08-15 | Undetermined | Adult | Brain | Nervous System |