Cancer Transcriptome Atlas

Human

Designed for comprehensive profiling of the tumor, tumor microenvironment, and tumor immune status, the Cancer Transcriptome Atlas (CTA) is the right tool for any immuno-oncology study. Profile 1800 targets simultaneously with spatial resolution- focused on 55 critical immune and tumor related pathways. GeoMx RNA assays contain in situ hybridization (ISH) probes conjugated to unique DNA indexing-oligos via a UV-photocleavable linker. Oligo sequences contain ROI indices mapping them back to tissue location, an RNA target identification sequence mapping them back to their ISH probes, and a unique molecular identifier (UMI) to deduplicate reads. Sequencing files are integrated back to slide images and ROI selections for spatially resolved RNA expression analysis.

Let Canopy run the CTA 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!

Benefits

Profiling over 1800 RNA targets simultaneously with spatial resolution in any region of interest from a single tissue section

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

Comprehensive RNA content designed for cancer biology research in any tissue

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

Details & Data

Curated Content for Cancer Biology

The CTA panel for GeoMx DSP is designed to profile all aspects of tumor and tumor microenvironment biology. Use this assay to:

Profile global immune response
Assess microenvironment immune activity
Quantify tumor reactivity to the immune response and therapeutic treatments
Measure clinically-derived gene sets including the 18-gene Tumor Inflammation Signature (TIS) known to be associated with response to PD-1/PD-L1 inhibitor pathway blockade, and the PAM50 signature known to be associated with breast cancer metastasis.

Annotation	# Genes	Annotation	# Genes	Annotation	# Genes	Annotation	# Genes
Angiogenesis	51	CT Antigens	31	Insulin Signaling	64	Notch Signaling	78
Antigen Presentation	104	Costimulatory Signaling	48	Interferon Signaling	89	Nucleic Acid Sensing	80
Apoptosis	62	Cytosolic DNA-sensing	30	Inerleukin Signaling	205	PDGF Signaling	34
Autophagy	14	Cytotoxicity	108	JAK-STAT Signaling	115	PI3-Akt	226
BCR Signaling	79	Death Receptor Signaling	118	Lymphocyte Regulation	89	Proteotoxic Stress	11
C-type Lectin Activation	64	DNA Damage Repair	155	Lymphocyte Trafficking	43	Regulation of Cell Motility	90
cAMP Signaling	68	ECM Organization	126	MAPK Signaling	220	TCR Signaling	52
Carbon Metabolism	48	EMT	81	Matrix Remodeling and Metastasis	115	TGF-beta Signaling	90
Cell Adhesion	207	Epigenetic Regulation	58	Metabolism	174	TLR Signaling	90
Cell Adhesion Signaling	117	FC Receptor Signaling	58	mTOR Signaling	35	Transcriptional Misregulation	118
Cell Cycle	139	FoxO Signaling	82	Myeloid Activity	174	Type I Interferon Signaling	48
Chemokine Signaling	119	Hedgehog Signaling	49	Neutrophil Activation	120	Type II Interferon Signaling	49
Circadian Clock	19	Hippo Signaling	71	NF-kB Signaling	105	Wnt Signaling	128
Complement System	43	Hypoxia	73	NK Cell Activation	108

Cancer Transcriptome Atlas Assay Design

Assess gene expression data for 1800 gene targets with spatial resolution with the CTA panel. Using morphology marker antibodies, such PanCk and CD45, assess immune profile of tissue to select ROIs. The ISH probes are conjugated to unique DNA-indexing oligos which are UV-photocleaved and then oligo sequences are sequenced on an Illumina sequencer. The DNA oligo sequences contain ROI indices mapping them back to their tissue location, an RNA target identification sequence matching them to their ISH probe, and a UMO to dedupe the reads.

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.

cta-roi_panck-and-cd45 — 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.

Complete Coverage for Cancer Biology

Designed for cancer biology research, the CTA provides complete coverage of tumor biology, the microenvironment, and the immune response, without sequencing unnecessary targets.

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