Whole Transcriptome Atlas


The Whole Transcriptome Atlas (WTA) panel empowers researchers to explore biology across a single tissue. The entire human transcriptome can be measured in each region of interest (ROI) to uncover biological changes at specific locations on the tissue sample. Over 18,000 protein-coding genes make up this panel, which is based on the human gene nomenclature committee (HUGO) database and cross-referenced in NCBI’s RefSeq database. The unique architecture of each probe delivers maximum sensitivity and confidence in each transcript counted. Explore pathways across the whole transcriptome in user defined regions of interest with the WTA panel.

Let Canopy run the WTA assay for you with our GeoMx DSP services, and deliver the data right to your inbox, getting you publishable data faster- inquire today about your next project!



Deliver both spatial precision and high plex gene expression analysis with over 18,000 protein-coding genes for a broad look at the biology of your tissue


ISH probes are conjugated to DNA-indexing oligos; these oligos contain ROI indices mapping them back to their tissue location, an RNA target ID sequence matching them to their ISH probes, and a UMI to dedup reads


Explore pathways across the whole transcriptome in user defined regions of interest


Canopy's GeoMx DSP Service includes consultative discussions with our team for ROI selection and data QC and analysis overview

Details & Data

A new way to look at biology

The WTA panel provides whole transcriptome coverage with probes specific to protein coding mRNA sequences. These sequences are based on the HUGO database and cross-referenced with the NCBI RefSeq database to give you confidence in each transcript. Along with a high specificity for their target molecules, DSP RNA probes are screened for a myriad of factors including melting temp, GC content, off target hits, and repetitive sequences. Each probe is assigned a unique DSP barcode for downstream molecular counting on the Illumina sequencer. The targeted nature of this panel avoids the many pitfalls of poly(A) pulldown techniques by delivering increased sensitivity even in heavily degraded tissues such as FFPE.

With GeoMx, researchers can explore pathways across the whole transcriptome in user defined regions of interest. Providing an unbiased view of 18,000 protein-coding genes, the WTA can unlock new pathways to e explored and enables RNA profiling in oncology, immunology, neuroscience, developmental biology and other diverse fields.

With 18,000 genes to target, its also important for the probes to be sensitive and also accurate enough to confidently count. GeoMx RNA assays contain in situ hybridization (ISH) probes conjugated to unique DNA indexing-oligonucleotides via a UV-photocleavable linker. After selecting regions of interest (ROIs), the DNA oligonucleotides are UV cleaved and then sequenced on an Illumina sequencer. DNA oligonucleotide sequences contain ROI indices mapping them back to their tissue location, an RNA target identification sequence matching them to their ISH probes, and a unique molecular identifier (UMI) to deduplicate reads. Sequenced oligonucleotides are processed then imported back into the GeoMx platform for integration with the slide images and ROI selections for spatially-resolved RNA expression.

ROI Selection

ROI selection is a critical step in the GeoMx DSP workflow.  Canopy’s service assists in ROI selection to make sure our clients are generating the best data for their project.  Once morphology marker staining is complete, a Canopy scientist will collaboratively review the images with our clients to select the ROIs for the project.  The ROIs provide the spatial resolution for the downstream gene expression analysis.

Figure 1: Data from tonsil tissue internally generated by Canopy Biosciences. A: Solid Tumor morphology makers were used to stain tissue slide; standard ROI selection methodology was used to generate ROIs in circular, square, and heptagonal shapes as well as ROI segmentation (ROI 003). B: PanCk and CD45 signal strength was measured.

Downstream Workflow

Following ROI selection, the sequences are collected, and library prep begins.  Samples are sequenced on the Illumina sequencer.  Indices and UMIs on the oligos maintain spatial information and sample specificity.  Sequencing data is relayed back to the GeoMx DSP for processing and integration with spatial images.

GeoMx DSP Data Analysis

Canopy’s GeoMx DSP service includes data consultation.  Once sequencing data is integrated back to GeoMx DSP instrument, a Canopy scientist schedules a consultation with the client.  This session is used to review the QC data from the project and provide an overview on the analysis suite.  From there the client should be able to do their own analysis and download data, figures and images for publication.

The GeoMx analysis suite combines whole tissue visualization with advanced ROI selection to enable spatial profiling of tissue sections by tracking the image data to corresponding profiling data. There are a number of normalization options and a variety of data visualization formats to export publication-quality figures.

Explore the Biology That Matters

The GeoMx Whole Transcriptome Atlas (WTA) provides an unbiased view of 18,000+ protein-coding genes. Unlock new pathways to be explored and profile gene expression oncology, immunology, neuroscience, developmental biology, and other diverse fields with the WTA panel and Canopy’s GeoMx DSP service.

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