run_metadata: 30269
This data as json
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| 30269 | SRR27747519 | SRX23412816 | SRS20268137 | SRP486180 | PRJNA1069776 | Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq | GSE254346 | Transcriptome Analysis | The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate topography and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified "midpoint" in hindbrain vestibular neuron development 36 hpf labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics. | All vestibular neurons replicate 2 | GSM8038038 | tissue:Hindbrain vestibular neurons|time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a|geo loc name:missing|collection date:missing | All vestibular neurons replicate 2 | Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files | Hindbrain vestibular neurons | Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red converted Kaede from late born green unconverted Kaede neurons. | Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1 | time:72 hpf 74 hpf type:Hindbrain vestibular neurons|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede|treatment:n/a | GSM8038038 | GSM8038038: All vestibular neurons replicate 2; Danio rerio; RNA Seq | GSM8038038 r1 | GSM8038038 | 1 | Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP486180 | loader:fastq load.py | Zebrafish-Replicate2_S2_L002_I1_001.fastq.gz Zebrafish-Replicate2_S2_L002_I2_001.fastq.gz Zebrafish-Replicate2_S2_L002_R1_001.fastq.gz Zebrafish-Replicate2_S2_L002_R2_001.fastq.gz | fastq fastq fastq fastq | 9495760675.0 | 68314825.0 | GSM8038038 r2 | 0:10 1:10 2:28 3:91 | A:2685940540;C:901627244;G:1612080998;T:1016532106;N:468187 | 10 | 10 | 28 | 91 | 2685940540 | 901627244 | 1612080998 | 1016532106 | 468187 | SRX23412816 | SRS20268137 | SRA1792542 | Neuroscience Institute, New York University Grossman School of Medicine | Neuroscience Institute, New York University Grossman School of Medicine | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2024-01-26 | Multi-stage | Multi-stage | Brain | Nervous System |