McClean: FISH (Ping)

Overview

This is a draft protocol. This will be optimized to measure transcriptional response from the pheromone and hyperosmotic stress pathway in S. cerevisiae

Solutions

FISH Probes

Fish probes are designed using the probe designed from BioSearch technologies and ordered from BioSearch technologies.

Reconstituting the Dried Probe Stock

The probe stock should be sufficient to provide up to 200 or more hybridizations. For frequent use, aliquots of the probe stock can be stored at +2 to +8 °C in the dark for up to a month. Redissolve the dried oligonucleotide probe blend in 200 μL of T₁₀E₁ buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0), to create a probe stock at a total oligo concentration of 25 μM. Mix well by vortexing and spin down.

Short-Term Storage & Daily Use

Dissolved probe mix should be subjected to a minimum number of freeze-thaw cycles. For daily and short-term use, the mix can be stored at 4°C in the dark for up to a month.

Long-Term Storage

Store the probes in the dark at -20°C for storage lasting longer than a month.

Buffer B

• 1.2M Sorbitol
• 100mM KHPO₄ pH 7.5

To make mix together:

• 8ml of 1M KH₂PO₄
• 41.5 ml of 1M K2₂HPO₄
• Sorbitol 10.93g

β-Mercaptoethanol

Fisher O3446I; Stored in the flammables cabinet.

Concanavalin A Solutions

• Concanavalin A Solution for Microfluidics
• Concanavalin A Solution without Ions

DAPI Stock Solution

• DAPI, dilactate, catalog #D9564 from Sigma

To make a 5 mg/mL DAPI stock solution (10.9 mM for dilactate), dissolve the contents of one vial (10 mg) in 2 mL of deionized water (dH2O). Note: This DAPI derivative is not very soluble in phosphate-buffered saline (PBS).

Storage: For long-term storage the stock solution can be aliquoted and stored at ≤–20°C. For shortterm storage the solution can be kept at 2–6°C, protected from light. When handled properly, DAPI solutions are stable for at least six months.

Vanadyl Ribonucleoside Complex (VRC)

Aliquoted and stored in the -20°C freezer. Stock solution is 200mM. Defrost the frozen stock from the freezer at room temperature. This can be reconsistuted to a green-black clear solution by incubating the tube at 65°C only if necessary.

Lyticase

• Resuspend Sigma cat #L5263 in 1X PBS to 25000U per ml.
• Store at -20°C in single use aliquots (50U).
• Use 50U in 1ml of spheroplast buffer for slow growing cells.

PBS 10X (RNase free)

Ambion #AM9624 or equivalent

Nuclease Free Water

Ambion #AM9932 or equivalent

Hybridization Buffer

• Dextran sulfate, #D6001 from Sigma or equivalent
• 20X saline-sodium citrate (SSC) (nuclease-free), catalog #82021-484 from VWR
• Formamide (deionized), catalog #AM9342 from Ambion or equivalent
• Nuclease-free water (to 10 mL final volume), catalog #AM9932 from Ambion or equivalent

Mix together 1g of Dextran sulfate, 1ml of 20x saline-sodium citrate (SSC), 1ml of formamide and bring everything up to 10ml with nuclease-free water.

WARNING: Formamide is a teratogen that is easily absorbed through the skin and should be used in a chemical fume hood. Be sure to let the formamide warm to room temperature before opening the bottle.

Wash buffer without DAPI (50 mL)

• 20X SSC, catalog #82021-484 from VWR or equivalent
• Formamide (deionized), catalog #AM9342 from Ambion or equivalent
• Nuclease-free water, catalog #AM9932 from Ambion or equivalent

Mix together 5ml of SCC, 5 ml of formamide (for 10% final concentration), and bring everything up to 50ml with nuclease-free water.

WARNING: Formamide is a teratogen that is easily absorbed through the skin and should be used in a chemical fume hood. Be sure to let the formamide warm to room temperature before opening the bottle.

Wash buffer w/DAPI (50 mL)

• DAPI, catalog #D9564 from Sigma or equivalent (Stock is at?)
• 20X SSC (5 mL), catalog #82021-484 from VWR or equivalent
• Formamide (deionized) (5 mL for 10% final concentration), catalog #AM9342 from Ambion or equivalent
• Nuclease-free water (to 50 mL final volume), catalog #AM9932 from Ambion or equivalent

Add together 5ml SSC, 5ml of formamide (for a final concentration of 10%), add DAPI to have a final concentration of 5ng/ml and then bring volume up to 50ml with nuclease-free water.

10% glucose

• α-D-Glucose, catalog #158968 from Sigma or equivalent
• Nuclease-free water, catalog #AM9932 from Ambion or equivalent

Weight out 10g of glucose into 70 ml of nuclease-free water. Dissolve glucose and bring volume up to 100ml with nuclease-free water. Autoclave.

Anti-fade buffer WITHOUT enzymes

• 10% glucose in nuclease-free water
• 1 M Tris-HCl, pH 8.0, catalog #AM9855G from Ambion or equivalent
• 20X SSC, catalog #82021-484 from VWR or equivalent
• Nuclease-free water, catalog #AM9932 from Ambion or equivalent
• Glucose oxidase (diluted to 3.7 mg/mL stock), catalog #G0543 from Sigma or equivalent
• Catalase, catalog C3155 from Sigma or equivalent

NOTE: Mix together 0.85 mL of nuclease-free water and add 100 µL of 20X SSC, 40 µL of 10% glucose and 10 µL of 1 M Tris-HCl. Vortex and then transfer 100 µL of this “GLOX” buffer to another tube, to which one should add 1 µL of the glucose oxidase stock and 1 µL of mildly vortexed catalase suspension. The remainder can be used as an equilibration buffer.

Anti-fade buffer WITH enzymes (“GLOX” buffer)

• 10% glucose in nuclease-free water
• 1 M Tris-HCl, pH 8.0, catalog #AM9855G from Ambion or equivalent
• 20X SSC, catalog #82021-484 from VWR or equivalent
• Nuclease-free water, catalog #AM9932 from Ambion or equivalent
• Glucose oxidase (diluted to 3.7 mg/mL stock), catalog #G0543 from Sigma or equivalent
• Catalase, catalog C3155 from Sigma or equivalent

NOTE: Mix together 0.85 mL of nuclease-free water and add 100 µL of 20X SSC, 40 µL of 10% glucose and 10 µL of 1 M Tris-HCl. Vortex and then transfer 100 µL of this “GLOX” buffer to another tube, to which one should add 1 µL of the glucose oxidase stock and 1 µL of mildly vortexed catalase suspension. The remainder can be used as an equilibration buffer.

Protocol

Fixing Cells

1. Grow culture to Klett ~50-100 in LFM media (can also use YPD or SC media). If you are measuring OD, grow cells to an OD of ~0.4-0.6
2. Fix cells by adding 32% paraformaldehyde directly to the culture to a final concentration of 6.4% (4ml culture + 1ml paraformaldehyde). Incubate at room temperature for 45 minutes.
3. Spin the cells down at 3000 xg for 5 minutes. Resuspend in 1.8 ml Buffer B and transfer to a 2 ml eppendorf.
4. Wash cells 3X with 1.8ml Buffer B by pipetting up and down gently. Spin down at 3000 xg for 5 minutes each time.
5. Resuspend pellet in 1002 μL spheroplast buffer plus VRC plus lyticase plus BME (890ul Buffer B + 100ul VRC + 10ul Lyt + 2ulBME).
6. Incubate at 37°C. Monitor the digestion every 10 minutes or so. Check the cells on the small scope by the nanodrop. Once you reach ~90% phase dark (digested) cells the digestion is done. The first time you try the protocol, this step will need to be optimized. Previous attempts suggest that about 15 minutes works well.
7. Spin 5 min at 3000 xg (do not spin too hard as cells are fragile due to lyticase).
8. Wash 3X with 1ml Buffer B, spinning at 2000 rpm for 5 minutes each wash.
9. Gently add 1ml 70% ethanol.
10. Incubate at 4°C overnight. Cells can be stored like this for about a week before hybridization (perhaps longer, this would need to be tested. The Botstein lab protocol seems to indicate that cells can be stored in this state at -20°C for up to several months).

Hybridization

1. Mix a small volume of the probe stock (1µL) with Hybridization Buffer to 100 µL final volume for each sample to be hybridized. Vortex and centrifuge the probe solution(s) briefly.
   • For the initial test of a probe-set it is best to start 4 separate hybridization reactions to determine which dilution of the probe stock is optimal for detection. Add 1 µl from each of each of the working dilutions (1:10, 1:5, 1:2.5 ) as well as the probe stock itself into separate aliquots of the hybridization solution. The working dilutions should be made into T₁₀E₁ (same as for the initial resuspension of the dried probe).
2. Gently aspirate the 70% ethanol off of the sample.
3. Incubate the yeast cells in 1ml of 0.1mg/mL concanavalin A (see Concanavalin A Solution (without ions) ) for 2 hours and then let settle onto the chambered coverglass pre-coated with concanavalin A. The volume of the wells of the 96-well plate is a maximum of 200μL, so add 100μL of cells, and let this settle. Depending on the density of cells this may be too much or too little and the amount of settling time or the volume of cells added may need to be adjusted. At trick is to load the cells, then monitor the settling and density at the bottom of the well using transmitted light on the Nikon microscope.
4. Add 100μL of wash buffer with the same percentage formamide (10%) as the hybridization buffer and let stand for 2-5 minutes.
5. Aspirate the wash buffer and then add 100 µL of hybridization solution plus probe.
6. Cover the wells with parafilm or tape during incubation to prevent drying of the hybridization solution during the incubation.
7. Incubate in a dark humidified chamber for 4 hours at 37°C. If stronger signals are desired for low expressed genes, the hybridization can be done overnight.
8. Add 100μL of wash buffer to the sample. Pipette up and down gently.
9. Incubate at 37°C for 30 minutes in the dark.
10. Aspirate the wash buffer, then re-suspend in another 100 mL of wash buffer with 5 ng/mL DAPI for nuclear counterstaining.
11. Incubate at 37°C for 30 minutes in the dark.
12. Aspirate the wash buffer and resuspend in 2x SSC.
13. Aspirate the SSC and add the GLOX buffer without enzymes for equilibration; incubate for 1-2 minutes.
14. Aspirate the buffer and add 100 µL of GLOX buffer to which the enzymes (glucose oxidase and catalase) have been added.
15. Proceed to imaging

Notes

Please feel free to post comments, questions, or improvements to this protocol. Happy to have your input!

*Megan N McClean The Buffer B protocol is not exactly 1.2M sorbitol because the volume of the sorbitol added is not taken into account, similarly the KHPO₄ concentration is slightly less than 100mM. This is the protocol that the Botstein lab uses, so I'm assuming that it works fine.

*Megan N McClean This protocol is in the process or being optimized. Steps that may need to be modified (there may be more, this is just what I can think of at the moment):

• DAPI concentration

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References

Botstein lab protocol: Botstein Lab FISH Protocol

Stellaris Protocols: Stellaris FISH Protocols

Contact

• Megan N McClean 14:01, 11 October 2011 (EDT)

or instead, discuss this protocol.