Aug 20, 2025
Single Cell Multiomics protocol for processing gDNA and mRNA
- Anala V. Shetty1,2,
- Clifford J. Steer1,2,3,
- Walter C. Low1,2,4
- 1Molecular, Cellular, Developmental Biology, and Genetics Graduate Program, University of Minnesota, Minneapolis, MN, USA;
- 2Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA;
- 3Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Minnesota, Minneapolis, MN, USA;
- 4Department of Neurosurgery, University of Minnesota, Minneapolis, MN, USA
Protocol Citation: Anala V. Shetty, Clifford J. Steer, Walter C. Low 2025. Single Cell Multiomics protocol for processing gDNA and mRNA. protocols.io https://dx.doi.org/10.17504/protocols.io.36wgqdnwyvk5/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: December 13, 2024
Last Modified: August 20, 2025
Protocol Integer ID: 115142
Keywords: single cell, multiomics approach, gDNA, mRNA, single cell gDNA, single cell mRNA, replication timing of single cell, gdna protocol, cdna from single cell, processing gdna, gdna, affordable single cell, cdna part of the protocol, replication timing, processing mrna, compatible with replication, mrna, smartseq2 technique, replication, standalone protocol
Funders Acknowledgements:
Clifford J. Steer
Grant ID: R01 DK117286
Clifford J. Steer and Walter Low
Grant ID: R01 DK117286-03S1
Clifford J. Steer and Walter Low
Grant ID: R01 AI173804-01
Abstract
Here, we developed an affordable single cell (sc)-multiomics approach to simultaneously extract and process gDNA and cDNA from single cells. The gDNA protocol can also be used as a standalone protocol. The cDNA part of the protocol was adopted from G&T (Macaulay et al. 2016) and uses the SMARTSeq2 technique for processing mRNA (Picelli et al. 2014). The gDNA was used to deduce copy number variation and replication timing of single cells. in cell lines. The gDNA protocol was compatible with replication timing computational pipelines like Kronos sc-RT (Gnan et. al 2022) and sc-Repliseq (Miura et. al 2020).
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