Spatial transcriptomics research - RocGene (Beijing) Technology Co., Ltd.

Application Requirements

Although spatial transcriptome technology can provide spatial distribution information of gene expression in tissue samples, the commonly used sequencing-based spatial transcriptome methods have problems such as sparse data and limited quantitative accuracy. In studies such as analyzing cell heterogeneity and tumor microenvironment, it is necessary to accurately and quantitatively verify the expression levels of specific genes in spatial transcriptome data to determine the true expression abundance of genes at different spatial locations and ensure the reliability of research results. Therefore, research institutions need a set of cost-effective detection solutions that can accurately quantify, stabilize, have strong sensitivity/specificity, and can be compatible with trace samples.

Solutions

Result Validation Solution - Archimed R Series + qPCR Premix

Supporting Reagents: High-sensitivity reverse transcription and PCR reaction Mix, improving reverse transcription efficiency and detection result accuracy.
Detection Platform: 1.33× higher sensitivity; Tube heating mode ensures more accurate detection results for trace samples; multiplex probe-based relative quantification achieves ultra-high detection efficiency.

Performance Enhancement Solution - ArchiCycler Series + Archimed R Series + qPCR Premix

Primer Validation: ArchiCycler gradient PCR supports user-defined annealing temperature with physical isolation and ±0.1℃ high-precision temperature control, enabling efficient confirmation of the optimal annealing temperature for primers.
Supporting Reagents: High-sensitivity reverse transcription and PCR reaction Mix, improving reverse transcription efficiency and detection result accuracy.
Detection Platform: 1.33× higher sensitivity; Tube heating mode ensures more accurate detection results for trace samples; multiplex probe-based relative quantification achieves ultra-high detection efficiency.

Application Scenarios

Sequencing Data Validation

In spatial transcriptomics research, sequencing data can reveal the spatial expression distribution of genes in tissues but may contain errors. High-sensitivity and high-accuracy real-time fluorescent quantitative PCR is required to accurately validate the expression levels of specific genes. For example, in tumor spatial transcriptomics research, it is necessary to clarify the expression of specific oncogenes (e.g., EGFR, KRAS) in the tumor core area, marginal area, and the boundary of normal tissues.

Gene Expression Related to Intercellular Interaction

Interactions between different cells in the tissue microenvironment affect physiological and pathological processes. Spatial transcriptomics localizes related genes, and real-time fluorescent quantitative PCR with good repeatability, strong specificity and multiplex detection capability can be used to deeply analyze their expression levels. For instance, in immune microenvironment research, study the expression of chemokines (CCL2, CXCL10), immune checkpoints (PD-1, PD-L1) and other genes related to the interaction between tumor cells and immune cells (e.g., T cells, macrophages).

Tracking Spatiotemporal Expression Changes of Genes

During embryo, seed development and other processes, spatiotemporal expression changes of genes finely regulate cell differentiation and tissue/organ formation. Spatial transcriptomics depicts the spatial map of gene expression, and real-time fluorescent quantitative PCR with good temperature uniformity, strong adaptability to trace samples and flexible performance adjustment is used to quantify gene expression at specific spatiotemporal points. For example, study the expression of neurodevelopment-related genes (Nestin, NeuroD1) in different germ layers and different developmental stages during mouse embryonic development.

Expression of Key Genes at Specific Spatial Positions

For cardiovascular and cerebrovascular diseases, neurodegenerative diseases, etc., clarifying the expression of key genes in specific regions of pathological tissues is crucial for revealing pathological mechanisms. Spatial transcriptomics localizes lesion regions, and real-time fluorescent quantitative PCR with precise temperature control and ultra-high resolution is needed to determine the expression of target genes. For example, in Alzheimer's disease research, detect the expression of Aβ amyloid-related genes (APP, BACE1) in specific brain regions (e.g., hippocampus) of the brain.

Detection Workflow

Result Validation Solution - Archimed R Series + qPCR Premix

Performance Enhancement Solution - ArchiCycler Series + Archimed R Series + qPCR Premix

Our Advantages

High-Efficiency Detection

All solutions support multiplex probe-based relative quantification. The independently developed probe-based relative quantification analysis method can determine the expression levels of multiple genes in an ultra-efficient and rapid manner, effectively reflecting the co-expression of multiple interacting genes.

Excellent Sensitivity and Specificity

High-performance self-developed enzyme system, combined with ultra-fast temperature ramping rate and 1.33× resolution instrument sensitivity, ensures high sensitivity and specificity of results.

Wide Applicability

Gradient temperature can be edited independently; physical isolation design ensures the performance of optimizing primer reaction conditions; ±0.1℃ temperature accuracy + Tube temperature control mode is more suitable for the needs of micro-volume reactions.

Success Cases

Scenario: A research team in Beijing used spatial transcriptomics technology to study the colorectal cancer tumor microenvironment and found that a set of genes related to tumor invasion in the tumor marginal area showed a differential expression trend.

Requirements: Validate the accuracy of expression quantification of differentially expressed genes in spatial transcriptomics data. The real-time fluorescent quantitative PCR originally used by the department was shared by the platform, making it impossible to complete a large number of expression validation experiments in a short time. A cost-effective and high-efficiency detection platform was needed to complete data validation within a short period.

Solution:

Researchers used laser capture microdissection (LCM) technology to obtain tissue samples from the tumor marginal area, tumor core area and paracancerous normal tissue area respectively, extracted RNA and reverse-transcribed it into cDNA using the high-sensitivity one-step RT-qPCR premix provided by Rocgene, and performed multi-gene relative quantification validation experiments with Archimed R6.

Results:

Relative quantification results showed that the expression trend of target genes was consistent with spatial transcriptomics data, and the quantification results were more accurate, confirming the high expression of genes in the tumor marginal area discovered by spatial transcriptomics technology. This provided strong data support for in-depth study of the mechanism of colorectal cancer tumor invasion, and also demonstrated the important value of Archimed R series instruments in the validation of gene expression quantification in spatial transcriptomics research.

On-site Usage Photos

Detection Results