Questions & Answers
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SupportGeneral
General Q&A
Sample Preparation
Chromium Controller
- How should the 10x Genomics gaskets and chips that have been used to run samples containing infectious agents be disposed of?
- If the Chromium Controller is placed in a biosafety cabinet, will the vibration from the hood/ biosafety cabinet affect Gel Bead-in-Emulsion (GEM) formation?
- Can the Chromium Controller be moved between different BSL level labs?
- What is the purpose of loading surrogate fluid in the unused wells of the Chromium Chip?
- How do I decontaminate my Chromium Controller?
- What are the specifications of the Chromium Controller?
Reagents
- How many freeze thaw cycles are the gel beads stable for?
- Why is it critical to load the wells in the specified order?
- Is there a plate magnetic separator recommended by 10x?
- What is the maximum number of thaw-freeze cycles for the i7 sample index plate?
- Can I mix reagents from different kits?
- What is the shelf life of 10x reagents?
GEM Generation & Barcoding
- Can samples be treated with UV light, which is known to cross-link DNA? How would UV treatment affect RNA in the sample?
- Can an additional temperature incubation step be included during GEM-RT Incubation ?
- During GEM-RT Incubation in the Single Cell Assays, can the 85°C (step 2) be extended for more than 5 min?
- Can Trizol be used as a substitute for Recovery Agent?
- Will Recovery Agent (PN 220016) inactivate infectious agent/s in a sample when processing GEMs in the 10x workflow?
- Which thermal cyclers are supported for use with GEMs?
Library Construction
- I have already started my experiment, what are the safe stopping points in the protocol?
- Can I use a melting curve analysis after the qPCR protocol to assess the quality of my 10x libraries?
- Why do I need to use qPCR to quantify my final library?
- How long can final libraries be stored at -20°C?
- How are SPRIselect volumes calculated?
Sequencing
- I stored my GEM-RT Products, cDNA, and/or final library for longer than recommended in the User Guide. Can I use them to complete the protocol for sequencing?
- Should I increase the number of reads per cell if I increase the number of antibodies?
- Do I need custom sequencing primers for 10x libraries?
- What is the recommended amount of PhiX to spike in 10x libraries?
- Why are there unequal ratios of the four oligos (or oligo dropout) in my 10x library after sequencing?
- How do you set up a NextSeq run on BaseSpace?
Software
- Cellranger job failed in stage code exit status 255
- Are the mkfastq pipelines interchangeable between products?
- [error] Barcode out of bounds (I1:0-14)
- How do I fix the mkfastq error "No bcl2fastq found on path"?
- Is it possible to get gene expression values on a cell by cell basis instead of on a cluster by cluster basis in Loupe Cell Browser?
- Create clusters of a given cell type in different samples in a combined cloupe file