Questions & Answers
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SupportGeneral
General Q&A across multiple products
Chromium Nuclei Isolation Kit
- When should I start the 10 minute lysis timer for the Nuclei Isolation Kit?
- How can I improve the yield of my nuclei for hard-to-dissociate tissues such as heart, muscle, and fibrous tissue using the Chromium Nuclei Isolation Kit?
- How can I optimize my nuclei suspension if I am using an untested tissue type in the Chromium Nuclei Isolation kit?
- How can I reduce myelin debris from brain in the Chromium Nuclei Isolation kit?
- What should I do if I have >5% of my nuclei suspension staining live?
- What if I do not get enough nuclei from 50mg of tissue using the Chromium Nuclei Isolation Kit?
Chromium X Series
- What USB formats are supported for use with the Chromium X/iX?
- What accompanies a Chromium X purchase?
- What accompanies a Chromium iX purchase?
- What is the Chromium iX Accessory Kit (PN-1000323)?
- What is a Chromium X Upgrade Kit (PN-1000327)?
- What are the specifications of the Chromium X/iX?
Sample Preparation
- How can I remove myelin from my brain samples?
- Can I freeze a cell or nuclei pellet or whole blood?
- Why should I filter bone marrow aspirates before isolating BMMCs?
- How should I ship blood and bone marrow for single-cell sequencing?
- How should I collect blood or bone marrow to preserve neutrophils for single cell sequencing?
- How should I collect bone marrow samples for single cell sequencing?
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
- Can I use Dynabeads™ MyOne™ SILANE that froze during shipment?
- How are the ratios of SPRIselect beads calculated in 10x assays?
- What are the best practices for using SPRIselect beads in 10x assays?
- 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?
GEM Generation & Barcoding
- What if I accidentally fill the 'No fill' row with glycerol when loading a NextGEM chip?
- 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?
Library Construction
- Is Single Index Kit T Set A the same as Chromium i7 Multiplex Kit?
- Is Single Index Kit N Set A the same as Chromium i7 Multiplex Kit N, Set A?
- 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?
Sequencing
- Which 10x Assays are compatible with long-read sequencing applications?
- Can I detect alternative transcript isoforms using 10x assays?
- 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 into 10x libraries?
Software
- My antibody t-SNE shows noodles or worms
- FASTQ header mismatch error
- IO error in FASTQ files
- Why do I have an alert in my web summary with 'Low Fraction of Valid UMIs'?
- My samples are analyzed with Cell Ranger v7.0. Should I rerun analysis using the latest Cell Ranger v7.1?
- How to generate FASTQs with BCL Convert for 10x gene expression products