3' Gene Expression
10x Genomics Universal 3' Gene Expression assay targets 3' ends of polyadenylated RNA. It generates transcriptome-wide gene expression measurements and has broad species compatibility. The method is compatible with suspensions of viable cells or intact nuclei.
Link to manufacturer's websiteFixed RNA profiling (Flex)
10x Genomics Flex is an assay for profiling gene expression from formaldehyde-fixed cells. The method is compatible with human and mouse cells. The samples can be stored for up to 12 months. This flexibility enables batch-processing samples, making it easier to run multi-site studies or analyze samples that require shipping or extended storage. The method is also compatible with sample multiplexing, bringing about significant cost savings in large-scale projects.
Link to manufacturer's website
Transcriptome-wide gene expression profiling in tissue context
Overview We offer 10 X Genomics’ Visium V2 and Visium HD applications for spatial transcriptomics analyses. The methods are based on positionally barcoded custom sample slides. The Visium V2 slide has capture areas of either 6.5 mm x 6.5 mm or 11 mm x 11 mm. The areas have barcoded spots of 55 µm with 100 µm center-to-center distance. Each spot features unique PCR barcodes, allowing spatial transcriptomics analysis to be performed in whole-genome wide level. The Visium HD Spatial Gene Expression slides contain 6.5 x 6.5 mm capture areas with a continuous grid of oligonucleotides arrayed in millions of 2 x 2 µm barcoded squares without gaps, achieving single cell–scale spatial resolution. The data is output at 2 µm, as well as multiple bin sizes. The 8 x 8 µm bin is the recommended starting point for visualization and analysis. Sample requirements Visium: We recommend using FFPE samples, freshly sectioned before the analysis. Optimal tissue thickness depends on the tissue type, but 10 um is optimal for most tissues. Before starting the Visium analysis, RNA quality will be measured using RNA extraction and capillary gel electrophoresis. Link to Visium
We work in collaboration with the Medical Bioinformatics Centre to develop data analysis solutions for single-cell transcriptomics data. Please contact mbc [at] utu.fi for more information.