Spatial proteomics is limited by detection sensitivity, multiplexing, and multi-modal integration, leaving a gap between discovery and clinical assays. Here we present Protein and nucleic Acid Serial Tyramide Amplification (PASTA), employing horseradish peroxidase-mediated oligonucleotide deposition and cyclical imaging for high-plex, multi-modal spatial profiling. Compatible with conjugated antibodies and in situ hybridization, PASTA enables simultaneous protein and RNA co-detection from FFPE samples, providing a cost-effective bridge from discovery to clinical validation.
The PASTA code and data are released to the academic community for non-commercial academic research only. Any commercial research use, integration into commercial products or services requires prior approvals.
An overview of the purpose of different scripts to reproduce the figures in the manuscript.
| File Name | Description |
|---|---|
paper_figures/PASTA_Fig1_Quantification.Rmd |
Code for plots in Figure 1 and corresponding Extended Data Figures 1-5 |
paper_figures/PASTA_Fig2_Quantification.Rmd |
Code for plots in Figure 2 and corresponding Extended Data Figures 6-10 |
paper_figures/PASTA_Fig2_PhenotypeMaps.ipynb |
Code for phenotype maps in Figure 2C and corresponding Extended Data Figure 7, 10B and Supplementary Figures 1-2 |
The code is designed to work with the data available on Zenodo. The "data" folder in Fig1_data.zip contains all necessary data to generate the quantification plots in Fig. 1 and Extended Data Fig. 1-5 using the above code. The "data" folder in Fig2_data.zip contains all necessary data to generate the quantification plots and phenotype maps in Fig. 2, Extended Data Fig. 7, and Supplementary Fig. 1-2 using the above code.
We are providing interested users with templates of the python scripts for PASTA automation on the OT-2 liquid handling platform. A thorough documentation can be found here
| File Name | Description |
|---|---|
automation/PASTA_oligoHRP_automation.py |
Flexible automation script for up to 4 samples and up to 32 cycles |
- Hendrik A. Michel
- Wenrui Wu
- Huaying Qiu
- Sizun Jiang
For inquiries regarding this repository, please contact Sizun Jiang (sjiang3@bidmc.harvard.edu) and Hendrik Michel (hmichel@bidmc.harvard.edu).
To cite this work, please cite: Michel et al. (2025), "PASTA: Versatile Tyramide-oligonucleotide Amplification for Multi-modal Spatial Biology", bioRxiv, 2025.04.30.651463; doi: 10.1101/2025.04.30.651463