- Add NIB medium (CelLytic™ PN Isolation/Extraction buffer) to a new, clean, sterile, and pre-refrigerated 60 mm petri-dish.
- Collect fresh roots from seven day-old Arabidopsis plants by separating the root from the aerial part of the plant with a razor blade.
- Transfer the roots with forceps into the 60 mm Petri dish. Be sure to expose the roots to the NIB medium. Note: Remove any piece of aerial plant tissue to avoid any contamination of the root samples.
- Finely chop the roots with a razor blade for about 5 minutes.
- Add additional NIB medium if needed to keep the root tissues moist .
- Incubate 15 minutes in the cold room using a gentle horizontal shaking (i.e., platform rockers).
- In an ice bucket, place a 50 ml Falcon tube with a 30 µm strainer mounted on a 40 µm strainer at the top.
- Pre-wet the 40 and 30 µm strainers with 500 µl of NIB medium before to filter the nuclei suspension. The tube should be slightly tilted on its side.
- Using wide-bore tips, slowly pipet the chopped roots-NIB mixture from step 6 onto the pre-wet strainers.
- Using wide-bore tips, slowly rinse the plate with 500 µl NIB medium to collect the remaining nuclei.
- Add the extra 500 µl chopped root-NIB medium onto the strainers to collect the remaining nuclei and to remove debris.
- The filtered nuclei sample is ready for fluorescence-activated nuclear sorting.
- After sorting, centrifuge nuclei at 1000 × g for 10 minutes at 4°C.
- Remove the supernatant.
- Add 3ml of PBS+.
- Gently resuspend the nuclei.
Reference
Thibivilliers S, Anderson D, Libault M (2020). Isolation of Plant Root Nuclei for Single Cell RNA Sequencing. Current Protocols in Plant Biology. 5(4). doi.org/10.1002/cppb.20120.