NanoString GeoMx® Digital Spatial Profiling with DRAGEN on BaseSpace™ Sequence Hub: Scaling NanoString spatial genomics with Illumina Sequencing

Updated: March 31, 2021 to announce additional regions where the app has been made publicly available.

Updated: March 3, 2021 to announce public availability of the Nanostring GeoMx app on BaseSpace Sequence Hub.

NanoString GeoMx® with DRAGEN on BaseSpace™ Sequence Hub: Scaling NanoString spatial genomics with Illumina Sequencing

Spatial genomics enables new capabilities that uses sequencing-based readout to encode spatial information with biological sample information such as expression profiling. NanoString is a partner that develops a spatial genomics solution called GeoMx Digital Spatial Profiler (DSP), which is a sample and library preparation solution that allows customers to encode and visualize spatial information from stained tissues. Illumina is collaborating with NanoString to pair their GeoMx DSP with NGS readout from Illumina sequencing instruments, in order to enable scalability in addressing large panels of genes, whole transcriptomes, and protein abundance from spatial samples.

We announced our collaboration earlier this year, and we’re excited to share more about what we are working on. Beyond simply enabling higher throughput by using NGS as a readout, teams from Illumina and NanoString have been working together to ensure the increasing volume of data is analyzed in a timely manner, and that the workflow between our companies’ instruments is streamlined to improve customer experiences. Today we are announcing early access for a DRAGEN-accelerated workflow that streamlines analysis for customers using both GeoMx and Illumina instruments for their spatial genomics workflows. Edit: As of March 31, 2021, this workflow is live for users of BaseSpace Sequence Hub in the US, Europe, Australia, and Canada.

In our initial release, customers will be able to use a cloud-based application hosted on Illumina’s BaseSpace Sequence Hub (BSSH) to analyze and format sequencing data for compatibility with GeoMx DSP.

Customers setting up their run on their Illumina instruments will first set up their runs to stream data to BSSH.

Once sequencing data is available in BSSH (which is available in a few minutes after sequencing is complete), users should first upload their configuration file from the GeoMx instrument into BSSH, before selecting the GeoMx NGS Pipeline from the Apps menu in BSSH.

After launching the application, users then configure their analysis in the app launch interface:

  • Select the FASTQ Biosamples to include in the analysis. These FASTQs are generated from the data coming from the sequencing instrument.
  • Select the configuration file that was uploaded earlier for the analysis. This configuration file comes from the “NGS Readout Package” from the GeoMx instrument, please see the user guide linked below for details.
  • Select an output folder where the results will be stored.
  • Launch the application.

Analysis will typically complete in 1 to 2 hours, for a typical experiment containing ~192 regions of interest (ROIs) and ~400 million reads. After the analysis completes, customers can download the results, and load them into their GeoMx DSP software for interactive visualization.

  • Select the analysis result:
  • Click on the Files tab, and find the “.zip” file:
  • Download the “…DCC.zip” file to your local computer:

Once loaded into GeoMx DSP, customers can then visualize and interact with their data.

For early access, this software pipeline will be available on BaseSpace Sequence Hub, Illumina’s cloud-based genomics computing environment. Edit: As of March 31, 2021, this workflow is live for users of BaseSpace Sequence Hub in the US, Europe, Australia, and Canada.

Please contact NanoString support at geomxsupport@nanostring.com to inquire about joining the early access program. And please stay tuned as we continue to streamline the customer experience and expand access to customers that may not have access to cloud software solutions.

Products mentioned here are for research use only, and are not for diagnostic use.

User Manual for GeoMx NGS Pipeline on Illumina DRAGEN via BaseSpace Sequence Hub

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