CHMI owns and operates its own MiniSeq. This instrument is ideal for a bacterial genome sequencing, PCR panel assays, and low-coverage QC runs prior to larger NovaSeq runs.
- Sequencing by Synthesis: 5 minute YouTube video
- MiniSeq system guide
- MiniSeq denature and dilute guide
- MiniSeq support site
- MiniSeq training videos
If you plan to sequence on the same day, place the flow cell at room temperature and put the reagent cartridge in a water bath to thaw before starting your pool. The flow cell needs to equilibrate for at least half an hour and the reagent cartridge needs even more time to thaw. You can also thaw the reagent cartridge in the fridge or cold room overnight. Once thawed, use within a week.
Denaturation and Dilution
The following protocol is based on the MiniSeq Denature and Dilute Guide (linked above), with few adjustments. The biggest change is that we do not vortex the libraries after denaturation.
Before proceeding to these steps, make sure your flow cell is out at room temperature and your reagent cartridge is thawing. In addition to these sequencing reagents, you will need pooled libraries, 20pM denatured PhiX, 1M Tris-HCl ph 8, 1N NaOH, MilliQ water, RSB, and hybridization buffer.
- In a 1.5mL tube labeled "1 nM", add the following, according to pool nM concentration:
2. In a 1.5mL tube, make a 0.1N dilution of NaOH by adding 900uL of MilliQ water and 100uL 1N NaOH. Vortex and set aside.
3. In another 1.5mL tube, make a 200mM dilution of Tris by adding 800uL of MilliQ water and 200uL 1M Tris. Vortex and set aside.
2. In another 1.5mL tube labeled "5 pM," combine 5ul 1nM pool with 5ul 0.1 N NaOH and pipette to mix.
3. Incubate for 5 minutes at room temperatures.
7. Immediately 5ul 200mM Tris and pipette to mix.
8. Add 985ul of hybridization buffer. Slowly pipette to mix or invert the tube. Your "5pM" tube now contains your denatured library pool at 5pM concentration.
10. Proceed to the final dilution of your samples. Label your new tube "Final" and add the appropriate volumes of hybridization buffer, 5pM library, and 20pM PhiX:
|Desired Loading Concentration pM||ul Hyb Buffer||ul 5pM Library Pool||ul 20pM PhiX for 1% Spike-In||ul 20pM PhiX for 5% Spike-In||ul 20pM PhiX for 20% Spike-In|
11. Invert to mix and keep on ice until ready to use.
Loading the Sequencer
Before loading, make sure your run has been programmed in Local Run Manager (on the MiniSeq) or another sample sheet template.
1. Make sure the flow cell has been at room temperature for at least 30 minutes to equilibrate. Bring it to the sequencer.
4. Press "Sequence" and log in to Basespace.
2. Open the container and remove the flow cell. Hold the flow cell to the light and inspect the for any scratches or defects.
3. Put some ethanol on a kim wipe, and slowly wipe the glass face of the flow cell in a single direction. Take a clean kim wipe and repeat to remove any excess ethanol or remaining dust.
5. Load the flow cell. Press the white button to release the old flow cell and push the clamp down gently to secure the new flow cell.The pins on the machine line up with the holes on the flow cell. Select Next.
6. Remove the Spent Reagents Container. There is a chemical waste carboy around the corner from the sequencer. The container does not have a lid. Empty it into the waste carboy near the NextSeq and return to its position. This waste contains formamide. Never dispose it down the sink and change gloves if you spill or drip.
7. Remove the old Reagent Cartridge from the sequencer. Remove the reservoir behind position #9. This contains trace amounts of formamide and is disposed in a bag for chemical waste pickup. The rest of the cartridge can be disposed in regular trash.
8. Return to your new, thawed reagent cartridge. Gently tilt it back and forth to check thaw and mix reagents.
9. Hold a p1000 tip in your hand and stab into the foil of well #16 on the reagent cartridge. Open up the foil of the well completely.
10. Pipette your denatured, diluted pool into the well. Pipette the entire contents of the well, including any that got into the cap. You will have about 500 µL total.
11. Load the reagent cartridge into the sequencer.
12. Follow the on-screen prompts, select your Basespace run, and confirm the parameters.
13. After the self-check, press Start!