u After cycle 5—Intensities appear after template registration, which requires the first 5 cycles of
sequencing. Although it is safe to end a run after cycle 1, ending after cycle 5 is recommended. Do not
end a run during cluster generation.
u Read 1 or Index 1 Read—End the run
before
paired-end resynthesis begins. The flow cell cannot be
saved for later rehybridization after paired-end resynthesis begins.
Required Consumables
A rehybridization run requires a new NextSeq reagent cartridge and buffer cartridge regardless of when the
run was stopped.
End the Current Run
1 Select End Run. When prompted to confirm the command, select Yes.
2 When prompted to save the flow cell, select Yes. Saving the flow cell does not ensure that the current run
will be salvageable. Note the expiration date for rehybridization.
3 Remove the saved flow cell and set aside at 2°C to 8°C until you are ready to set up the rehybridization
run.
NOTE
You can store the flow cell up to 7 days at 2°C to 8°C in the plastic clamshell case
without
the desiccant
package. For best results, rehybridize the saved flow cell within 3 days.
Perform a Manual Wash
1 From the Home screen, select Perform Wash.
2 From the Wash Selection screen, select Manual Post-Run Wash. See
Perform a Manual Wash
on page
24.
NOTE
If you have not removed the reagent cartridge and buffer cartridge from the stopped run, you can use them
for the manual wash. Otherwise, perform the manual wash with the reagent wash cartridge and buffer wash
cartridge.
Set Up a New Run on the BaseSpace Prep Tab
1 If the instrument is configured for BaseSpace or BaseSpace Onsite, set up a new run on the Prep tab
using the same parameters as the original run.
TIP
Click the Pools tab, select the appropriate Pool ID to retain the previous run settings, and then assign a
unique name for the new run.
Set Up a Run on the Instrument
1 Prepare a new reagent cartridge.
2 If the saved flow cell was stored, allow it to reach room temperature (15–30 minutes).
3 Clean and load the saved flow cell.
Document # 15046563 v04
For Research Use Only. Not for use in diagnostic procedures.
32
NextSeq 500 System Guide
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