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
- Why are we making direct download to a networked Chromium X Series instrument the default path for updates starting with firmware v2.0?
- What accessories are required to run GEM-X (Single Cell 3’ v4 or Immune Profiling 5’ v3)?
- Are clicking noises made by the Chromium X Series expected when running GEM-X Chips?
- Are there additional resources to help troubleshoot network connectivity issues for Chromium X Series?
- What USB formats are supported for use with the Chromium X Series?
- What accompanies a Chromium X Series purchase?
Sample Preparation
- What sample types have been tested with Cell Fixation Protocol for GEM-X Single Cell 3' & 5' Assays (CG000776)?
- 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?
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
- If there are shipment delays, is it acceptable to use Dynabeads™ MyOne™ SILANE that have been stored at room temperature or frozen?
- 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 should I do if there is reagent on the Chromium X Series Chip Holder after a GEM-X run?
- How do I diagnose and report a wetting failure with GEM-X assays?
- How do I diagnose and report a clog failure with GEM-X assays?
- 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 ?
Library Construction
- What is the difference between Amp Mix (PN-2000047) and Library Amp Mix (PN-2000531)?
- Which region should I select when determining the average fragment size of my library?
- 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?
- How long can final libraries be stored at -20°C?
Sequencing
- What considerations are there for sequencing 10x Genomics libraries on NextSeq 1000/2000 Sequencing Systems with XLEAP SBS kits?
- What index combinations should I select when sequencing low plex pools of 10x Genomics Libraries generated with the Dual Index TT or Dual Index TS plates?
- Why has the loading concentration on the NovaSeq 6000 Illumina sequencing platform been updated for Next GEM library types?
- Which 10x Genomics library types are compatible with sequencing on the Element AVITI™ System?
- What sequencing configuration should I use?
- How to setup a 10x Genomics sample sheet in Illumina's BaseSpace for demultiplexing
Software
- My samples are analyzed with Cell Ranger v8.0. Should I upgrade to the latest Cell Ranger v9.0?
- How do I generate single cell ATAC or multiome ATAC FASTQ files from NextSeq or NovaSeq X?
- My samples are analyzed with Cell Ranger v7.1. Should I rerun analysis using the latest Cell Ranger v7.2?
- My antibody t-SNE shows noodles or worms
- How do I solve the error "cluster must have the same length as the number of barcodes" when using a merged Seurat object?
- How are data normalized for the multi-sample comparison (pseudo-bulk differential expression) calculation in Loupe Browser?