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MAN-10152-01 for software v2.5
Finalizing
For NGS readout:
continued
6. Establish which GeoMx Seq Code plate should
be associated with the Plate Barcode in the
Readout Group Information grid.
7. Click the Update button.
8. Select the Finalize and Download Readout
Package button.
9. When asked to confirm the Readout Group
selection, click Yes.
10. Insert a USB drive into the instrument.
11. Click OK in the Readout Package Successfully
Created window to save these files to the USB: :
• Lab Worksheet contains information on the
contents of each well of each plate and can be
useful when doing library preparation and pooling.
• Configuration File will be used by the GeoMx
NGS Pipeline software to convert the Illumina
FASTQ files into DCC files.
• Seq Code UDI Indices file is needed for your
NGS Illumina platform run except when using the
NextSeq 1000/2000.
• For NextSeq 1000/2000 users, a
samplesheet.csv and whitelist.txt replace the
Seq Code UDI Indices file.
12. NextSeq 1000/2000 users with their GeoMx DSP
linked to their BaseSpace Sequence Hub
workgroup: Click Send to BaseSpace to send the
run details to the BaseSpace workgroup. A
notification that the run has been created appears
in the Notifications bell. Access through the
BaseSpace Sequence Hub to start the run, check
progress, and download results. See
BaseSpace Admin on page 85
DSP NGS Readout User Manual
for more details.
FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.
For nCounter readout:
continued
2. The first time a Hyb Code Pack lot
number is used, a pop-up window will
appear. Click New Lot to continue
finalizing the plate.
3. If you have just completed your run, the
Status for each row of your collection
plate that contained aspirate should read
Collected. Once you finalize, the status
for each row should read Finalized.
4. Select the Finalize button.
5. Insert a USB drive into the instrument.
6. Select the Download button in the
Definition File category to initiate the
download of the Cartridge Definition File
(CDF) to the USB drive. The CDF is
transferred to the nCounter MAX/FLEX
platform (see the
Readout User Manual
not edit the contents of the CDF.
7. Select the Download button in the
Library Prep Information category to
initiate the download of a worksheet to
use for reference during hybridization
setup. This worksheet also contains
information needed to set up readout on
the nCounter SPRINT platform.
Illumina
and the
GeoMx
(MAN-10153)
GeoMx DSP Instrument User Manual
GeoMx DSP nCounter
(MAN-10089). Do
63
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