Questions & Answers
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SupportSingle Cell Multiome ATAC + Gene Expression
Simultaneous profiling of 3' gene expression and chromatin accessibility from the same cell.
General
- Where should I expect cells from different sample types to be located in the Peaks Targeting plot?
- How does the data compare between fresh and frozen samples in the Multiome assay?
- How does the Gene Expression data compare between whole cells and nuclei?
- Where can I find the cells with good GEX and ATAC data in the Cross Sensitivities Plot?
- How does the Single Cell Multiome ATAC + GEX sensitivity compare to the standalone 3’ and ATAC assays?
Sample Requirements
- Are OCT-embedded samples compatible with the Single Cell Multiome ATAC + Gene Expression assay?
- How can I assess whether a tissue sample is a good candidate for Single Cell ATAC or Single Cell Multiome ATAC + Gene Expression assays?
- Can I use RNase-rich tissue samples for single cell gene expression or Multiome assays?
- Can I use fixed samples as input to the Multiome assay?
- Can RIN score be used for sample quality estimation before starting the Multiome assay?
- Is granulocyte sorting a requirement?
Nuclei Isolation
- How do I prepare and store 10% IGEPAL CA-630 and IGEPAL CO-360 stock solutions for nuclei isolations?
- Which nuclei isolation protocol should I use for the Single Cell Multiome ATAC + Gene Expression assay?
- How much residual membrane is acceptable when preparing nuclei for the Single Cell ATAC or Single Cell Multiome ATAC + Gene Expression assays?
- What are the differences in the nuclei isolation protocols among the 3', standalone ATAC and Multiome (ATAC+GEX) assays?
- What cleanup steps are compatible with my Multiome sample?
- Can I store the Diluted Nuclei Buffer, Lysis Buffers or Wash Buffers used in the Multiome assay?
Workflow
- How do I determine the average fragment size of a Single Cell ATAC or Multiome ATAC final library?
- Should I optimize transposition times for ATAC v1.1, v2 or Multiome assays?
- Can I purchase nuclei buffer for my ATAC or Multiome experiment?
- Why do I see an increased High Molecular Weight peak at 2000bp in the Multiome ATAC library trace?
- What is the purpose of the quenching reaction?
- Does the transposition reaction damage mRNA or promote nuclei leakage?
Sequencing
- At what concentration should standalone ATAC or Multiome ATAC libraries be loaded for the NovaSeq 6000 XP workflow?
- Why can I not pool Multiome ATAC and Standalone ATAC libraries on certain sequencers?
- Can I make Single index GEX libraries using the 10x Multiome ATAC + RNA assay?
- Can I sequence Multiome libraries on the Nextseq 1000/2000?
- I installed a custom sequencing recipe on my NextSeq 500/550, why can't I input 24 bp in the i5 indexing read?
- Why do I need a custom recipe when sequencing Multiome ATAC libraries on the NextSeq 500/550?
Software
- How can I analyze only my Multiome Gene Expression library with Cell Ranger on 10x Genomics Cloud Analysis?
- What is the difference between Promoter Sum, and Nearby Gene Sum in Loupe Browser?
- How do I modify the search distance of feature linkages in my multiome analysis?
- What would I observe if I mismatched Multiome ATAC and GEX data from different samples?
- Where can I find the barcode whitelist(s) for Single Cell Multiome (ATAC + GEX) product?
- Why does the ATAC R2 read have to be 16 bp?