Geomx Dsp Workflow - nanoString GeoMx DSP User Manual

MAN-10152-01 for software v2.5

GeoMx DSP Workflow

GeoMx DSP Workflow
The GeoMx Digital Spatial Profiler (DSP) is a novel platform developed by NanoString. This
product relies on antibody or nucleic acid probes coupled to photocleavable oligonucleotide tags.
After probes hybridize to targets in slide-mounted tissue sections, the oligonucleotide tags are
released from discrete regions of the tissue via UV exposure. Released tags are quantitated by
nCounter technology or Illumina Next Generation Sequencing (NGS). Counts are mapped back
to tissue location, yielding a spatially resolved digital profile of analyte abundance
6).
Day 1: Slide Staining. Prepare slides and incubate biological targets with UV- cleavable
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probes. Prepare manually or using the BOND RX/RX
®
Leica Biosystems .
Day 2: Process Slides on GeoMx DSP. Load prepared slides into the GeoMx DSP
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instrument and enter slide/study information. Slides are scanned to capture fluorescent
images used to select regions of interest (ROIs). The instrument collects UV-cleaved oligos
from the ROIs into the wells of a collection plate.
For NGS readout:
Day 3: Transfer the collected aspirates to a
PCR plate and perform Library Prep with
Seq Code primers. Pool and purify the
products, then Sequence on an Illumina
NGS instrument.
Day 4 : Process FASTQ sequencing files
into digital count conversion (DCC) files
using NanoString's GeoMx NGS Pipeline
on Illumina DRAGEN™ accessed via
BaseSpace™ Sequence Hub, or using
GeoMx NGS Pipeline standalone software.
Upload DCC files on to the GeoMx DSP.
Day 4 or 5: Create a Data Analysis study in the Data Analysis suite and perform quality-
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control checks and data analysis, and generate analysis plots.
FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.
GeoMx DSP Instrument User Manual
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Fully Automated IHC/ISH Stainer from
For nCounter readout:
Day 2, continued : Transfer the collected
aspirates to a hybridization plate along with
GeoMx Hyb Code reagents. Hybridization
occurs overnight.
Day 3 : Pool wells and Process on an
nCounter MAX/FLEX or Pro Analysis
System or SPRINT Profiler.
reporter count conversion (RCC) files to the
GeoMx DSP.
(see Figure
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