Jan 23, 2025

Public workspaceMultiome protocol - Stanford TMC

DOI
https://dx.doi.org/10.17504/protocols.io.kqdg3qy3ev25/v1
  • bqzhao 1,
  • Thomas Karathanos1
  • 1Stanford University
  • Human BioMolecular Atlas Program (HuBMAP) Method Development Community
    Tech. support email: [email protected]
Thomas Karathanos
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DOI: https://dx.doi.org/10.17504/protocols.io.kqdg3qy3ev25/v1
Protocol Citation: bqzhao , Thomas Karathanos 2025. Multiome protocol - Stanford TMC. protocols.io https://dx.doi.org/10.17504/protocols.io.kqdg3qy3ev25/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: January 23, 2025
Last Modified: January 23, 2025
Protocol Integer ID: 118920
Keywords: multiome protocol, multiome, intestinal sample, experiments on intestinal sample, part of the human biomolecular atlas program, human biomolecular atlas program, stanford tmc overview of protocol, rna, stanford tmc overview, stanford tmc, seq
Abstract
Overview of protocol followed for multiome (RNA-seq & ATAC-seq) experiments on intestinal samples at Stanford TMC, as part of the Human Biomolecular Atlas Program.
Troubleshooting
Steps
Isolate nuclei from frozen tissues and prepare for ATAC-seq following the Omni-ATAC protocol described by Corces et al.: Link
The original protocol (without the nuclei extraction from frozen tissues portion) is described in more detail here: Link
Download CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User_Guide_RevG.pdfCG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User_Guide_RevG.pdf4.7MB
Follow the 10x Genomics protocol for Single Cell Multiome ATAC + Gene Expression from a dissociated sample: Link

Protocol references
Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396

10x Genomics. Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. Rev. G, 2024, https://cdn.10xgenomics.com/image/upload/v1728078404/support-documents/CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User_Guide_RevG.pdf.pdf.