Developmental transcriptional atlas of the Drosophila melanogaster VNC (neurons - loom version)

This object contains scRNA-seq counts data of the Drosophil malanogaster VNC atlas presented in "A Developmental Atlas of the Drosophila Nerve Cord Uncovers a Global Temporal Code for Neuronal Identity" (Cachero et al. 2025, doi.org/10.1101/2025.07.16.664682). This dataset comprises neurons and neuronal precursors. Data were collected from 92 individual animals, covering four developmental stages (6, 24, 36 and 48 hours after puparium formation) and both sexes. Each stage–sex condition is represented by 5 to 18 biological replicates, covering between 5 to 11 different genotypes.

Two umap embeddings are stored in the object:

UMAPallages: calculated before stage integration
umap: calculated after integration

Cellular metadata:

Sex: sex of the animal the cell originated from
Stage: developmental stage of the animal the cell originated from
birthtime: predicted neurogenesys period (primary, early secondary, secondary)
maturation: maturation state of the neuron
hemilineage: predicted hemilineage
hemilineage_stem: predicted hemilineage for less mature neurons subset
soma_neuromere: predicted soma neuromere

soma_neuromere_MCNS: predicted soma neuromere matching annotation from MCNS dataset for 01B (T1>T2, T2>T3, T3>A)
precursorsType: whether neuroblast (NB), ganglion mother cell (GMC), immature post mitotic neuron (earlyNeuron) or more mature neuron (neuron). Applies only to precursors subset
fru_clone: fruitless clone predicted identity
fru_dsx: whether neuron expresses fru, dsx or both. Applies only to secondary neurons
amines: predicted aminergic identity
neurotransmitter: predicted neurotransmitter identity