Cancer Genomics Center

Single Cell Multiome ATAC + Gene Expression (Multiome)

Chromium Single Cell Multiome ATAC + Gene Expression provides multiomic analysis for the same single cell. Simultaneously profile gene expression and open chromatin from the same cell, across thousands of cells, with Chromium Single Cell Multiome ATAC + Gene Expression. This pipeline provides a unified view of a cell's gene expression profile and its epigenomic landscape. Increase the resolution of cell states, identify drivers of differential gene expression, and discover cells with similar transcriptional profiles but functionally different chromatin landscapes by leveraging two modalities at once.

Highlights

• Multiply your power of discovery with combined epigenomic and gene expression profiling using the assay for transposaseaccessible chromatin (ATAC) to identify regions of open chromatin alongside RNA-seq
• Gain deeper insights into cell types and states with linked transcriptional and epigenomic analyses
• Understand gene regulatory networks by linking open chromatin regions with gene expression profiles at single cell resolution
• Easily interpret epigenetic profiles with key expression marker

Sample Submission requirements

Service	Sample Type	Minimum Amount	Morphology of nuclei	Optimal concentration
Multime	Nuclei	50,000	Intact membrane	Contact us for info

• Single cells are suspended in 1x nuclei buffer with DTT and RNase inhibitor
• Samples have to be sent to core before 1 PM
• The nuclei will be checked the quality and the core has the rights to determine if the samples are qualified for the experiment
• Please check the core (cgc@uth.tmc.edu or 713-500-7933) for the detail information.

Service Workflow

Data analysis with Cell Ranger ARC

The Single Cell Multiome ATAC + Gene Expression software suite consists of Cell Ranger ARC for the analysis and Loupe Browser for the visualization of chromatin accessibility and 3' gene expression data from the same cell produced by the 10x platform. The set of analysis pipelines in this suite perform sample demultiplexing, barcode processing, identification of open chromatin regions, and simultaneous counting of transcripts and peak accessibility in single cells. Additionally, the pipelines perform secondary analyses like dimensionality reduction, clustering, differential analysis, and feature linkage between peaks and genes that aid in data interpretation.

Useful documents

• Chromium Next GEM Multiome User Guide
• Grant Application Support

Sample preparation webinar

Recording: https://10xgenomics.zoom.us/rec/share/WBreUC7kp8YBphiFiBm3caNY4lVREJzkGK9eH-yvgtWqHV72O9fGH50xoejM8coi.nIy34oQhfX-q8tVZ

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