Best Practises for Successful CosMx SMI Runs

We are excited to share key best practices for selecting optimal samples for successful CosMx™ SMI single-cell spatial runs at 1000-plex. Leveraging NanoString’s latest software updates (released on 13/11/2024) and our proprietary workflows at Next Level Genomics, we ensure superior quality and reliable data outcomes for your spatial experiments.

Software Updates (13/11/2024)

CosMx SMI Software v1.4 includes significant enhancements:

• Run Time Estimator: Real-time cycling time estimation during Field of View (FOV) selection, optimizing RNA and protein assay throughput.
• Cloud Software Updates: Direct software updates enabled via Control Center using Windows Admin credentials.
• Reduced UV Cleave Time: Faster reporter cycles, higher throughput, reduced UV damage to tissue, improved focus stability, and longer UV source lifetime.
• Improved Distortion Correction: Enhanced measurement precision and accuracy.
• Support for CosMx Whole Transcriptome (WTx) Panel: Preparation for future product launch.
• User Experience Improvements: Including enhanced autofocus, optimized image quality, streamlined cloud uploads, automated disk space checks, clearer error messaging, and instrument consumables reset functionality.

Best Practices for Sample Selection

Tip 1: Evaluate Tissue Block Quality

High-quality tissue blocks are foundational for successful spatial data generation.

• Tissue Fixation: Use recommended fixatives (10% NBF or 4% PFA) with fixation times of 24-72 hours based on tissue type.
• Ischemic Time: Shorter ischemic times yield better RNA quality.
• Sample Storage: Freshest samples typically yield the best results, but older FFPE samples can still perform well depending on storage conditions. At Next Level Genomics, we successfully achieved 100+ mean transcripts per cell from a flow cell sectioned 12 years prior. Optimal storage conditions—especially storing samples at 4°C with desiccant—are critical for preserving sample integrity. Even ambient temperature storage can maintain sample quality if properly paired with desiccant.
• Proprietary Advantage: Next Level Genomics offers comprehensive evaluations, ensuring ideal fixation, minimal ischemic impact, and optimal storage practices to maintain high-quality samples.

Tip 2: Ensure High-Quality Tissue Sections

Proper tissue sectioning maximizes assay sensitivity and specificity.

• Recommended thickness: FFPE (5 µm), Frozen (5-10 µm).
• Use sections within two weeks to preserve RNA integrity.
• Avoid artifacts such as folds, tears, and uneven thickness.
• Proprietary Advantage: Our experts utilize optimized techniques and rigorous quality control (including H&E staining) to guarantee sample excellence.

Tip 3: Address Tissue Heterogeneity and Autofluorescence

Optimized FOV placement enhances data interpretability.

• Pre-screen sections with H&E staining to avoid necrosis or autofluorescence areas.
• Consider tissue heterogeneity for representative sampling.
• Proprietary Advantage: We offer advanced autofluorescence mitigation and precise FOV strategies tailored to your scientific objectives.

Next Level Genomics – Your Partner in Spatial Genomics

Our proprietary workflows and dedicated support streamline complex spatial studies, ensuring robust and insightful results.

Contact us to discover how our proprietary solutions can elevate your next CosMx™ spatial project.