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Representative Results






Purification of Low-abundant Cells in the Drosophila Visual System

Published: September 26th, 2018



1Department of Neurobiology, Harvard Medical School

Here, we present a cell dissociation protocol for efficiently isolating cells present at low abundance within the Drosophila visual system through fluorescence activated cell sorting (FACS).

Recent improvements in the sensitivity of next generation sequencing have facilitated the application of transcriptomic and genomic analyses to small numbers of cells. Utilizing this technology to study development in the Drosophila visual system, which boasts a wealth of cell type-specific genetic tools, provides a powerful approach for addressing the molecular basis of development with precise cellular resolution. For such an approach to be feasible, it is crucial to have the capacity to reliably and efficiently purify cells present at low abundance within the brain. Here, we present a method that allows efficient purification of single cell clones in genetic mosaic experiments. With this protocol, we consistently achieve a high cellular yield after purification using fluorescence activated cell sorting (FACS) (~25% of all labeled cells), and successfully performed transcriptomics analyses on single cell clones generated through mosaic analysis with a repressible cell marker (MARCM). This protocol is ideal for applying transcriptomic and genomic analyses to specific cell types in the visual system, across different stages of development and in the context of different genetic manipulations.

The Drosophila visual system is an outstanding model for studying the genetic basis of development and behavior. It comprises a stereotyped cellular architecture1 and an advanced genetic toolkit for manipulating specific cell types2,3. A major strength of this system is the ability to autonomously interrogate gene function in cell types of interest with single cell resolution, using genetic mosaic methods4,5. We sought to combine these genetic tools with recent advances in next generation sequencing to perform cell type-specific....

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1. Planning Before the Experiment

  1. Before starting the experiment, perform a small-scale pilot experiment to confirm if the genetics work as expected to specifically label the desired cells.
    1. As a first pass, use immunohistochemistry and light microscopy to determine if unwanted cells are labeled. Ideally, genetic markers will be specific within the retina and optic lobe (Figure 3). Only optic lobes are used for cell dissociation and so labeling in the .......

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General scheme
A general scheme of the protocol is shown in Figure 1. The protocol is divided into three major parts: fly work, sample preparation, sequencing and data analysis. The "Planning before the experiment" session of the protocol is not included in the general scheme for simplicity.

A calendar of the major parts of the protocol.......

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This protocol is simple and not technically difficult to execute, but there are several key steps that if overlooked will cause a considerable reduction in cellular yield. (Step 2.3.2.) It is crucial that crosses are healthy, and that the food does not dry out. Regular watering of crosses is essential to maximize the number of flies available for dissection that are of the right genotype and at the correct stage of development. How often crosses need to be watered will vary depending on the food used and the housing cond.......

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This research was funded by the NINDS of the National Institutes of Health under award number K01NS094545, andgrants from the Lefler Center for the Study of Neurodegenerative Disorders. We acknowledge Liming Tan and Jason McEwan for valuable conversations.


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Name Company Catalog Number Comments
Liberase TM Roche 5401127001 Proteolytic enzyme blend
NaCl Sigma-Aldrich S3014
KCl Sigma-Aldrich P9541
NaH2PO4 Sigma-Aldrich S9638
NaHCO3 Sigma-Aldrich  S5761
Glucose Sigma-Aldrich G0350500
L-Glutathione Sigma-Aldrich G6013
Heat Inactivated Bovine Serum Sigma-Aldrich F4135
Insulin Solution Sigma-Aldrich I0516
L-Glutamine Sigma-Aldrich G7513
Penicillin-Streptomycin Solution Sigma-Aldrich P4458
Schneider's Culture Medium Gibco 21720024
Papain Worthington LK003178
2-Mercaptoethanol  Sigma-Aldrich M6250-100ML
RNeasy Micro Kit Qiagen 74004 RNA purification kit
RNase-free DNase Qiagen 79254
SuperScript II Reverse Transcriptase Life Technologies 18064-014
dNTP Mix Life Technologies R0191
MgCl2 Solution Sigma-Aldrich M1028-10X1ML
Betaine Solution Sigma-Aldrich B0300-1VL
RNaseOUT Life Technologies 10777-019
Q5 High-Fidelity 2x Master Mix New England Biolabs M0492S
MinElute PCR Purification Kit Qiagen 28004
Nextera XT DNA Library Prepration Kit Illumina FC-131-1024
Nextera XT Index Kit Illumina FC-131-1001
Test Tube with Cell Strainer Snap Cap Falcon 352235
Bottle-Top Vacuum Filter Systems Corning CLS431153
ThermoMixer F1.5 Eppendorf 5384000020
FACSAria Flow Cytometer BD Biosciences 656700
HiSeq 2500 Sequencing System Illumina SY–401–2501

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