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Encyclopedia of Experiments

Single Cell Dissociation of Caenorhabditis elegans: A Method to Isolate Live Cells


This video describes a method to dissociate whole worms into a single-cell suspension suitable for FACS or immunoprecipitation of intact cells.


This protocol is an excerpt from Germany et al, Isolation of Specific Neuron Populations from Roundworm Caenorhabditis elegans, J. Vis. Exp. (2019).

1. Preparation and collection of aged worms for cell isolation

NOTE: Explained below is the isolation of cholinergic neurons from the transgenic unc-17::GFP strain (OH13083) obtained from the Caenorhabditis Genetics Center (CGC) strain repository at the University of Minnesota. It is imperative to maintain sterile conditions to prevent contamination from fungi or bacteria.

  1. Prepare and synchronize worms via the bleaching method as described by T. Stiernagle. For aging experiments, plate worms onto nematode growth medium (NGM) plates containing 25 µM water solution of fluorodeoxyuridine (FuDR) to reduce egg production and arrest egg hatching. Inspect agar plates regularly to prevent contamination or egg hatching as this will cause unreliable results.
    NOTE: For unc-17::GFP cells, typically three 100 mm x 15 mm NGM plates are used to isolate a sufficient amount of cells of interest.
  2. Collect worms and prepare buffers for cell isolation.
    1. Collect worms in a 15 mL conical tube. Wash worms from plate with 1.5 mL of M9 buffer (1 mM MgSO4, 85 mM NaCl, 42 mM Na2HPO4·7H2O, 22 mM KH2PO, pH 7.0) and centrifuge for 5 min at 1,600 x g. Discard supernatant and wash worms with 1 mL of M9 buffer. Repeat centrifugation and wash for a total of five times to remove as much E. coli contamination as possible.
      NOTE: Adding antibiotics (50 µg/mL), such as ampicillin, at this step can help reduce bacterial contamination.
    2. For two samples, prepare 2 mL of sodium dodecyl sulfate-dithiothreitol (SDS-DTT) lysis buffer: 200 mM DTT, 0.25% (w/v) SDS, 20 mM HEPES (pH 8.0), and 3% (w/v) sucrose.
    3. Prepare 15 mL of isolation buffer (118 mM NaCl, 48 mM KCl, 2 mM CaCl2, 2 mM MgCl2, 25 mM HEPES [pH 7.3]) and store it on ice.
      NOTE: Both the SDS-DTT lysis buffer and isolation buffer must be made fresh before each experiment.
  3. Cuticle disruption and single cell isolation
    1. Centrifuge animals collected in step 1.2.1 for 5 min at 1,600 x g. Remove all supernatant and suspend worms in 1 mL of M9 media and transfer to 1.5 mL microcentrifuge tube.
    2. Pellet worms with centrifugation at 1,600 x g for 5 min.
    3. Add 200 µL of SDS-DTT lysis buffer to worms and incubate for 5 min at room temperature (RT). Worms should appear to be “winkled” along the body if viewed under a light microscope.
      NOTE: Prolonged exposure to SDS-DTT lysis buffer may result in death of worms, which can be monitored by observing worms. Worms that are dead will elongate and will not curl.
    4. Add 800 µL of ice-cold isolation buffer and mix by gently flicking tube.
    5. Pellet worms for 1 min at 13,000 x g at 4 °C, remove supernatant and wash with 1 mL of isolation buffer.
    6. Repeat step 1.3.5 for a total of five times, carefully removing isolation buffer each time.
    7. Add 100 µL of protease mixture from Streptomyces griseus (15 mg/mL) (Table of Materials) dissolved in isolation buffer to the pellet and incubate for 10−15 min at RT.
      NOTE: As with the SDS-DTT lysis buffer, the extended protease digestion may result in excessive cleavage of proteins along the plasma membrane, preventing isolation of surface exposed GFP via magnetic beads.
    8. During incubation with protease mixture, apply mechanical disruption by pipetting samples up and down against the bottom of the 1.5 mL microcentrifuge tube with a 200 µL micropipette tip for ~60−70 times. Keep the pipette tip against the wall of the microcentrifuge tube with constant pressure to properly disassociate cells.
    9. To determine the stage of digestion, remove a small volume (~1−5 µL) of the digestion mixture, drop it on a glass slide and inspect it using a tissue culture microscope. After 5−7 min of incubation, worm fragments should have visibly reduced cuticle and a slurry of cells will be readily visible.
    10. Halt reaction with 900 μL of commercially available cold Leibovitz’s L-15 medium supplemented with 10% fetal bovine serum (FBS) and penicillin-streptomycin (final concentration at 50 U/mL penicillin and 50 μg/mL streptomycin).
    11. Pellet isolated fragments and cells by centrifugation for 5 min at 10,000 x g at 4 °C. Wash the pelleted cells with 1 mL of cold L-15-supplemented media twice more to ensure that excess debris and cuticle is removed.
    12. Resuspend pelleted cells in 1 mL of L-15-supplemented media and leave on ice for 30 min. Take the top layer, approximately 700−800 µL, to a microcentrifuge tube. This layer contains cells without cell debris and will be used in the subsequent isolation of cells of interest.
    13. Following manufacturer’s instructions, use an automated cell counter or hemocytometer to measure the cell density of 10−25 µL of isolated cells.

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Name Company Catalog Number Comments
Agar, Molecular Biology Grade VWR A0930
CaCl2 Sigma C5670
Contess Automated Cell Counter Invitrogen Z359629
DTT USBiological D8070
FBS Omega Scientific FB-02
Fluorodeoxyuridine Sigma F0503
HEPES Sigma H3375
KCl Amresco O395
KH2PO4 USBiological P5110
Leibovitz's L-15 Medium Gibco 21083027
MgCl2 Sigma M8266
MgSO4 USBiological M2090
Na2HPO4·7H2O USBiological S5199
NaCl VWR X190
NaOCl (Bleach) Clorox
Penicillin-Streptomicen Fisher Scientific 15140122
Pronase E Sigma 7433 protease mixture from Streptomyces griseus
SDS Amresco O227
SMT1-FLQC fluorescence stereomicroscope Tritech Research
Sucrose USBiological S8010


Single Cell Dissociation of <em>Caenorhabditis elegans</em>: A Method to Isolate Live Cells
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Source: Germany, E. M., et al. Isolation of Specific Neuron Populations from Roundworm Caenorhabditis elegans. J. Vis. Exp. (2019).

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