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scRNAseq docs: switch to the vfb-scRNAseq (VFBseq) datasets — do not merge until the data release is live #531

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Clare72 merged 2 commits into from
Nov 5, 2026
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scRNAseq docs: switch to the vfb-scRNAseq (VFBseq) datasets — do not merge until the data release is live #531

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scRNAseq docs: the 17 VFBseq datasets from vfb-scRNAseq
Clare72 Oct 27, 2026
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scRNAseq docs: Sample, Assay and Clustering queries; stage and tissue…
Clare72 Nov 2, 2026
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86 changes: 52 additions & 34 deletions content/en/docs/Data/scRNAseq/_index.md
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Expand Up @@ -16,14 +16,20 @@ sequencing itself is not VFB's; the anatomical annotation and the cross-linking

{{< vfb-figures set="scrnaseq" >}}

Data comes from [FlyBase](https://flybase.org/), which takes it from the
[Single Cell Expression Atlas](https://www.ebi.ac.uk/gxa/sc/home). The studies include
the [Fly Cell Atlas](https://flycellatlas.org/) and the
VFB curates these datasets itself, in
[vfb-scRNAseq](https://github.com/VirtualFlyBrain/vfb-scRNAseq). For each study, the
clusters are the authors' own, taken with their cell-type annotations from GEO,
ArrayExpress, the paper or the authors' published analysis, and each cluster is mapped
to the Drosophila Anatomy Ontology term for the cell type it is composed primarily of. Clusters
that no anatomy term describes well enough are held back rather than given a vague
term, so every cluster VFB shows has a cell type. Expression is summarised per cluster
from the authors' count data. The studies include the
[Fly Cell Atlas](https://flycellatlas.org/) and the
[Aging Fly Cell Atlas](https://hongjielilab.org/afca/).

## Finding clusters and genes

Clusters for a cell type are reached through the `Single cell transcriptomics data for…`
Clusters for a cell type are reached through the `scRNAseq data for…`
query on that cell type's Term Info pane. Datasets themselves are found by searching for
`scRNAseq` and filtering to `Dataset`.

Expand All @@ -40,40 +46,52 @@ _Only genes with extent > 0.2 in a cluster are included._
The same queries are available through
[VFB_connect](https://vfb-connect.readthedocs.io/en/stable/API_reference.html#transcriptomics-queries).

## Samples, assays and clusterings

Each dataset also has pages for what was sequenced and how it was analysed:

- **Samples**: the dissected tissue, with its stage, tissue, sex and the fly stock,
FlyBase strain or genotype it came from.
- **Assays**: the sequencing libraries made from each Sample, linked to their GEO, SRA
and BioSample records.
- **Clusterings**: the authors' analyses, each with its clusters and the Samples its
cells came from. A dataset can have several, for example one per stage.

A dataset's Term Info offers `Clusterings in…`, `Samples in…` and `Assays in…`, and a
Clustering offers its clusters, Samples and Assays. Cluster tables show the stages and
tissues of the Samples behind each cluster, apart from any stage the cluster itself was
given from its expression. From a stock, strain, allele or split combination,
`scRNAseq samples from…` and `scRNAseq clusters from samples of…` find the data from
those flies. See the [Queries Reference](/docs/website-features/queries/#how-a-scrnaseq-dataset-is-organised).

## 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.
reported by the original study. Ordered by cluster count. Datasets that span several
stages are listed once on [Datasets by stage](/docs/data/stages/), at their earliest.

| Dataset | Stage | Study | Clusters | Genes |
|---|---|---|---|---|
| [scRNAseq_2022_FCA_MIXED](https://flybase.org/reports/FBlc0004785) | Adult | Single-nucleus RNA-seq on cells from 5-days old female and male flies | 497 | 11,079 |
| [scRNAseq_2022_FCA_MALE](https://flybase.org/reports/FBlc0004307) | Adult | Single-nucleus RNA-seq on cells from 5-days old male flies | 422 | 10,978 |
| [scRNAseq_2022_FCA_FEMALE](https://flybase.org/reports/FBlc0003846) | Adult | Single-nucleus RNA-seq on cells from 5-days old female flies | 411 | 8,169 |
| [scRNAseq_2022_Calderon](https://flybase.org/reports/FBlc0007797) | Embryo | The continuum of Drosophila embryonic development at single-cell resolution | 274 | 2,166 |
| [scRNAseq_2023_AFCA_D30_FEMALE](https://flybase.org/reports/FBlc0006424) | Adult | Single-nucleus RNA-seq on cells from 30-days old female flies | 179 | 4,987 |
| [scRNAseq_2023_AFCA_D70_FEMALE](https://flybase.org/reports/FBlc0007348) | Adult | Single-nucleus RNA-seq on cells from 70-days old female flies | 176 | 5,458 |
| [scRNAseq_2023_AFCA_D50_FEMALE](https://flybase.org/reports/FBlc0006888) | Adult | Single-nucleus RNA-seq on cells from 50-days old female flies | 175 | 4,595 |
| [scRNAseq_2023_AFCA_D50_MALE](https://flybase.org/reports/FBlc0007071) | Adult | Single-nucleus RNA-seq on cells from 50-days old male flies | 172 | 4,878 |
| [scRNAseq_2023_AFCA_D30_MALE](https://flybase.org/reports/FBlc0006611) | Adult | Single-nucleus RNA-seq on cells from 30-days old male flies | 168 | 4,857 |
| [scRNAseq_2023_AFCA_D70_MALE](https://flybase.org/reports/FBlc0007532) | Adult | Single-nucleus RNA-seq on cells from 70-days old male flies | 161 | 4,835 |
| [scRNAseq_2023_AFCA_D30](https://flybase.org/reports/FBlc0006423) | Adult | Single-nucleus RNA-seq on cells from 30-days old flies | 99 | 5,312 |
| [scRNAseq_2023_AFCA_D70](https://flybase.org/reports/FBlc0007347) | Adult | Single-nucleus RNA-seq on cells from 70-days old flies | 95 | 5,592 |
| [scRNAseq_2023_AFCA_D50](https://flybase.org/reports/FBlc0006887) | Adult | Single-nucleus RNA-seq on cells from 50-days old flies | 95 | 5,015 |
| [scRNAseq_2021_Ozel](https://flybase.org/reports/FBlc0005659) | Pupa | Single-cell RNA-seq study of pupal and adult optic lobes | 66 | 4,770 |
| [scRNAseq_2020_Kurmangaliyev](https://flybase.org/reports/FBlc0006237) | Pupa | Single-cell RNA-seq study of the pupal optic lobe | 62 | 5,975 |
| [scRNAseq_2018_Davie](https://flybase.org/reports/FBlc0006090) | Adult | Single-cell RNA-seq study of the aging brain | 59 | 6,111 |
| [scRNAseq_2020_Hormann](https://flybase.org/reports/FBlc0006305) | Adult | Single-cell RNA-seq study of visual motion-sensing neurons | 40 | 4,014 |
| [scRNAseq_2021_Mokashi_CTRL](https://flybase.org/reports/FBlc0005420) | Adult | Single-cell RNA-seq study of adult brain without alcohol exposure | 39 | 3,097 |
| [scRNAseq_2021_Baker_CTRL](https://flybase.org/reports/FBlc0005515) | Adult | Single-cell RNA-seq study of adult brain without cocaine exposure | 36 | 3,329 |
| [scRNAseq_2020_Allen](https://flybase.org/reports/FBlc0005603) | Adult | Single-cell RNA-seq study of adult ventral nerve cords | 20 | 3,085 |
| [scRNAseq_2022_Konstantinides](https://flybase.org/reports/FBlc0006404) | Larva | Single-cell RNA-seq study of larval optic lobes | 14 | 5,530 |
| [scRNAseq_2023_Saavedra](https://flybase.org/reports/FBlc0006361) | Adult | Single-cell RNA-seq study of the adult thorax | 11 | 1,726 |
| [scRNAseq_2019_Avalos](https://flybase.org/reports/FBlc0005362) | L1 larva | Single-cell RNA-seq study of first instar larval brains upon starvation | 10 | 6,463 |
| [scRNAseq_2021_IngSimmons](https://flybase.org/reports/FBlc0006191) | Embryo | 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](/blog/2022/01/01/vfb-content-report/) after each
data release; the machine-readable version is
| [scRNAseq data from Özel (2021)](https://virtualflybrain.org/reports/VFBseq_00001758) | Pupa, adult | Neuronal diversity and convergence in a visual system developmental atlas | 522 | 8,138 |
| [scRNAseq data from Li (2022), 10x](https://virtualflybrain.org/reports/VFBseq_00000538) | Adult | Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly | 335 | 12,747 |
| [scRNAseq data from Kurmangaliyev (2020)](https://virtualflybrain.org/reports/VFBseq_00000001) | Pupa | Transcriptional Programs of Circuit Assembly in the Drosophila Visual System | 232 | 7,473 |
| [scRNAseq data from Calderon (2022)](https://virtualflybrain.org/reports/VFBseq_00002863) | Embryo | The continuum of Drosophila embryonic development at single-cell resolution | 223 | 4,539 |
| [scRNAseq data from Li (2022), Smart-seq2](https://virtualflybrain.org/reports/VFBseq_00000777) | Adult | Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly | 211 | 15,011 |
| [scRNAseq data from Lu (2023)](https://virtualflybrain.org/reports/VFBseq_00001468) | Adult | Aging Fly Cell Atlas identifies exhaustive aging features at cellular resolution | 143 | 5,399 |
| [scRNAseq data from Allen (2020)](https://virtualflybrain.org/reports/VFBseq_00002728) | Adult | A single-cell transcriptomic atlas of the adult Drosophila ventral nerve cord | 106 | 6,264 |
| [scRNAseq data from Xie (2021)](https://virtualflybrain.org/reports/VFBseq_00002581) | Prepupa, pupa, adult | Temporal evolution of single-cell transcriptomes of Drosophila olfactory projection neurons | 92 | 8,317 |
| [scRNAseq data from Davie (2018)](https://virtualflybrain.org/reports/VFBseq_00000243) | Adult | A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain | 82 | 6,704 |
| [scRNAseq data from Konstantinides (2022)](https://virtualflybrain.org/reports/VFBseq_00002364) | L3 larva | A complete temporal transcription factor series in the fly visual system | 75 | 7,154 |
| [scRNAseq data from Hörmann (2020)](https://virtualflybrain.org/reports/VFBseq_00002461) | Pupa | A combinatorial code of transcription factors specifies subtypes of visual motion-sensing neurons in Drosophila | 40 | 3,874 |
| [scRNAseq data from Brunet Avalos (2019)](https://virtualflybrain.org/reports/VFBseq_00003150) | L1 larva | Single cell transcriptome atlas of the Drosophila larval brain | 28 | 6,772 |
| [scRNAseq data from Mokashi (2021)](https://virtualflybrain.org/reports/VFBseq_00003188) | Adult | Developmental Alcohol Exposure in Drosophila: Effects on Adult Phenotypes and Gene Expression in the Brain | 26 | 3,664 |
| [scRNAseq data from Baker (2021)](https://virtualflybrain.org/reports/VFBseq_00003265) | Adult | The Drosophila brain on cocaine at single-cell resolution | 22 | 3,634 |
| [scRNAseq data from Li (2017)](https://virtualflybrain.org/reports/VFBseq_00002527) | Pupa, adult | Classifying Drosophila Olfactory Projection Neuron Subtypes by Single-Cell RNA Sequencing | 22 | 7,562 |
| [scRNAseq data from Saavedra (2023)](https://virtualflybrain.org/reports/VFBseq_00003198) | Adult | REPTOR and CREBRF encode key regulators of muscle energy metabolism | 14 | 1,402 |
| [scRNAseq data from Ing-Simmons (2021)](https://virtualflybrain.org/reports/VFBseq_00002844) | Embryo | Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning | 13 | 6,763 |

Clusters a study left untyped, or typed only as a generic cell or neuron, are not
loaded, so these counts can be lower than the study's own. Counts here are of what VFB
holds, and are regenerated with the [content report](/blog/2022/01/01/vfb-content-report/)
after each data release; the machine-readable version is
[scRNAseq_DataSets.tsv](https://github.com/VirtualFlyBrain/VFB_reporting_results/blob/master/scRNAseq_DataSets.tsv).
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