GEM Generation & Barcoding

• How should I proceed with my Fixed RNA Profiling samples if I experience a clog or wetting failure?
• Why is GEM storage at -20°C not a validated stopping point in the Fixed RNA Profiling assay?

Sequencing

• Why are the "Reads Mapped Confidently to the Probe Set" or "Reads Mapped Confidently to the Filtered Probe Set" metrics in my Fixed RNA Profiling web summary file low?
• What sequencing parameters should be used for Fixed RNA Profiling gene expression libraries?
• Can I pool Fixed RNA Profiling gene expression libraries with other 10x Genomics libraries for sequencing?
• What Illumina sequencers are supported for Fixed RNA Profiling libraries?

Library Construction

• Why does my Fixed RNA Profiling library look unexpected or have low yield?
• What is the expected size and concentration of Fixed RNA Profiling Libraries?
• Why do I need a different sample index plate (Dual Index Kit TT) to make Fixed RNA Profiling Feature Barcode libraries?
• What dual index plate is compatible with the Chromium Fixed RNA Profiling?

Sample Preparation

• How can I improve my cell/nuclei recovery using the Fixed RNA Profiling Assay?
• How should I prepare my Liberase TH solution for the Isolation of Cells from FFPE Tissue Sections for Chromium Fixed RNA Profiling Demonstrated Protocol?
• How should I prepare my FFPE block upstream of the Isolation of Cells from FFPE Tissue Sections for Chromium Fixed RNA Profiling Demonstrated Protocol?
• What sample types are compatible with the Isolation of Cells from FFPE Tissue Sections for Chromium Fixed RNA Profiling Demonstrated Protocol?
• What block QC is available prior to the Isolation of Cells from FFPE Tissue Sections for Chromium Fixed RNA Profiling Demonstrated Protocol?
• How should I transport my FFPE curls for Isolation of Cells from FFPE Tissue Sections for Chromium Fixed RNA Profiling Demonstrated Protocol?

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General

• Can I use fewer than the minimum recommended number of cells/nuclei during probe hybridization with the Fixed RNA Profiling Assay?
• Can the Enhancer be kept at 42°C or 65°C for longer periods of time?
• Is the Fixed RNA Profiling assay compatible with intracellular staining?
• Which thermal cyclers are compatible with the Fixed RNA Profiling assay?

Software

• Is it expected to see a significant background signal from genomic DNA in Chromium Fixed RNA Profiling data?
• What does the term coverage mean in Fixed RNA Profiling?
• Is it possible to integrate fixed RNA profiling data with 3' or 5' gene expression data?
• Can I use PDX/xenograft tissue with Fixed RNA Profiling?
• Does Cell Ranger normalize UMI counts based on the coverage of genes in Fixed RNA Profiling?
• How do I use Cell Ranger aggr to aggregate Fixed RNA Profiling datasets?