Questions & Answers
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SupportSingle Cell Gene Expression
3' gene expression profiling at scale with single cell resolution.
High Throughput Single Cell Gene Expression
- Can I use Cell Ranger aggr to combine data from HT kits with data from standard kits? Will there be chemistry batch effects?
- What workflows and reagent kits are compatible with the Next GEM Single Cell 3’HT v3.1 assay?
- Why is the number of barcodes called in Cell Ranger equal to the Targeted Cell Recovery for HT?
Low Throughput
3' Gene Expression LT articles
- Why is the lower supported limit different for the Single Cell Gene Expression LT product, compared to the standard product?
- I have a low starting number of cells. Should I process my sample using the LT or the standard Single Cell Gene Expression kit?
- What workflows and reagent kits are compatible with the Next GEM Single Cell 3’ v3.1 LT assay?
- Why is the Next GEM Chip L kit not available for purchase separately?
- Is cell counting different for the Next GEM Single Cell 3’ v3.1 LT assay?
- Are fewer partitions generated for the Next GEM Single Cell 3’ v3.1 LT assay when compared to other single cell applications?
Sample Prep - Cells
- What can I do if my single cell/ nuclei suspension contains a high amount of debris?
- Can I use methanol fixation with the 3’ Single Cell Gene Expression assay?
- Can I store samples in a tissue storage solution?
- What are the best practices for dissociating tissue samples into single cells?
- How should I store my single-cell suspension for scRNA-seq?
- What Demonstrated Protocols for sample preparation are compatible with 3' Feature Barcoding?
Sample Prep-Nuclei
- Why were the lysis conditions updated in protocol CG000124 for Isolation of Nuclei for Single Cell RNA Sequencing?
- How do you isolate nuclei from snap-frozen tissue for 3’ gene expression profiling?
- What are the best practices for working with nuclei samples for 3' single-cell gene expression?
- How can I run a lysis timeline to optimize nuclei isolation for 3' single-cell gene expression?
- How can I isolate nuclei for 3' Gene Expression profiling?
Reagents
GEM Generation & Barcoding
Post GEM-RT Cleanup & cDNA Amplification
Library Construction
- What metrics could be affected by using an unsupported thermal cycler to prepare single cell gene expression libraries?
- Why are different index plates required for different library types?
- Can I use the SI Primer together with Dual Index Plate TT when preparing Single Cell 3' Gene Expression libraries?
- Can I use Dual Index Plates with 3' v3.1 Single Index reagent kits?
- What are the protocol differences between Single Cell 3' v3.1 Single Index and 3' v3.1 Dual Index?
- Are dual index plates shared across 10x assays?
Feature Barcoding - CRISPR Screening
- Why does my CRISPR Screening library trace have additional peaks?
- Which Capture Sequence and sgRNA integration site should I use for 3' CRISPR Screening experiments?
- Do you recommend enriching for transduced cells?
- What should I consider when designing my 3' or 5' CRISPR pool?
- What is MOI and how do I assess it?
- What resources are available for my CRISPR experimental design?
Sequencing
- What concentration should I load my libraries at for sequencing?
- What is 'read pairs per cell' and how does it relate to sequencer yield?
- Which Illumina SBS kit should I select for sequencing?
- Can I perform shallow sequencing to assess the quality of Single Cell 3' Gene Expression libraries?
- Are index sequences shared across dual index plates?
- Is nucleotide diversity in the index read important for Illumina sequencing?
Software
- Should I upgrade Cell Ranger to v7.1 for cell multiplexing analysis?
- What are the cell calling updates in Cell Ranger v7.1 and its impact on Single Cell Gene Expression data?
- Is filtering of ribosomal and mitochondrial genes in nuclei data needed?
- Nuclei aggregates in a barcode rank plot
- Why are some mapping metrics in Cell Ranger higher for nuclei data?
- Can we aggregate nuclei and cellular data on Cell Ranger aggr?