This research was supported by ERA-CVD-2019 and ANR-JCJC-2020 to SS. We thank the Genomics and Bioinformatics facility (GBiM) from the U 1251/Marseille Medical Genetics lab and the anonymous reviewers for providing valuable comments.

The animal procedure adopted in this study was approved by the animal ethics committees of the Aix-Marseille University (C2EA-14) and was carried out according to protocols approved by the appointed national ethical committee for animal experimentation (Minist&#232;re de l&#39;Education Nationale, de l&#39;Enseignement Sup&#233;rieur et de la Recherche; Authorization Apafis N&#176;33927-2021111715507212).
1. Setting up the timed mating prior to dissection
<ol>
	<li>To genera...

Nuclei Isolation from Mouse Cardiac Progenitor Cells at Single-Cell Resolution

<ol>
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Genetics. 16 (12), 716-726 (2015).</li><li>Macaulay, I. C., Ponting, C. P., Voet, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-cell+multiomics:+Multiple+measurements+from+single+cells.">Single-cell multiomics: Multiple measurements from single cells.</a> Trends in Genetics. 33 (2), 155-168 (2017).</li><li>Buenrostro, J. D., Wu, B., Chang, H. Y., Greenleaf, W. 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D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-cell+chromatin+accessibility+reveals+principles+of+regulatory+variation.">Single-cell chromatin accessibility reveals principles of regulatory variation.</a> Nature. 523 (7561), 486-490 (2015).</li><li>Denisenko, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Systematic+assessment+of+tissue+dissociation+and+storage+biases+in+single-cell+and+single-nucleus+RNA-seq+workflows.">Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows.</a> Genome Biology. 21 (1), 130 (2020).</li><li>Safabakhsh, S., et al. <a target="_blank" 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Cell Multiome ATAC + Gene Expression Reagent Kits User Guide.</a> 10x Genomics. , (2022).</li><li>Jia, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single+cell+RNA-seq+and+ATAC-seq+analysis+of+cardiac+progenitor+cell+transition+states+and+lineage+settlement.">Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement.</a> Nature Communications. 9 (1), 4877 (2018).</li><li>Wang, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-cell+dual-omics+reveals+the+transcriptomic+and+epigenomic+diversity+of+cardiac+non-myocytes.">Single-cell dual-omics reveals the transcriptomic and epigenomic diversity of cardiac non-myocytes.</a> Cardiovascular Research. 118 (6), 1548-1563 (2022).</li><li>Wang, Z., et al. <a target="_blank" 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C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Integrated+multi-omic+characterization+of+congenital+heart+disease.">Integrated multi-omic characterization of congenital heart disease.</a> Nature. 608 (7921), 181-191 (2022).</li><li>Chen, Z., Wei, L., Duru, F., Chen, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-cell+RNA+sequencing:+In-depth+decoding+of+heart+biology+and+cardiovascular+diseases.">Single-cell RNA sequencing: In-depth decoding of heart biology and cardiovascular diseases.</a> Current Genomics. 21 (8), 585-601 (2020).</li><li>Machado, L., Relaix, F., Mourikis, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stress+relief:+Emerging+methods+to+mitigate+dissociation-induced+artefacts.">Stress relief: Emerging methods to mitigate dissociation-induced artefacts.</a> Trends in Cell Biology. 31 (11), 888-897 (2021).</li><li>Tabula Muris, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-cell+transcriptomics+of+20+mouse+organs+creates+a+Tabula+Muris.">Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris.</a> Nature. 562 (7727), 367-372 (2018).</li><li>Machado, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tissue+damage+induces+a+conserved+stress+response+that+initiates+quiescent+muscle+stem+cell+activation.">Tissue damage induces a conserved stress response that initiates quiescent muscle stem cell activation.</a> Cell Stem Cell. 28 (6), 1125-1135 (2021).</li><li>Haghverdi, L., Lun, A. T. L., Morgan, M. D., Marioni, J. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Batch+effects+in+single-cell+RNA-sequencing+data+are+corrected+by+matching+mutual+nearest+neighbors.">Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.</a> Nature Biotechnology. 36 (5), 421-427 (2018).</li><li>Yang, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SMNN:+Batch+effect+correction+for+single-cell+RNA-seq+data+via+supervised+mutual+nearest+neighbor+detection.">SMNN: Batch effect correction for single-cell RNA-seq data via supervised mutual nearest neighbor detection.</a> Briefings in Bioinformatics. 22 (3), 097 (2021).</li><li>Stefanovic, S., Christoffels, V. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=GATA-dependent+transcriptional+and+epigenetic+control+of+cardiac+lineage+specification+and+differentiation.">GATA-dependent transcriptional and epigenetic control of cardiac lineage specification and differentiation.</a> Cellular and Molecular Life Sciences. 72 (20), 3871-3881 (2015).</li><li>Gunthel, M., Barnett, P., Christoffels, V. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development,+proliferation,+and+growth+of+the+mammalian+heart.">Development, proliferation, and growth of the mammalian heart.</a> Molecular Therapy. 26 (7), 1599-1609 (2018).</li><li>Stefanovic, S., Etchevers, H. 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The analysis of the cellular composition of the developing heart by combined snRNA-seq and snATAC-seq studies provides a deeper understanding of the origin of congenital heart disease26. Several research laboratories have studied the effects of cardiac tissue cryopreservation on snRNA-seq27. Conducting snRNA-seq and snATAC-seq using fresh micro-dissected tissue from mouse models of human disease can be logistically challenging when comparing different experimental condition...

Among birth defects, congenital heart defects (CHDs) are the most common, occurring in about 1% of live births each year1,2. Genetic mutations are identified in only a minority of cases, implying that other causes, such as abnormalities in gene regulation, are involved in the etiology of CHD2,3. Cardiac development is a complex process of diverse and interacting cell types, making the identification of causal noncoding mutations and their effects on gene regulation challenging. Organogenesis of the heart begins with cellular progenitors that give rise to different subtypes of cardiac cells, including myocardial, fibroblast, epicardial, and endocardial cells4,5.&#160;Single-cell genomics is emerging as a key method for studying heart development and assessing the impact of cellular heterogeneity in health and disease6. The development of multi-omics methods for the simultaneous measurement of different parameters and the expansion of computational pipelines has facilitated the discovery of cell types and subtypes in the normal and diseased heart6. This article describes a reliable single-nucleus isolation protocol for frozen cardiac progenitor cells obtained from mouse embryos that is compatible with downstream snRNA-seq and snATAC-seq (as well as snRNA-seq and snATAC-seq combined)7,8,9.
ATAC-seq is a robust method that allows the identification of regulatory open chromatin regions and the positioning of nucleosomes10,11. This information is used to draw conclusions about the location, identity, and activity of transcription factors. The activity of chromatin factors, including remodelers, as well as the transcriptional activity of RNA polymerase, can, thus, be analyzed since the method is highly sensitive for measuring quantitative changes in chromatin structure1,2. Thus, ATAC-seq provides a robust and impartial approach to uncovering the mechanisms controlling transcriptional regulation in a specific cell type. ATAC-seq protocols have also been validated to measure chromatin accessibility in single cells, revealing variability in the chromatin architecture within cell populations10,12,13.
Although there have been notable advances in the field of single cells in recent years, the main difficulty is the processing of the fresh samples needed to perform these experiments14. To circumvent this difficulty, various tests have been carried out with the aim of conducting analyses such as snRNA-seq and snATAC-seq with frozen cardiac tissue or cells15,16.
Several platforms have been used to analyze single-cell genomics data17. The widely used platforms for single-cell gene expression and ATAC profiling are platforms for multiple microfluidic droplet encapsulation17. As these platforms use microfluidic chambers, debris or aggregates can clog the system, resulting in non-usable data. Thus, the success of single-cell studies depends on the accurate isolation of individual cells/nuclei.
The protocol presented here uses a similar approach to recent studies using snRNA-seq and snATAC-seq to understand congenital heart defects18,19,20,21,22,23. This procedure utilizes the enzymatic dissociation of freshly microdissected cardiac tissue followed by the cryopreservation of mouse cardiac progenitor cells. After thawing, the viable cells are purified and processed for nuclear isolation. In this work, this protocol was successfully used to obtain snRNA-seq and snATAC-seq data from the same nuclear preparation of mouse cardiac progenitor cells.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>2100 Bioanalyzer Instrument</td>
			<td>Agilent</td>
			<td></td>
			<td>No catalog number</td>
		</tr>
		<tr>
			<td>5M Sodium chloride (NaCl)</td>
			<td>Sigma</td>
			<td>59222C-500ML&#160;</td>
			<td></td>
		</tr>
		<tr>
			<td>BSA 10%&#160;</td>
			<td>Sigma</td>
			<td>A1595-50ML</td>
			<td></td>
		</tr>
		<tr>
			<td>Chromium Next GEM Chip J Single Cell Kit, 16 rxns</td>
			<td>10X Genomics</td>
			<td>1000230</td>
			<td></td>
		</tr>
		<tr>
			<td>Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 4 rxns (including Nuclei Buffer 20X)</td>
			<td>10X Genomics</td>
			<td>1000285</td>
			<td></td>
		</tr>
		<tr>
			<td>Countess cell counting chamber slides</td>
			<td>Invitrogen</td>
			<td>C10283</td>
			<td></td>
		</tr>
		<tr>
			<td>Countess III FL</td>
			<td>Thermofisher</td>
			<td></td>
			<td>No catalog number</td>
		</tr>
		<tr>
			<td>Digitonin (5%)</td>
			<td>Thermofisher</td>
			<td>BN2006</td>
			<td></td>
		</tr>
		<tr>
			<td>DMSO</td>
			<td>Sigma</td>
			<td>D2650-5x5ML</td>
			<td></td>
		</tr>
		<tr>
			<td>DNA LoBind Tubes&#160;</td>
			<td>Eppendorf</td>
			<td>22431021</td>
			<td></td>
		</tr>
		<tr>
			<td>D-PBS</td>
			<td>Thermofisher</td>
			<td>14190094</td>
			<td>Sterile and RNase-free</td>
		</tr>
		<tr>
			<td>Dual Index Kit TT Set A 96 rxns</td>
			<td>10X Genomics</td>
			<td>1000215</td>
			<td></td>
		</tr>
		<tr>
			<td>Falcon 15 mL Conical Centrifuge Tubes&#160;</td>
			<td>Fisher Scientific&#160;</td>
			<td>352096</td>
			<td></td>
		</tr>
		<tr>
			<td>Falcon 50 mL Conical Centrifuge Tubes&#160;</td>
			<td>Fisher Scientific&#160;</td>
			<td>10788561</td>
			<td></td>
		</tr>
		<tr>
			<td>HI-FBS</td>
			<td>Thermofisher</td>
			<td>A3840001</td>
			<td>Heat inactivated</td>
		</tr>
		<tr>
			<td>High sensitivity DNA kit</td>
			<td>Agilent</td>
			<td>5067-4626</td>
			<td></td>
		</tr>
		<tr>
			<td>Igepal CA-630</td>
			<td>Sigma</td>
			<td>I8896-50ML</td>
			<td></td>
		</tr>
		<tr>
			<td>LIVE/DEAD Viability/Cytotoxicity Kit</td>
			<td>Thermofisher</td>
			<td>L3224</td>
			<td></td>
		</tr>
		<tr>
			<td>MACS Dead Cell Removal kit: Dead Cell Romoval MicroBeads, Binding Buffer 20X</td>
			<td>Miltenyi Biotec</td>
			<td>130-090-101</td>
			<td></td>
		</tr>
		<tr>
			<td>MACS SmartStrainers (30 &#181;m)</td>
			<td>Miltenyi Biotec</td>
			<td>130-098-458</td>
			<td></td>
		</tr>
		<tr>
			<td>Magnesium chloride (MgCl2)</td>
			<td>Sigma</td>
			<td>M1028-100ML</td>
			<td></td>
		</tr>
		<tr>
			<td>Milieu McCoy 5A&#160;</td>
			<td>Thermofisher</td>
			<td>16600082</td>
			<td></td>
		</tr>
		<tr>
			<td>MS Columns</td>
			<td>Miltenyi Biotec</td>
			<td>130-042-201</td>
			<td></td>
		</tr>
		<tr>
			<td>NovaSeq 6000 S2</td>
			<td>Illumina</td>
			<td></td>
			<td>No catalog number</td>
		</tr>
		<tr>
			<td>Penicillin Streptomycin (Pen/Strep)</td>
			<td>Thermofisher</td>
			<td>15070063</td>
			<td></td>
		</tr>
		<tr>
			<td>PluriStrainer Mini 40&#181;m</td>
			<td>PluriSelect</td>
			<td>V-PM15-2021-12</td>
			<td></td>
		</tr>
		<tr>
			<td>Rock inhibitor</td>
			<td>Enzo Life Sciences</td>
			<td>ALX-270-333-M005</td>
			<td></td>
		</tr>
		<tr>
			<td>Single Index Kit N Set A, 96 rxn</td>
			<td>10X Genomics</td>
			<td>1000212</td>
			<td></td>
		</tr>
		<tr>
			<td>Standard 90mm Petri dish Sterilin</td>
			<td>Thermofisher</td>
			<td>101R20</td>
			<td></td>
		</tr>
		<tr>
			<td>Sterile double-distilled water</td>
			<td>Thermofisher</td>
			<td>R0582</td>
			<td></td>
		</tr>
		<tr>
			<td>Trizma Hydrochloride solution (HCl)</td>
			<td>Sigma</td>
			<td>T2194-100ML&#160;</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypan Blue stain (0.4%)</td>
			<td>Invitrogen</td>
			<td>T10282</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypsin 0.05% - EDTA 1X</td>
			<td>Thermofisher</td>
			<td>25300054</td>
			<td></td>
		</tr>
		<tr>
			<td>Tween20</td>
			<td>Sigma</td>
			<td>P9416-50ML&#160;</td>
			<td></td>
		</tr>
		<tr>
			<td>Wide orifice filtered pipette tips 200 &#956;l</td>
			<td>Labcon</td>
			<td>1152-965-008-9</td>
			<td></td>
		</tr>
		<tr>
			<td>ZEISS SteREO Discovery.V8</td>
			<td>ZEISS</td>
			<td></td>
			<td>No catalog number</td>
		</tr>
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</table>

nuclei isolation from mouse cardiac progenitor cells for epigenome and gene expression profiling at single-cell resolution

The developing heart is a complex structure containing various progenitor cells controlled by complex regulatory mechanisms. The examination of the gene expression and chromatin state of individual cells allows the identification of the cell type and state. Single-cell sequencing approaches have revealed a number of important characteristics of cardiac progenitor cell heterogeneity. However, these methods are generally restricted to fresh tissue, which limits studies with diverse experimental conditions, as the fresh tissue must be processed at once in the same run to reduce the technical variability. Therefore, easy and flexible procedures to produce data from methods such as single-nucleus RNA sequencing (snRNA-seq) and the single-nucleus assay for transposase-accessible chromatin with high-throughput sequencing (snATAC-seq) are needed in this area. Here, we present a protocol to rapidly isolate nuclei for subsequent single-nuclei dual-omics (combined snRNA-seq and snATAC-seq). This method allows the isolation of nuclei from frozen samples of cardiac progenitor cells and can be combined with platforms that use microfluidic chambers.

Author Spotlight: Nuclei Isolation from Mouse Cardiac Progenitor Cells for Epigenome and Gene Expression Profiling at Single-Cell Resolution  

Nuclei Isolation from Mouse Cardiac Progenitor Cells for Epigenome and Gene Expression Profiling at Single-Cell Resolution

The main objective of this protocol is to study the interaction of genetic and environmental factors in the context of heart development and their contribution to congenital heart defects. Single nuclei approaches such as single nuclei RNA-seq and single nuclei ataxic are emerging as key methods to study cellular heterogeneity in health and disease during heart development. One limiting step of these experiments is that all the sample have to be run simultaneously.While working with all the experimental conditions, collecting fresh enough material is for all the condition simultaneously could be challenging. Although there have been a significant progress in the field in single cell for recent years, the main difficulty is processing free samples. Avoiding the difficulty is extremely benefit to identify the molecular mechanism underlying congenital heart disease defects.This protocol describes the steps to follow for successfully isolating high quality nuclei from frozen cardiac cell suspension obtained from mouse embryos. And our protocol is compatible with downstream single nuclei RNA-seq and single nuclei ataxic. We hope that this procedure will help interested researchers and encourage them to use this powerful method for their research.

Compared to the preparation of single-cell suspensions for single-cell approaches, the preparation of single-nuclei suspensions is much more challenging and requires a higher degree of resolution and processing. The key factor for successful combined snRNA-seq and snATAC-seq is a clean and intact nuclei suspension. The protocol for efficient nuclei isolation must be adapted to each tissue type and condition (fresh or frozen). Here, an optimized protocol is described for the isolation of nuclei from frozen mouse embryonic...

Watch this Scientific Journal Video about Nuclei Isolation from Mouse Cardiac Progenitor Cells for Epigenome and Gene Expression Profiling at Single-Cell Resolution at JoVE.com

Here, we present a protocol describing cell nuclei preparation. After microdissection and enzymatic dissociation of cardiac tissue into single cells, the progenitor cells were frozen, followed by isolation of pure viable cells, which were used for single-nucleus RNA sequencing and the single-nucleus assay for transposase-accessible chromatin with high-throughput sequencing analyses.

The developing heart is a complex structure containing various progenitor cells controlled by complex regulatory mechanisms. The examination of the gene ...

nuclei-isolation-from-mouse-cardiac-progenitor-cells-for-epigenome