microbiome block

Single cell Multiomics-10XGenomics MRL


Simultaneous capture of gene expression and open chromatin signatures from the same cell with Chromium Single Cell Multiome ATAC + Gene Expression allows multimodality and high resolution functional characterization of genomics and transcriptional states. This assay uses a Gel Bead-in-Emulsion (GEMs) concept to capture individual cell signals. In this workflow, two libraries are constructed that include a 3’ gene expression library and one ATAC-seq library. About 10K individual cells are input in each library and 30-40K paired sequencing reads are generated on gene expression library and 50K reads on ATAC-seq library. These libraries are sequenced on NovaSeq6k platforms to generate 300-600 Million sequences per sample. RAW sequencing data is analyzed using the Cell Ranger pipeline and visualized through Loupe browser tools.


We use the following 10X Genomics kits and platforms for sequencing library preparation and sequencing.

  • Chromium Next GEM Single cell 3’ Kit v3.1
  • ATAC-seq kit
  • Dual Index Kit TT Set A 96rxn
  • Chromium Next GEM Chip G Single cell kit, 16 rxn
  • NovaSeq6k-S4

Key Features

  • Single cell gene expression analysis
  • Chromatin state signature
  • High resolution cell type and state characterization
  • Precise gene expression regulation analysis
  • Cell type composition

Third-Party Resources

Cell Ranger and Loupe Browser | Single cell data analysis and data visualization tools

The Loupe Browser is a desktop application that provides interactive visualization functionality to analyze data from different 10x Genomics solutions. Cell Ranger and Loupe Browser