Our Blog

C. elegans Agarose pad

Agarose pad method for C. elegans embryos, larvae and adult worms.

To get an accurate temperature using our CherryTemp temperature controller and ensure the accurate control we provide, samples must be placed close to the thermalisation chip (<500µm). This protocol is suitable for C. elegans embryo, larva and adult. For larva and adult, skip steps 5-7.


World fastest heater and cooler system for microscopy

Get information about how to thermalize your cells


Step 1 : Align 3 microscope slides and stick lab tape on the 2 external ones (lengthwise).

Agarose pad protocol for C elegans_Fig-01

Step 2: Drop melted agarose (50 to 100µl) on the middle one. Diameter of the pad must be around 1cm diameter.

Agarose pad protocol for C elegans_Fig-02

Step 3: Top the agarose with another clean slide, placed perpendicularly. Apply gentle pressure and allow agarose to solidify.

Agarose pad protocol for C elegans_Fig-03

Step 4: After agarose has solidified, gently remove the top slide. Agarose is ready to use, and the pad will be less than 500µM width.

Agarose pad protocol for C elegans_Fig-04

Step 5: Pick young adults into pre-cooled M9 medium (16°C).


Step 6: Dissect them by cutting at both end of the uterus using a scalpel and #15 blade to release the embryos.


Step 7: Choose the embryos of the desired stage and transfer them to a cover slip using a mouth pipette.


Step 8: Top the coverslip with our dedicated spacer. Pile-up several spacers for a particular height.

Agarose pad protocol for C elegans_Fig-05

Step 9: Transfer the pad onto the CherryTemp chip (engravements facing down, cover slip and liquid microfluidic chamber facing up). The pad must be centred on the thermalising pattern.

Agarose pad protocol for C elegans_Fig-06

Step 10: Add the embryos in a 5µl drop of M9 on the agar pad.

Agarose pad protocol for C elegans_Fig-07

Step 11: Top with a spacer (1) and high-resolution glass coverslip (2). The mounted sample is ready for observation in an upright microscope configuration.

Agarose pad protocol for C elegans_Fig-08

Step 12: Flip the mounted sample 180° for an inverted microscope configuration.

Agarose pad protocol for C elegans_Fig-09


Methods adapted from J. Dumont and J.C. Canman labs (2016) as well as various protocoles available on the Hyman lab and the worm atlas website and from our user’s feedback.

T. Davies, S. Sundaramoorthy, S.N. Jordan,M. Shirasu-Hiza, J. Dumont and J.C. Canman, 2016, “Using fast-acting temperature-sensitive mutants to study cell division in Caenorhabditis elegans“, Methods in Cell Biology, Volume 137, ISSN 0091-679X, http://dx.doi.org/10.1016/bs.mcb.2016.05.004 

Related Videos

Checkout other protocols


CherryTemp thermal stage

Discover the CherryTemp Heater Cooler

Ultra-fast shifts and temperature accuracy at the sample level

Learn more

This is a unique website which will require a more modern browser to work! Please upgrade today!