1. Neuroscience
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Cellular diversity in the Drosophila midbrain revealed by single-cell transcriptomics

  1. Vincent Croset
  2. Christoph Daniel Treiber  Is a corresponding author
  3. Scott Waddell  Is a corresponding author
  1. University of Oxford, United Kingdom
Research Article
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Cite this article as: eLife 2018;7:e34550 doi: 10.7554/eLife.34550


To understand the brain, molecular details need to be overlaid onto neural wiring diagrams so that synaptic mode, neuromodulation and critical signaling operations can be considered. Single-cell transcriptomics provide a unique opportunity to collect this information. Here we present an initial analysis of thousands of individual cells from Drosophila midbrain, that were acquired using Drop-Seq. A number of approaches permitted the assignment of transcriptional profiles to several major brain regions and cell-types. Expression of biosynthetic enzymes and reuptake mechanisms allows all the neurons to be typed according to the neurotransmitter or neuromodulator that they produce and presumably release. Some neuropeptides are preferentially co-expressed in neurons using a particular fast-acting transmitter, or monoamine. Neuromodulatory and neurotransmitter receptor subunit expression illustrates the potential of these molecules in generating complexity in neural circuit function. This cell atlas dataset provides an important resource to link molecular operations to brain regions and complex neural processes.

Data availability

Sequencing data have been deposited in SRA under accession code SRP128516. Digital Expression Matrix is provided as supplementary file.

The following data sets were generated

Article and author information

Author details

  1. Vincent Croset

    Center for Neural Circuits and Behaviour, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  2. Christoph Daniel Treiber

    Center for Neural Circuits and Behaviour, University of Oxford, Oxford, United Kingdom
    For correspondence
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6994-091X
  3. Scott Waddell

    Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, United Kingdom
    For correspondence
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4503-6229


Wellcome (200846/Z/16/Z)

  • Scott Waddell

Bettencourt Schueller Foundation

  • Scott Waddell


  • Vincent Croset


  • Christoph Daniel Treiber

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Mani Ramaswami, Trinity College Dublin, Ireland

Publication history

  1. Received: December 21, 2017
  2. Accepted: April 18, 2018
  3. Accepted Manuscript published: April 19, 2018 (version 1)
  4. Version of Record published: April 30, 2018 (version 2)


© 2018, Croset et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.


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