run_metadata: 49093
This data as json
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| 49093 | SRR7723466 | SRX4579978 | SRS3674265 | 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 ß 42 Aß42 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 | pubmed:31018142;pubmed:34685728;pubmed:35681503 | PBS Control | GSM3334110 | tissue:Telencephalon|treatment:PBS Control | PBS Control | 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 PBS 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:PBS Control | GSM3334110 | GSM3334110: PBS Control; Danio rerio; RNA Seq | GSM3334110 2 | 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:GSM3334110 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP157997 | dangling references:treat as unmapped | PBS_possorted_genome_bam.bam | 10X Genomics bam file | 6292411773.0 | 110393189.0 | GSM3334110 r11 | 0:57 | A:1933363206;C:1158155764;G:1296886350;T:1901320452;N:2686001 | 57 | 1933363206 | 1158155764 | 1296886350 | 1901320452 | 2686001 | SRX4579978 | SRS3674265 | SRA759092 | GEO | AG KIZIL, German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association | 1 | 0.87993 | 0.28191 | 0.77861 | 0.50645 | 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 |