研究目的
To provide an independent, comprehensive description of the DSP technology including an overview of NanoString’s capture and antibody barcode conjugation chemistries, experimental workflow, data output and analysis methods, and to discuss the DSP technology in the context of other highly multiplexed immunohistochemistry methods.
研究成果
The NanoString DSP platform offers significant opportunities for high-dimensional interrogation of tissue samples, with robust detection of high abundance protein and RNA targets and good reproducibility. However, careful consideration of experimental design and data interpretation is necessary due to the platform's technical complexities and limitations, particularly in single-cell analyses and data normalization.
研究不足
The review highlights the need for careful consideration of the DSP platform's technical performance, sensitivity, and reproducibility. It notes the challenges in single-cell analyses, including the arbitrary definition of 'positive' expression and the difficulty in interpreting data from low abundance markers. The review also points out the platform's inability to reconstruct an image of the interrogated sample, limiting spatial information to the predefined regions of interest.
1:Experimental Design and Method Selection:
The review discusses the NanoString Digital Spatial Profiling (DSP) platform, focusing on its capability for highly multiplexed, spatial assessment of protein and/or RNA targets in tissues. It outlines the platform's use of oligonucleotide barcodes conjugated via a photocleavable linker to primary antibodies or nucleic acid probes for detection.
2:Sample Selection and Data Sources:
The review considers the use of fresh frozen or FFPE samples for DSP analysis, highlighting the impact of pre-analytical variables on protein and RNA quality.
3:List of Experimental Equipment and Materials:
The DSP platform is detailed, including its components and the nCounter platform for data analysis.
4:Experimental Procedures and Operational Workflow:
The workflow involves sample staining and imaging, region of interest selection, and collection and analysis of data. The process includes UV illumination of selected regions to liberate attached oligos from antibodies or RNA probes, followed by collection and enumeration of these oligos.
5:Data Analysis Methods:
The review discusses the normalization of data to account for technical and biological variance, including the use of ERCC probes for technical normalization and reference targets for cellularity normalization.
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