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 website

    Fixed 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

    We offer 10 X Genomics’ Visium HD WT panel (probe-based assay) and Visium HD 3’ (poly(A) RNA detection) applications for spatial transcriptomics analyses. The Visium HD Spatial Gene Expression slides contain 6.5 x 6.5 mm (WT panel and 3’) or 11 x 11 mm (only for WT panel) 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 for whole transcriptome. 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 for Visium HD: For Visium HD WT panel either FFPE, fresh frozen (FF) or fixed frozen (FxF) tissue sections can be used, but please do not section your samples before coordinating the sample processing with us first. Visium HD 3’ is only compatible with FF tissue sections. Optimal tissue thickness depends on the tissue type, but 5 µm (FFPE) and 10 µm (FF/FxF) are optimal for most tissues. Before starting the Visium HD analysis, RNA quality will be measured using RNA extraction and capillary gel electrophoresis.

    Sample compatibility: Visium HD WT panel is compatible with human, mouse and rat tissues, and the sections can be stained either with H&E or IF with specific markers. Visium HD 3’ is species-agnostic and enables for example detection of isoforms, BCR/TCR and SNVs, but only H&E staining is used for morphological information. Link to Visium HD
    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.  

    Last updated on February 21, 2025