Project description:Spatial transcriptomic technologies are promising tools to reveal fine anatomical profiles of tissues. In the case of methodologies utilizing barcoded probe arrays, achieving a balance among probe barcoding complexity, cost, gene capture sensitivity, and spatial resolution is crucial for accelerating the spreading speed of spatial transcriptomic in basic science and clinical work. Here, we developed spatially cellular-level RNA-capture probe arrays using miniaturized microfluidic and microarray technologies. By leveraging the predetermined and cost-effective probe fixation characteristics of this methodology, we significantly reduced the consumable cost of the probe array to $0.31/mm2 and fabrication time to approximately 2 hours. Furthermore, the modification of the RNA-capture probe on sequencing slides by microfluidic chip does not rely on large imaging or printing instruments. Notably, the efficiency of the transcript captured by the probe array is even comparable to conventional single-cell RNA sequencing. Based on this technology, the stacked three-dimensional transcriptome atlas and the spatial cell heterogeneity of mouse brains were successfully visualized. Taken together, we present an experimental and analytical framework for the spatial investigation of mouse brain structures and cell phenotypes.
Project description:cDNA and cRNA hybridization technologies have different, probe-specific sensitivities. We used samples from an etanercept trial (GSE11903) to explore in a real-life setting the uniqueness of each platform.
Project description:Proteomic technologies based on mass spectrometry (MS) have greatly evolved in the past years, and nowadays it is possible to routinely identify thousands of peptides from complex biological samples in a single LC-MS/MS experiment. Despite the advancements in proteomic technologies, the scientific community still faces important challenges in terms of depth and reproducibility of proteomics analyses. Here, we present a multicenter study designed to evaluate long-term performance of LC-MS/MS platforms within the Spanish Proteomics Facilities Network (ProteoRed-ISCIII). The study was performed under well-established standard operating procedures, and demonstrated that it is possible to attain high qualitative and quantitative reproducibility over time. Our study highlights the importance of deploying platform quality assessment metrics in multi-laboratory studies in early LC-MS/MS system troubleshooting.
Project description:Assessment of different subcellular localizations (membrane, cytosol, nucleus) of estrogen receptors by multi-epitope protein expression in 200 NSCLC specimens and matched non-cancerous tissues and ESR-1 probe mapping meta-analysis of Affymetrix 2.0 plus data in 1398 NSCLC tumors and normal lung tissues and 39 NSCLC cell lines led us to the conclusion that ERα extranuclear variants are the main ERs in NSCLC. In order to further analyze these effects we treated A549 and H520 cell lines with 17β-estradiol, 17β-estradiol-BSA (plasma membrane impermeable conjugate) and tamoxifen for 3h, in order to investigate early transcriptional effects and responsiveness to estrogen agonists and antagonists. The aim of this study was to demonstrate the functionality of NSCLC ERs and decipher which genes, canonical pathways and networks are affected by each treatment.