Single Cell RNA Sequencing Data
scRNAseq Data available on Virtual Fly Brain.
VFB integrates single-cell and single-nucleus RNA sequencing data by connecting it to anatomy: each cluster from a published study is annotated with the Drosophila Anatomy Ontology term for the cell type it corresponds to, so that a query for a cell type returns its transcriptomic clusters alongside its images and connectivity. The sequencing itself is not VFB’s; the anatomical annotation and the cross-linking are.
Data comes from FlyBase, which takes it from the Single Cell Expression Atlas. The studies include the Fly Cell Atlas and the Aging Fly Cell Atlas.
Finding clusters and genes
Clusters for a cell type are reached through the Single cell transcriptomics data for…
query on that cell type’s Term Info pane. Datasets themselves are found by searching for
scRNAseq and filtering to Dataset.
Genes in a cluster can be filtered by function and sorted by expression level and by extent — the proportion of cells in the cluster expressing the gene. As with other VFB result tables, the list exports as CSV.
Only genes with extent > 0.2 in a cluster are included.
The same queries are available through VFB_connect.
Datasets
Gene counts are after the extent filter above, so they are lower than the gene count reported by the original study. Ordered by cluster count.
| Dataset | Study | Clusters | Genes |
|---|---|---|---|
| scRNAseq_2022_FCA_MIXED | Single-nucleus RNA-seq on cells from 5-days old female and male flies | 497 | 11,079 |
| scRNAseq_2022_FCA_MALE | Single-nucleus RNA-seq on cells from 5-days old male flies | 422 | 10,978 |
| scRNAseq_2022_FCA_FEMALE | Single-nucleus RNA-seq on cells from 5-days old female flies | 411 | 8,169 |
| scRNAseq_2022_Calderon | The continuum of Drosophila embryonic development at single-cell resolution | 274 | 2,166 |
| scRNAseq_2023_AFCA_D30_FEMALE | Single-nucleus RNA-seq on cells from 30-days old female flies | 179 | 4,987 |
| scRNAseq_2023_AFCA_D70_FEMALE | Single-nucleus RNA-seq on cells from 70-days old female flies | 176 | 5,458 |
| scRNAseq_2023_AFCA_D50_FEMALE | Single-nucleus RNA-seq on cells from 50-days old female flies | 175 | 4,595 |
| scRNAseq_2023_AFCA_D50_MALE | Single-nucleus RNA-seq on cells from 50-days old male flies | 172 | 4,878 |
| scRNAseq_2023_AFCA_D30_MALE | Single-nucleus RNA-seq on cells from 30-days old male flies | 168 | 4,857 |
| scRNAseq_2023_AFCA_D70_MALE | Single-nucleus RNA-seq on cells from 70-days old male flies | 161 | 4,835 |
| scRNAseq_2023_AFCA_D30 | Single-nucleus RNA-seq on cells from 30-days old flies | 99 | 5,312 |
| scRNAseq_2023_AFCA_D70 | Single-nucleus RNA-seq on cells from 70-days old flies | 95 | 5,592 |
| scRNAseq_2023_AFCA_D50 | Single-nucleus RNA-seq on cells from 50-days old flies | 95 | 5,015 |
| scRNAseq_2021_Ozel | Single-cell RNA-seq study of pupal and adult optic lobes | 66 | 4,770 |
| scRNAseq_2020_Kurmangaliyev | Single-cell RNA-seq study of the pupal optic lobe | 62 | 5,975 |
| scRNAseq_2018_Davie | Single-cell RNA-seq study of the aging brain | 59 | 6,111 |
| scRNAseq_2020_Hormann | Single-cell RNA-seq study of visual motion-sensing neurons | 40 | 4,014 |
| scRNAseq_2021_Mokashi_CTRL | Single-cell RNA-seq study of adult brain without alcohol exposure | 39 | 3,097 |
| scRNAseq_2021_Baker_CTRL | Single-cell RNA-seq study of adult brain without cocaine exposure | 36 | 3,329 |
| scRNAseq_2020_Allen | Single-cell RNA-seq study of adult ventral nerve cords | 20 | 3,085 |
| scRNAseq_2022_Konstantinides | Single-cell RNA-seq study of larval optic lobes | 14 | 5,530 |
| scRNAseq_2023_Saavedra | Single-cell RNA-seq study of the adult thorax | 11 | 1,726 |
| scRNAseq_2019_Avalos | Single-cell RNA-seq study of first instar larval brains upon starvation | 10 | 6,463 |
| scRNAseq_2021_IngSimmons | Single-cell RNA-seq study of gastrulating embryos | 9 | 6,423 |
Not every cluster carries an anatomical annotation: many are non-neural or were not resolved to a cell type in the source study. Counts here are of what VFB holds, and are regenerated with the content report after each data release; the machine-readable version is scRNAseq_DataSets.tsv.