When the run pauses, a dialog box opens with options to raise the sippers and empty the full container.
Empty Spent Reagents Container
1 Select Raise Sippers.
2 Remove the spent reagents container and discard the contents appropriately.
3 Return the empty container to the buffer compartment.
4 Select Continue. The run resumes automatically.
Rehybridization Workflow
A rehybridization run might be necessary if metrics generated during the first few cycles show
intensities below 2500. Some low-diversity libraries can show intensities below 1000, which is expected
and cannot be resolved with rehybridization.
NOTE
The End Run command is final. The run cannot be resumed, run consumables cannot be reused, and
sequencing data from the run are not saved.
When you end a run, the software performs the following steps before the run ends:
u Places the flow cell in a safe state.
u Unlocks the flow cell RFID for a later run.
u Assigns a rehybridization expiration date to the flow cell.
u Writes the run logs for completed cycles. A delay is normal.
u Bypasses the automatic post-run wash.
When you start a rehybridization run, the software performs the following steps to perform the run:
u Creates a run folder based on a unique run name.
u Checks that the flow cell rehybridization date has not expired.
u Primes reagents. A delay is normal.
u Skips the clustering step.
u Removes the previous Read 1 primer.
u Hybridizes a fresh Read 1 primer.
u Continues through Read 1 and the remainder of the run based on specified run parameters.
Points to End a Run for Rehybridization
Later rehybridization is possible only if you end the run at the following points:
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.
Document # 1000000041922 v01
For Research Use Only. Not for use in diagnostic procedures.
46
NextSeq 550Dx Research Mode Instrument Reference Guide
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