Nov 15, 2025

Public workspaceEpi Multiome ATAC + Gene Expression – Stanford Bone Marrow TMC

DOI
https://dx.doi.org/10.17504/protocols.io.j8nlkyjw5g5r/v1
  • Patricia Favaro1,
  • Jumana Afaghani1,
  • Sean Bendall1
  • 1Stanford University
  • Human BioMolecular Atlas Program (HuBMAP) Method Development Community
    Tech. support email: [email protected]
Patricia Favaro
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DOI: https://dx.doi.org/10.17504/protocols.io.j8nlkyjw5g5r/v1
Protocol Citation: Patricia Favaro, Jumana Afaghani, Sean Bendall 2025. Epi Multiome ATAC + Gene Expression – Stanford Bone Marrow TMC. protocols.io https://dx.doi.org/10.17504/protocols.io.j8nlkyjw5g5r/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: November 13, 2025
Last Modified: November 17, 2025
Protocol Integer ID: 232249
Keywords: ATAC, HuBMAP, Tissue Map Center (TMC), Multiome, Gene Expression, bone Marrow, 10x genomics single cell multiome nuclei isolation protocol, 10x genomics single cell multiome, epi multiome atac, quality nuclei suitable for downstream atac, stanford bone marrow tmc fresh, human whole bone marrow aspirate, gene expression multimodal profiling, gene expression, mononuclear cell, downstream atac, nuclei isolation protocol
Funders Acknowledgements:
HuBMAP NIH
Grant ID: U54HL165445
Abstract
Fresh human whole bone marrow aspirates (25 mL; AllCells) were collected and processed on the same day. Mononuclear cells were isolated by Ficoll density gradient centrifugation followed by red blood cell lysis. CD34⁺ hematopoietic stem and progenitor cells were enriched by magnetic selection (STEMCELL Technologies, catalog # 17856). Equal numbers of CD34⁺ and CD34⁻ cells (5×10⁵ each) were then pooled at a 1:1 ratio. Nuclei were extracted following the 10x Genomics Single Cell Multiome nuclei isolation protocol (see links below), generating high-quality nuclei suitable for downstream ATAC + gene expression multimodal profiling.
Troubleshooting
Steps
Nuclei isolation from fresh CD34⁺ and CD34⁻ cells: link
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression library preparation: link
Acknowledgements
This work was supported by HuBMAP NIH grant U54HL165445.