TITLE: L1 stage C. elegans dissociation for FACS isolation and RNA-seq analysis of intestine-specific cells
AUTHORS: Robert TP Williams, Erin Osborne Nishimura

[DESCRIPTION]
This protocol is for generating a single cell suspension suitable for isolation of intestine-specific cells through Fluorescence Activated Cell Sorting (FACS) from L1 stage C. elegans. This protocol utilizes treatment with SDS-DTT solution and Pronase E to disrupt the cuticle. Worms are mechanically homogenized with a dounce homogenizer.

[STEPS]
SECTION: Before beginning
1. Prepare reagents in advance


L15-10 Buffer: Mix 500 ml Leibovitz's L-15 Medium, 50 ml Fetal Bovine Serum (heat inactivated), 50 ul of 100x Penicillin-Streptomycin solution and 7.7 g sucrose. Filter with 0.2 micron pore filter. Store at 4ºC.

Egg Buffer: Mix 29.5 ml of 2M NaCl, 12 ml of 2M KCl, 1 ml of 1M CaCl2, 1 ml of MgCl2, 12.5 ml of 1M HEPES-NaOH pH 7.2 and 435 ml molecular grade water. Filter with 0.2 micron pore filter. Store at 4ºC.

Pronase E solution (15 mg/ml): Weigh 150 mg of Protease from Streptomyces griseus (Sigma P8811-1G) into a 15 ml tube. Dissolve the enzyme in 10 ml of Egg Buffer. Nutate the solution for approximately 10 minutes until dissolved. Prepare 1 ml aliquots in 1.5 ml tubes. Store aliquots at -20ºC.
SECTION: Before beginning
2. On day of protocol:

Cool swinging bucket centrifuge to 4ºC
Thaw pronase aliquots at room temperature
Place L15-10 and egg buffer on ice
Wash and sterilize dounce homogenizer and pestle A (1ml H20, 1ml 70% EtOH)
SECTION: Before beginning
3. Starting material: 
Worm suspension in 15 ml tube (material generated from this protocol)
Strains: N2, fluorescent sorting strain

Perform this protocol on both strains in parallel

Note: The volumes for chemical and enzymatic treatments in this protocol require an L1 pellet less than 200 uL. If L1 pellet exceeds 200 ul, utilize 2x the L1 pellet volume.
SECTION: SDS-DTT Treatment
7. Once the worm suspension is free of E. coli, centrifuge worm suspension at 2,000 rcf for 1 minute 

SECTION: SDS-DTT Treatment
8. Resuspend the worm pellet in 1 ml of M9 and transfer to a 1.5 ml tube.
SECTION: SDS-DTT Treatment
9. Pellet the worms again at 2,000 rcf for 1 minute.
SECTION: SDS-DTT Treatment
10. Transfer 10 ul of L1 worm pellet to 1ml of Qiazol and store at -80°C for downstream RNA analysis
SECTION: SDS-DTT Treatment
11. Resuspend the worm pellet in 200 ul of fresh SDS-DTT solution
SECTION: SDS-DTT Treatment
12. Incubate for 2 min room temperature to digest the cuticle
NOTE: 
- Worms should look ruffled, and pharynx should change from thin and elongated to short and round
- Incubation exceeding 2 min will damage the sample
SECTION: SDS-DTT Treatment
13. Quench reaction by adding 800 ul of ice cold egg buffer
SECTION: SDS-DTT Treatment
14. Pellet worms at 13,000 rcf for 15 seconds at 4ºC
SECTION: SDS-DTT Treatment
15. Decant the supernatant and replace with 1 ml of ice-cold egg buffer
SECTION: SDS-DTT Treatment
16. Repeat the egg buffer wash for a total of 5 washes
SECTION: Pronase E Treatment
17. Resuspend the SDS-DTT treated worms in 200 ul of 15 mg/ml Pronase E
SECTION: Pronase E Treatment
18. Incubate for 30 minutes at room temperature nutating to digest the cuticle
SECTION: Cell dissociation
24. Transfer the worm suspension to a 2 ml glass dounce homogenizer
SECTION: Cell dissociation
25. Perform 100 strokes with dounce pestle A to generate a worm slurry
SECTION: Cell dissociation
26. Visually confirm worm dissociation by viewing a 2 ul sample of worm slurry on a fluorescent microscope
SECTION: Cell dissociation
27.2. Pellet undissociated worms at 100 rcf for 1 minute at 4ºC in swinging bucket centrifuge

NOTES:
- This step will separate the dissociated cells from intact worms
- Cells will remain in the supernatant
- Intact and partially dissociated worms will remain in the pellet
- Ensure your cell type of interest is not lost during this step. 
- Visually confirm fluorescent cells are present in the supernatant. 
- Visually confirm fluorescent cells are not present in the pellet. 
- You may need to reduce the centrifuge speed and/or time if fluorescent cells are in the pellet of this step.
SECTION: Measure approximate cell concentration
31. Load 10 ul of cell suspension to a Bio-Rad TC20 automated cell counting slide. Also can use a hemocytometer.
SECTION: Measure approximate cell concentration
33. Dilute the sample to    if above this concentration with L15-10
SECTION: Measure approximate cell concentration
34. Microscopically confirm fluorescent cells are present in the cell counting slide
SECTION: Measure approximate cell concentration
32. This protocol should yield between   to    total cells

SECTION: Measure approximate cell concentration
35. If the total cell yield is less than    cells and many intact worms remain, repeat the SDS-DTT, Pronase E and dounce homogenization steps
SECTION: Pronase E Treatment
19. Quench the Pronase E treatment by adding 1 ml of L15-10
SECTION: Pronase E Treatment
20. Pellet the worms at 13,000 rcf for 15 seconds at 4°C
SECTION: Pronase E Treatment
21. Decant the supernatant and resuspend the worms in 1 ml of L15-10
SECTION: Pronase E Treatment
22. Pellet the worms at 13,000 rcf for 15 seconds at 4°C
SECTION: Pronase E Treatment
23. Resuspend the worms in 1ml of L15-10
SECTION: Cell dissociation
27.3. Aspirate 1 ml of the cell-containing supernatant. Keep the pipette away from the pelleted worm debris.
SECTION: Cell dissociation
27.4. Dispense the cell suspension though a 35-micron nylon mesh filter into a 5 ml flow cytometry tube
SECTION: Cell dissociation
28. Resuspend remaining worm slurry in 1ml of L15-10
SECTION: Cell dissociation
30. - Transfer 70 ul of cells to 1 ml of Qiazol and store at -80°C for downstream RNA analysis
- Continue to step 31
- Retain the remaining ~2ml of cells for FACS
SECTION: Harvest L1 Worms
4. Harvest the synchronized L1 worms by washing the plates with fresh M9. 
SECTION: Harvest L1 Worms
5. Pass the harvested L1 suspension through a 20 micron filter. This will filter any contaminating debris (agar chunks, partially bleached worm chunks) and any unhatched or dead embryos.
SECTION: Harvest L1 Worms
6. Pellet the worms in a 15 ml tube for 1 min at 2,000 rcf. Discard the supernatant and repeat M9 washes until the supernatant is free of visible E. coli.
SECTION: Cell dissociation
27. Harvest the cells
SECTION: Cell dissociation
27.1. Transfer worm slurry to 1 ml centrifuge tube
SECTION: Cell dissociation
29. For the sorting strain, perform an additional round of dissociation and cell harvest (Steps 24-28). You will perform a total of two to three homogenization cycles, until few intact worms remain.

Total cell suspension volumes:
- Control strain = 1ml
- Sorting strain = 2-3ml
SECTION: Measure approximate cell concentration
36. Move on to FACS protocol