Questions & Answers
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SupportSingle Cell Gene Expression Flex
Fixed RNA Profiling
General
- Can GEM-X Flex customers perform TotalSeq™️-B Singleplex experiments?
- What Flex Gene Expression applications are compatible with TotalSeq™️ antibodies?
- Why isn’t TotalSeq™️-B compatible with Flex Gene Expression for Multiplexed Samples?
- Can the Enhancer be kept at 42°C or 65°C for longer periods of time?
- Is the Flex Gene Expression assay compatible with intracellular protein labeling?
Custom Probe Design
- What workflow modifications are required when performing CRISPR Screening with the Single Cell Gene Expression Flex assay?
- How do I pool custom probes for a Single Cell Gene Expression Flex + CRISPR experiment?
- How do I design custom probes for CRISPR Guide Capture for use with the Single Cell Gene Expression Flex Assay?
- How do I design custom probes to detect fluorescent reporters EGFP and/or RFP?
Sample Preparation
- Can dissociated FFPE samples be flow sorted for use with the Fixed RNA Profiling assay?
- Does the FFPE Demonstrated Protocol produce a suspension of single nuclei, single whole cells or a mixture of both?
- Can I use Flow Sorting with fixed whole blood samples?
- What QC is available before, during, and after running the Flex Gene Expression assay with FFPE samples?
- Can I use OCT embedded fresh frozen tissue with the Flex Gene Expression assay?
- Can formaldehyde from alternative vendors be used for sample fixation in the Flex Gene Expression assay?
GEM Generation & Barcoding
Sequencing
- What sequencing configuration is required for antibody libraries derived from using Proteintech Group (PTG) antibodies mixed with Biolegend antibodies, generated from multiplexing experiments using Flex Gene Expression?
- What sequencing configuration is required for Proteintech Group (PTG)-derived antibody libraries generated from multiplexing experiments using Flex Gene Expression?
- Why are the "Reads Mapped Confidently to the Probe Set" or "Reads Mapped Confidently to the Filtered Probe Set" metrics in my Flex Gene Expression web summary file low?
- What sequencing parameters should be used for Flex Gene Expression libraries?
Software
- How does Single Cell Flex data generated from GEM-X chips compare to Flex data generated from NextGEM chips?
- Cell Ranger detected a lower number of cells than expected in my FFPE samples with the Fixed RNA Profiling (Flex) assay. Can I change cell calling parameters to recover more cells?
- Why do you recommend a T nucleotide at the 25th position of custom probes in the Technical Note for custom probe design for Flex and Visium assays?
- How do I analyze CRISPR screening + Single Cell Gene Expression Flex data in Cell Ranger?
- Is trajectory analysis compatible with the Fixed RNA Profiling (Flex) assay?
- How can I get FASTQ files by sample for a multiplexed Flex library?