General

• Can I pool less than 4 or 16 samples when using the Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples?
• What is the maximum number of cells that can be targeted per barcode when using the Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples?
• Can I ship fixed single cell/nuclei samples for use with the Fixed RNA Profiling Assay?
• Can I use fewer than the minimum recommended number of cells/nuclei during sample fixation or 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?

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Sample Preparation

• Can formaldehyde from alternative vendors be used for sample fixation in the Fixed RNA Profiling Assay?
• Can I use formalin fixed tissue as input for the Gene Expression Flex assay?
• Can an FFPE tissue slide be used as input for the Isolation of Cells from FFPE Tissue Sections Demonstrated Protocol (CG000632)?
• Can I use Xylene alternatives for Tissue Deparaffinization during the Isolation of Cells from FFPE Tissue Sections Demonstrated Protocol (CG000632)?
• What are the validated stopping points for sample storage in the Fixed RNA Profiling assay?
• Why was the -20°C optional sample storage recommendation removed from the Fixed RNA Profiling assay?

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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?

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?

Sequencing

• Why was the percentage of PhiX for NovaSeq increased for Multiplexed Fixed RNA Profiling libraries sequenced on NovaSeq?
• 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?

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?