The authors would like to thank the entire team at the Oregon Health Sciences University for taking care of the non-human primate colony and for tissue acquisition. Additionally, Vanderbilt Technologies for Advanced Genomics provided technical expertise and experimental design advice. DTC was supported by an F31 pre-doctoral fellowship from the NIH/NIDK (1F31DK135164). PK was supported by the NIH/NIDDK (1R01DK128187). MG was supported by a VA Merit award (I01 BX005399), the NIH/NIDDK (1R01DK135032, 1R01DK128187), and the JDRF (2-SRA-2024-1455-S-B). Work at the Oregon National Primate Research Center (ONPRC) was supported by P51OD011092 for operational support of the Center.

Islet retrieval was conducted in accordance with the guidelines of the Institutional Animal Care and Use Committee (IACUC) of the Oregon National Primate Research Center (ONPRC) and Oregon Health and Science University and was approved by the ONPRC IACUC. The ONPRC abides by the Animal Welfare Act and Regulations enforced by the United States Department of Agriculture (USDA) and the Public Health Service Policy on Humane Care and Use of Laboratory. The protocol herein was applied to islets from fetal Rhesus macaques that were necropsied on gestational day 145 (Rhesus macaque gestation is typically 173-175 days). The details of the reagents and the equipment used for this study are listed in the Table of Materials.
1. Islet isolation
<ol>
	<li>Excise fetal pancreata from surrounding tissues9 and place it in ice-cold phosphate-buffered saline.</li>
	<li>Remove the pancreas from PBS and inflate it with collagenase P (0.6 mg/mL) via cannulation of the pancreatic duct using a 33 G rodent brain cannula injector.</li>
	<li>Divide the pancreas into six sections with sterile surgical scissors and digest for 27-30 min at 37 &#176;C in collagenase solution.</li>
	<li>Prepare RT media by combining 10% FBS and 100 U/mL penicillin/streptomycin into RPMI 1640.</li>
	<li>Pour off collagenase and add 10 mL of RT media.</li>
	<li>Gently shake for 1 min to disrupt the remaining connective tissue.</li>
	<li>Remove undigested material by straining through a 500 &#181;m filter.</li>
	<li>Wash the islets twice with 50 mL of RT media.</li>
	<li>Incubate the islets in bovine DNase I (0.8 U/mL) in a 37 &#176;C water bath for 10 min.</li>
	<li>Culture the islets overnight in RT media with bovine DNase I (0.4 U/mL) at 37 &#176;C with 5% CO2.</li>
	<li>Ship islets in specialized packaging at ambient temperature with temperature control gel packs.</li>
</ol>
2. Sample banking for long-term storage
<ol>
	<li>Assess islets for size using a scaled reticle and note the degree of acinar and ductal tissue in preparation.</li>
	<li>Handpick islets with an automated pipette into a 60 mm dish containing 5 mL of 2.8 mM glucose DMEM. 
	NOTE: It is imperative to minimize the amount of acinar tissue and ductal tissue that will be stored in the final islet preparation. Details of ideal islets for use are reported in a previous protocol9.</li>
	<li>Pick islets into a 1.5 mL tube and spin at ~300 x g for 5 min at 4 &#176;C.</li>
	<li>Resuspended the islets in calcium and magnesium-free 1x PBS.</li>
	<li>Spin for 5 min at ~300 x g at 4 &#176;C. Discard the supernatant.</li>
	<li>Repeat steps 2.3-2.5 twice more.</li>
	<li>Flash freeze the islets in a 1.5 mL tube for 10 s in liquid nitrogen.</li>
	<li>Store the pellet at -80 &#176;C until the day of nuclear isolation.</li>
</ol>
3. Cellular fractionation for isolation of nuclei and cytoplasmic fraction
<ol>
	<li>Preparation of buffers for nuclei extraction (Table 1).
	<ol>
		<li>Ensure that the bench, pipettes, and reagents are RNase-free.</li>
		<li>Prepare the wash, concentrated lysis, lysis dilution, and diluted nuclei buffers according to Table 1.</li>
		<li>Prepare 0.1x lysis buffer in a 5 mL tube using the lysis dilution buffer to dilute the concentrated lysis buffer.</li>
	</ol>
	</li>
	<li>Tissue homogenization
	<ol>
		<li>Remove the samples from -80 &#176;C freezer and immediately place them on ice.</li>
		<li>Add 500 &#181;L of 0.1x lysis buffer to the tissue pellets and incubate for 3 min on ice.</li>
		<li>Using a disposable RNase-free pellet pestle, gently homogenize the tissue 15 times on ice.</li>
		<li>Incubate the samples on ice for 10 min.</li>
		<li>Add 500 &#181;L of wash buffer to the homogenate and gently pipette on ice.</li>
		<li>Prime a 30 &#181;m pre-separation filter by adding 300 mL of wash buffer to the filter over a 5 mL tube.</li>
		<li>Filter the 1 mL cellular homogenate using the 30 &#181;M pre-separation filter into the 5 mL tube.</li>
		<li>Spin the filtered homogenate at 500 x g for 5 min in a swinging bucket centrifuge at 4 &#176;C.</li>
	</ol>
	</li>
	<li>Collection and storage of supernatant for metabolomics
	<ol>
		<li>Remove 1 mL of the supernatant from step 3.2.8 with a pipette and add to a 1.5 mL cryovial on ice.</li>
		<li>Immediately freeze the supernatant at -80 &#176;C. This supernatant will be used for metabolomics.</li>
	</ol>
	</li>
	<li>Preparation of nuclei for single nucleus RNA- and ATAC-sequencing
	<ol>
		<li>Gently resuspend the nuclei pellet by adding 1 mL of wash buffer to the pellet dropwise. Slowly pipette 5 times.</li>
		<li>Spin the washed pellet at 1000 x g for 5 min in a swinging bucket centrifuge at 4 &#176;C.</li>
		<li>Repeat steps 3.4.1 and 3.4.2 once more.</li>
		<li>After the final wash, resuspend the nuclei in 1 mL of wash buffer. Keep nuclear preparation on ice.</li>
		<li>Aspirate 10 &#181;L of nuclei suspension with a pipette and mix with 10 &#181;L of 0.4% Trypan blue by gently pipetting.</li>
		<li>Add 10 &#181;L of the nuclei and Trypan blue mixture to an automated cell counter slide with a pipette and place it in the instrument.</li>
		<li>Determine nuclei concentration in nuclei/&#181;L. 
		NOTE: Unlike cellular preparations for single-cell RNA sequencing, automated cell counters will detect nuclei as dead cells. No more than 95% of this preparation should be live on automated cell counters. If more than 5% of the nuclear population is live, the nuclei suspension can be filtered an additional time through the 30 &#181;m pre-separation filter and spun for 5 min at 1000 x g at 4 &#176;C. Nuclei concentration can then be recalculated as outlined in step 3.4.6.</li>
		<li>Based on the desired targeted nuclei recovery, resuspend nuclei to the necessary concentration using 1x nuclei buffer and proceed to single nucleus RNA and ATAC sequencing library preparation10.</li>
	</ol>
	</li>
</ol>
4. Preparation of cytosolic fraction for capillary electrophoresis- mass spectrometry (CE-MS)
<ol>
	<li>Combine 80 &#181;L of cytosolic fraction collected in step 3.3.1 with 20 &#181;L of nanopure water containing internalized standards.</li>
	<li>Proceed with CE-MS and analysis as previously described11,12,13.</li>
</ol>

From RNA to Metabolites: Multi-Omic Profiling of Non-Human Primate Fetal Islets

<ol>
	<li>Christensen, A. A., Gannon, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+beta+cell+in+type+2+diabetes.">The beta cell in type 2 diabetes.</a> Curr Diab Rep. 19 (9), 81 (2019).</li><li>Elsakr, J. M., Gannon, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Developmental+programming+of+the+pancreatic+islet+by.">Developmental programming of the pancreatic islet by.</a> Trends Dev Biol. 10, 79-95 (2017).</li><li>Salzberg, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Risk+factors+and+lifestyle+interventions.">Risk factors and lifestyle interventions.</a> Prim Care. 49 (2), 201-212 (2022).</li><li>Pound, L. D., Kievit, P., Grove, K. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+non-human+primate+as+a+model+for+type+2+diabetes.">The non-human primate as a model for type 2 diabetes.</a> Curr Opin Endocrinol Diabetes Obes. 21 (2), 89-94 (2014).</li><li>Kang, R. B., 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-nucleus+RNA+sequencing+of+human+pancreatic+islets+identifies+novel+gene+sets+and+distinguishes+&#946;-cell+subpopulations+with+dynamic+transcriptome+profiles.">Single-nucleus RNA sequencing of human pancreatic islets identifies novel gene sets and distinguishes &#946;-cell subpopulations with dynamic transcriptome profiles.</a> Genome Med. 15 (1), 30 (2023).</li><li>Basile, 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=Using+single-nucleus+RNA-sequencing+to+interrogate+transcriptomic+profiles+of+archived+human+pancreatic+islets.">Using single-nucleus RNA-sequencing to interrogate transcriptomic profiles of archived human pancreatic islets.</a> Genome Med. 13 (1), 128 (2021).</li><li>Cab&#233;, C. M., 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=High-quality+brain+and+bone+marrow+nuclei+preparation+for+single+nuclei+multiome+assays.">High-quality brain and bone marrow nuclei preparation for single nuclei multiome assays.</a> J Vis Exp. (202), e65715 (2023).</li><li>. Nuclei from embryonic mouse brain for single cell multiome ATAC + gex sequencing Available from: <a target="_blank" href="https://www.10xgenomics.com">https://www.10xgenomics.com</a> (2022)</li><li>Elsakr, J. M., Deeter, C., Ricciardi, V., Gannon, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+non-human+primate+pancreatic+islet+oxygen+consumption.">Analysis of non-human primate pancreatic islet oxygen consumption.</a> J Vis Exp. (154), e60696 (2019).</li><li>. Chromium next gem single cell multiome ATAC + gene expression reagent kits user guide Available from: <a target="_blank" href="https://www.10xgenomics.com">https://www.10xgenomics.com</a> (2022)</li><li>Maruyama, A., 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=Extraction+of+aqueous+metabolites+from+cultured+adherent+cells+for+metabolomic+analysis+by+capillary+electrophoresis-mass+spectrometry.">Extraction of aqueous metabolites from cultured adherent cells for metabolomic analysis by capillary electrophoresis-mass spectrometry.</a> J Vis Exp. (148), e59551 (2019).</li><li>Ooga, T., 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=Metabolomic+anatomy+of+an+animal+model+revealing+homeostatic+imbalances+in+dyslipidaemia.">Metabolomic anatomy of an animal model revealing homeostatic imbalances in dyslipidaemia.</a> Mol Biosyst. 7 (4), 1217-1223 (2011).</li><li>Ohashi, 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=Depiction+of+metabolome+changes+in+histidine-starved+Escherichia+coli+by+CE-TOFMS.">Depiction of metabolome changes in histidine-starved Escherichia coli by CE-TOFMS.</a> Mol Biosyst. 4 (2), 135-147 (2008).</li><li>Chiou, J., 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+identifies+pancreatic+islet+cell+type&#8211;+and+state-specific+regulatory+programs+of+diabetes+risk.">Single-cell chromatin accessibility identifies pancreatic islet cell type&#8211; and state-specific regulatory programs of diabetes risk.</a> Nat Genetics. 53 (4), 455-466 (2021).</li><li>Pang, Z., 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=Metaboanalyst+6.0:+Towards+a+unified+platform+for+metabolomics+data+processing,+analysis+and+interpretation.">Metaboanalyst 6.0: Towards a unified platform for metabolomics data processing, analysis and interpretation.</a> Nucleic Acids Res. , 253 (2024).</li><li>Willency, J. A., Lin, Y., Pirro, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Targeted+metabolomics+in+human+and+animal+biofluids+and+tissues+using+liquid+chromatography+coupled+with+tandem+mass+spectrometry.">Targeted metabolomics in human and animal biofluids and tissues using liquid chromatography coupled with tandem mass spectrometry.</a> STAR Protoc. 5 (1), 102884 (2024).</li><li>Behnke, J. -. S., Urner, L. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Emergence+of+mass+spectrometry+detergents+for+membrane+proteomics.">Emergence of mass spectrometry detergents for membrane proteomics.</a> Anal Bioanal Chem. 415 (18), 3897-3909 (2023).</li><li>Ouimet, C. M., D'amico, C. I., Kennedy, R. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advances+in+capillary+electrophoresis+and+the+implications+for+drug+discovery.">Advances in capillary electrophoresis and the implications for drug discovery.</a> Expert Opin Drug Discov. 12 (2), 213-224 (2017).</li><li>Alexandrov, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spatial+metabolomics+and+imaging+mass+spectrometry+in+the+age+of+artificial+intelligence.">Spatial metabolomics and imaging mass spectrometry in the age of artificial intelligence.</a> Annu Rev Biomed Data Sci. 3, 61-87 (2020).</li><li>Ewald, J. 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=Web-based+multi-omics+integration+using+the+analyst+software+suite.">Web-based multi-omics integration using the analyst software suite.</a> Nat Protoc. 19, 1467-1497 (2024).</li></ol>

The authors declare no conflicts of interest.

Historically, the methods of nuclear isolation for single nucleus RNA- and ATAC-sequencing have utilized buffers containing detergents that are incompatible with liquid chromatography-mass spectrometry (LC-MS), a common technique used for metabolite quantification16,17. The current protocol allows for the combination of transcriptomic and metabolomic techniques from the same sample preparation by using a gentle detergent for cellular fractionation, and following ...

The pancreatic islets of Langerhans are critical for the management of glucose tolerance throughout the lifespan. Failure to properly tune blood glucose levels via the glucose-lowering hormone, insulin, or the glucose-raising hormone, glucagon results in Diabetes Mellitus1. Modifiable risk factors to minimize diabetes risk include exercise and diet. In addition, it is becoming clear that maternal diet during pregnancy also has an effect on offspring susceptibility to diabetes in adulthood2,3. Thus, methods are needed to analyze the effects of maternal diet and other exposures, such as medications used during pregnancy, on the insulin-producing beta cells in model organisms during development. For example, islets from fetal non-human primate (NHP) offspring can be evaluated for the effects of developmental exposures. Similar to humans, NHPs typically have singleton births and vary in their physiological response to Western-style diet feeding4. While the gestation and fetal development of NHPs shares many similarities with humans, making them a highly relevant species for metabolic programming studies, challenges to performing comparative bioinformatic assays on NHP offspring include a restricted mating season and intermittent sample collection. Therefore, approaches that allow for long-term storage prior to sample processing and analysis are ideal. This protocol describes the preparation of samples for single nucleus RNA-sequencing, ATAC-sequencing, and bulk cytoplasmic metabolomics.
Studies by others in the islet biology field have demonstrated overlap in the genetic signatures observed in samples prepared via single-cell RNA Sequencing and single-nucleus RNA sequencing5,6. Both methods allow for the identification of transcripts that contribute to distinguishing features amongst various cell types within the islet population. Through the use of gentle detergents on flash-frozen tissue, intact nuclei can simultaneously be used for ATAC sequencing, which allows for the determination of accessible chromatin regions. Combining single-nucleus RNA-sequencing with ATAC-sequencing allows for better characterization of gene regulatory networks7.
The preparation of samples for metabolomics has traditionally been limited by the need for a high sample volume input for liquid chromatography. In addition, careful consideration must be given to the buffers used during sample preparation to avoid false NMR peaks in mass spectrometric data. Given the low number of samples that are challenging and costly to acquire in primate studies, allocation of islets from different offspring toward transcriptomic versus metabolomic experiments can be difficult. Thus, this protocol makes use of the normally discarded cytosolic fraction generated during cellular fractionation for single-nucleus experiments. This method allows for the simultaneous characterization of transcripts and open chromatin regions that define cellular subsets in fetal islets while quantitatively measuring the metabolites produced within islets (Figure 1). This protocol is adapted from a demonstrated protocol published by 10x genomics for the isolation of nuclei from flash-frozen embryonic mouse brain tissue (version CG000366 Rev D8)7.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>33 G rat brain cannula injector</td>
			<td>Protech International</td>
			<td>8IC315IS5SPC</td>
			<td>For duct cannulation and pancreas inflation</td>
		</tr>
		<tr>
			<td>Penicillin/Streptomycin</td>
			<td>Fisher</td>
			<td>15-140-122</td>
			<td>For RT media</td>
		</tr>
		<tr>
			<td>FBS</td>
			<td>Millipore/Sigma</td>
			<td>F4135-500ML</td>
			<td>For RT media</td>
		</tr>
		<tr>
			<td>RPMI 1640</td>
			<td>Thermo Fisher Scientific</td>
			<td>11-875-135</td>
			<td>For RT media</td>
		</tr>
		<tr>
			<td>Collagenase P</td>
			<td>Sigma Aldrich</td>
			<td>11213865001</td>
			<td>For digestion of pancreas</td>
		</tr>
		<tr>
			<td>Bovine Dnase I</td>
			<td>Sigma Aldrich</td>
			<td>11284932001</td>
			<td>For RT media and isolation</td>
		</tr>
		<tr>
			<td>Dextrose</td>
			<td>Fisher</td>
			<td>D16-1</td>
			<td>Final concentration will be 2.8 mM</td>
		</tr>
		<tr>
			<td>Calcium Chloride</td>
			<td>Fisher</td>
			<td>C4901-500G</td>
			<td>Final concentration will be 0.5 mM</td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>Gibco</td>
			<td>15630-080</td>
			<td>Final concentration will be 10 mM</td>
		</tr>
		<tr>
			<td>Bovine Serum Albumin (BSA) Fraction 5</td>
			<td>Research Products International</td>
			<td>A30075100</td>
			<td>Final concentration will be 0.5 mg/mL</td>
		</tr>
		<tr>
			<td>Dulbecco&#39;s Modified Eagle Medium</td>
			<td>Gibco</td>
			<td>11966025</td>
			<td>For handpicking islets</td>
		</tr>
		<tr>
			<td>20x Nuclei Buffer</td>
			<td>10X Genomics</td>
			<td>2000153/2000207</td>
			<td></td>
		</tr>
		<tr>
			<td>Digitonin (5%)</td>
			<td>Thermo Fisher Scientific</td>
			<td>BN2006</td>
			<td>Digitonin may need to be warmed to 65 &#176;C to dissolve white precipitate</td>
		</tr>
		<tr>
			<td>MACS SmartStrainers (30 &#181;M)</td>
			<td>Miltenyi Biotec</td>
			<td>130-098-458</td>
			<td></td>
		</tr>
		<tr>
			<td>MACS BSA Stock Solution (10%)</td>
			<td>Miltenyi Biotec</td>
			<td>130-091-376</td>
			<td></td>
		</tr>
		<tr>
			<td>IGEPAL CA-630</td>
			<td>Sigma Aldrich</td>
			<td>i8896</td>
			<td>Prepare a 10% stock using MilliQ water</td>
		</tr>
		<tr>
			<td>Trizma Hydrochloride Solution, pH 7.5</td>
			<td>Sigma Aldrich</td>
			<td>T2319-1L</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Chloride Solution, 5 M</td>
			<td>Sigma Aldrich</td>
			<td>S6546-1L</td>
			<td></td>
		</tr>
		<tr>
			<td>Magnesium Chloride Solution, 1 M</td>
			<td>Sigma Aldrich</td>
			<td>M1028-100mL</td>
			<td></td>
		</tr>
		<tr>
			<td>Sigma Protector Rnase inhibitor</td>
			<td>Sigma Aldrich</td>
			<td>3335402001</td>
			<td></td>
		</tr>
		<tr>
			<td>DTT</td>
			<td>Research Products International</td>
			<td>D11000-5.0</td>
			<td></td>
		</tr>
		<tr>
			<td>Rnase-Free Disposable Pellet Pestles</td>
			<td>Fisher Scientific</td>
			<td>12-141-368</td>
			<td></td>
		</tr>
		<tr>
			<td>Tween 20</td>
			<td>Fisher Bioreagents</td>
			<td>BP337-500</td>
			<td>Prepare a 20% stock using MilliQ water</td>
		</tr>
		<tr>
			<td>Nuclease-Free Water</td>
			<td>Promega</td>
			<td>PR-P1193</td>
			<td></td>
		</tr>
		<tr>
			<td>DNA LoBind Tubes (5 mL)</td>
			<td>Eppendorf</td>
			<td>30108310</td>
			<td></td>
		</tr>
		<tr>
			<td>Cryovials (1.5 mL)</td>
			<td>VWR</td>
			<td>20170-225</td>
			<td></td>
		</tr>
		<tr>
			<td>Posi-Click Tubes (0.6 mL)</td>
			<td>Denville</td>
			<td>C-2177</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypan Blue (0.4%)</td>
			<td>Thermo Fisher Scientific</td>
			<td>T-10282</td>
			<td></td>
		</tr>
		<tr>
			<td>Dual-Chamber Cell Counting Slides</td>
			<td>Bio-Rad</td>
			<td>1450011</td>
			<td></td>
		</tr>
		<tr>
			<td>MiiliQ Ultrapure Water System</td>
			<td>Millipore/Sigma</td>
			<td>7003/05/10/15</td>
			<td></td>
		</tr>
		<tr>
			<td>5 kDa cut-off filter</td>
			<td>HMT Metabolome Technologies</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Internal Standards</td>
			<td>HMT Metabolome Technologies</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>P10, P20, P200, and P1000 Pipettes</td>
			<td>Eppendorf</td>
			<td>2231000602</td>
			<td></td>
		</tr>
		<tr>
			<td>Pipette Tips, 10 &#181;L</td>
			<td>VWR</td>
			<td>76322-528</td>
			<td></td>
		</tr>
		<tr>
			<td>Pipette Tips, 1000 &#181;L</td>
			<td>Thermo Fisher Scientific</td>
			<td>21-236-2A</td>
			<td></td>
		</tr>
		<tr>
			<td>Pipette Tips, 20 &#181;L</td>
			<td>Genesee Scientific</td>
			<td>23-404</td>
			<td></td>
		</tr>
		<tr>
			<td>Pipette Tips, 200 &#181;L</td>
			<td>USA Scientific</td>
			<td>1120-8810</td>
			<td></td>
		</tr>
		<tr>
			<td>Phase Contrast Microscope</td>
			<td>Olympus</td>
			<td>BX41-PH-B</td>
			<td></td>
		</tr>
		<tr>
			<td>Countess II Automated Cell Counter</td>
			<td>Thermo Fisher Scientific</td>
			<td>AMQAX1000</td>
			<td></td>
		</tr>
		<tr>
			<td>DPBS (1x)&#160;</td>
			<td>Gibco</td>
			<td>14190-144</td>
			<td></td>
		</tr>
		<tr>
			<td>Allegra X-30R Centrifuge</td>
			<td>Beckman-Coulter</td>
			<td>B06315</td>
			<td></td>
		</tr>
		<tr>
			<td>RNase-ZAP</td>
			<td>Sigma Aldrich</td>
			<td>R2020</td>
			<td></td>
		</tr>
	</tbody>
</table>

preparation of frozen non-human primate fetal islets for combined single nuclei rna-sequencing and atac-sequencing, and bulk metabolomics

One challenge in studies using tissue collected from multiple cohorts is avoiding batch effects when preparing for large-scale multi-omic experiments, such as combined single-cell RNA sequencing and metabolomics. The method in the current study utilizes flash-frozen pancreatic islets from fetal non-human primates collected over a span of two years for input into single-nucleus RNA sequencing and ATAC sequencing assays. The cytosolic fraction generated during nuclear extraction was retained for downstream capillary electrophoresis-mass spectrometry and subsequent metabolite quantification. This method allows for bulk analysis of metabolites that contribute to the changing transcriptomic and epigenomic landscapes within experimental conditions. It is applicable to many tissue types and maximizes the amount of information that can be extracted from samples that are not readily available. As the contribution of metabolism to the establishment of cellular identity via epigenetic modifications becomes more appreciated, techniques that allow for identifying the contribution of metabolites in specific cell types are timely and necessary.

The quality of the sequencing outputs is highly dependent on the quality of the nuclear input. Nuclear blebbing and damage to the outer nuclear membrane will result in ambient RNA and DNA contamination in the analysis, which will introduce noise in the data. A pure nuclear extract will have minimal evidence of nuclei encapsulated with cytoplasmic components (Figure 2A) or overdigestion, evidenced by bursting nuclei (Figure 2B). An ideal nuclear input will contai...

Author Spotlight: Multi-Layered Approach to Understand Postnatal Functions of Pancreatic Islets in Non-Human Primates

This protocol describes procedures to isolate high-quality nuclei from frozen non-human primate pancreatic islets for use in single-nucleus simultaneous RNA sequencing and ATAC sequencing while preserving the bulk cytosolic fraction for metabolomic analyses from the same samples.

Preparation of Frozen Non-Human Primate Fetal Islets for Combined Single Nuclei RNA-Sequencing and ATAC-Sequencing, and Bulk Metabolomics

One challenge in studies using tissue collected from multiple cohorts is avoiding batch effects when preparing for large-scale multi-omic experiments, ...

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JoVE Journal

Developmental Biology

417 Views.  Vanderbilt University. This protocol describes procedures to isolate high-quality nuclei from frozen non-human primate pancreatic islets for use in single-nucleus simultaneous RNA sequencing and ATAC sequencing while preserving the bulk cytosolic fraction for metabolomic analyses from the same samples.

Video: Author Spotlight: Multi-Layered Approach to Understand Postnatal Functions of Pancreatic Islets in Non-Human Primates

Preparation of Drosophila Larval Samples for Gas Chromatography-Mass Spectrometry (GC-MS)-based Metabolomics

Recent advances in the field of metabolomics have established the fruit fly Drosophila melanogaster as a powerful genetic model for studying animal metabolism. By combining the vast array of Drosophila genetic tools with the ability to survey large swaths of intermediary metabolism, a metabolomics approach can reveal complex interactions between diet, genotype, life-history events, and environmental cues. In addition, metabolomics studies can discover novel enzymatic mechanisms and uncover previously unknown connections between seemingly disparate metabolic pathways. In order to facilitate more widespread use of this technology among the Drosophila community, here we provide a detailed protocol that describes how to prepare Drosophila larval samples for gas chromatography-mass spectrometry (GC-MS)-based metabolomic analysis. Our protocol includes descriptions of larval sample collection, metabolite extraction, chemical derivatization, and GC-MS analysis. Successful completion of this protocol will allow users to measure the relative abundance of small polar metabolites, including amino acids, sugars, and organic acids involved in glycolysis and the TCA cycles.

Preparation of Drosophila Larval Samples for Gas Chromatography-Mass Spectrometry GC-MS-based Metabolomics

This protocol describes how to prepare Drosophila larvae for GC-MS-based metabolomic analysis.

Recent advances in the field of metabolomics have established the fruit fly Drosophila melanogaster as a powerful genetic model for studying animal ...

Intravenous and Intra-amniotic In Utero Transplantation in the Murine Model

In utero transplantation (IUT) is a unique and versatile mode of therapy that can be used to introduce stem cells, viral vectors, or any other substances early in the gestation. The rationale behind IUT for therapeutic purposes is based on the small size of the fetus, the fetal immunologic immaturity, the accessibility and proliferative nature of the fetal stem or progenitor cells, and the potential to treat a disease or the onset of symptoms prior to birth. Taking advantage of these normal developmental properties of the fetus, the delivery of hematopoietic stem cells (HSC) via an IUT has the potential to treat congenital hematologic disorders such as sickle cell disease, without the required myeloablative or immunosuppressive conditioning required for postnatal HSC transplants. Similarly, the accessibility of progenitor cells in multiple organs during development potentially allows for a more efficient targeting of stem/progenitor cells following an IUT of viral vectors for gene therapy or genome editing. Additionally, IUT can be used to study normal developmental processes including, but not limited to, the development of immunologic tolerance. The murine model provides a valuable and affordable means to understanding the potential and limitations of IUT prior to pre-clinical large animal studies and an eventual clinical application. Here, we describe a protocol for performing an IUT in the murine fetus through intravenous and intra-amniotic routes. This protocol has been used successfully to elucidate the necessary conditions and mechanisms behind in utero hematopoietic stem cell transplantation, tolerance induction, and in utero gene therapy.

Intravenous and Intra-amniotic In Utero Transplantation in the Murine Model

We describe a protocol for performing an in utero transplantation (IUT) through intravenous and intra-amniotic routes of injection in the murine model. This protocol can be used to introduce cells, viral vectors, and other substances into the unique immune-tolerant fetal environment.

In utero transplantation (IUT) is a unique and versatile mode of therapy that can be used to introduce stem cells, viral vectors, or any other substances ...

Culturing and Measuring Fetal and Newborn Murine Long Bones

Long bones are complex and dynamic structures, which arise from endochondral ossification via a cartilage intermediate. The limited access to healthy human bones makes particularly valuable the use of mammalian models, such as mouse and rat, to look into different aspects of bone growth and homeostasis. Additionally, the development of sophisticated genetic tools in mice allows more complex studies of long bone growth and asks for an expansion of techniques used to study bone growth. Here, we present a detailed protocol for ex vivo murine bone culture, which allows the study of bone and cartilage in a tightly controlled manner while recapitulating most of the in vivo process. The method described allows the culture of a range of bones, including tibia, femur, and metatarsal bones, but we have focused mainly on tibial culture here. Moreover, it can be used in combination with other techniques, such as time-lapse live imaging or drug treatment.

Here, we present a method for ex vivo culture of long murine bones at both fetal and newborn stages, suitable for analyzing bone and cartilage development and homeostasis in controlled conditions while recapitulating the in vivo process.

Long bones are complex and dynamic structures, which arise from endochondral ossification via a cartilage intermediate. The limited access to healthy ...

Analysis of Non-Human Primate Pancreatic Islet Oxygen Consumption

The measurement of oxygen consumption in spheroid clusters of cells, such as ex vivo pancreatic islets, has historically been challenging. We demonstrate the measurement of islet oxygen consumption using a 96-well microplate designed for the measurement of oxygen consumption in spheroids. In this assay, spheroid microplates are coated with a cell and tissue adhesive on the day prior to the assay. We utilize a small volume of adhesive solution to encourage islet adherence to only the bottom of the well. On the day of the assay, 15 islets are loaded directly into the base of each well using a technique that ensures optimal positioning of islets and accurate measurement of oxygen consumption. Various aspects of mitochondrial respiration are probed pharmacologically in non-human primate islets, including ATP-dependent respiration, maximal respiration, and proton leak. This method allows for consistent, reproducible results using only a small number of islets per well. It can theoretically be applied to any cultured spheroids of similar size.

This protocol demonstrates the accurate and reproducible measurement of oxygen consumption in non-human primate pancreatic islets. The islet loading techniques and coating of the microplate provide a framework for efficient measurement of respiration in other types of cultured spheroids.

The measurement of oxygen consumption in spheroid clusters of cells, such as ex vivo pancreatic islets, has historically been challenging. We demonstrate ...

Preparation of 3D Decellularized Matrices from Fetal Mouse Skeletal Muscle for Cell Culture

The extracellular matrix (ECM) plays a crucial role in providing structural support for cells and conveying signals that are important for various cellular processes. Two-dimensional (2D) cell culture models oversimplify the complex interactions between cells and the ECM, as the lack of a complete three-dimensional (3D) support can alter cell behavior, making them inadequate for understanding in vivo processes. Deficiencies in ECM composition and cell-ECM interactions are important contributors to a variety of different diseases. 
One example is LAMA2-congenital muscular dystrophy (LAMA2-CMD), where the absence or reduction of functional laminin 211 and 221 can lead to severe hypotony, detectable at or soon after birth. Previous work using a mouse model of the disease suggests that its onset occurs during fetal myogenesis. The present study aimed to develop a 3D in vitro model permitting the study of the interactions between muscle cells and the fetal muscle ECM, mimicking the native microenvironment. This protocol uses deep back muscles dissected from E18.5 mouse fetuses, treated with a hypotonic buffer, an anionic detergent, and DNase. The resultant decellularized matrices (dECMs) retained all ECM proteins tested (laminin &#945;2, total laminins, fibronectin, collagen I, and collagen IV) compared to the native tissue. 
When C2C12 myoblasts were seeded on top of these dECMs, they penetrated and colonized the dECMs, which supported their proliferation and differentiation. Furthermore, the C2C12 cells produced ECM proteins, contributing to the remodeling of their niche within the dECMs. The establishment of this in vitro platform provides a new promising approach to unravel the processes involved in the onset of LAMA2-CMD, and has the potential to be adapted to other skeletal muscle diseases where deficiencies in communication between the ECM and skeletal muscle cells contribute to disease progression.

In this work, a decellularization protocol was optimized to obtain decellularized matrices of fetal mouse skeletal muscle. C2C12 myoblasts can colonize these matrices, proliferate, and differentiate. This in vitro model can be used to study cell behavior in the context of skeletal muscle diseases such as muscular dystrophies.

The extracellular matrix (ECM) plays a crucial role in providing structural support for cells and conveying signals that are important for various ...

Genetic Modification of Primate Cerebral Organoids

Targeted Microinjection and Electroporation of Primate Cerebral Organoids for Genetic Modification

The cerebral cortex is the outermost brain structure and is responsible for the processing of sensory input and motor output; it is seen as the seat of higher-order cognitive abilities in mammals, in particular, primates. Studying gene functions in primate brains is challenging due to technical and ethical reasons, but the establishment of the brain organoid technology has enabled the study of brain development in traditional primate models (e.g., rhesus macaque and common marmoset), as well as in previously experimentally inaccessible primate species (e.g., great apes), in an ethically justifiable and less technically demanding system. Moreover, human brain organoids allow the advanced investigation of neurodevelopmental and neurological disorders.
As brain organoids recapitulate many processes of brain development, they also represent a powerful tool to identify differences in, and to functionally compare, the genetic determinants underlying the brain development of various species in an evolutionary context. A great advantage of using organoids is the possibility to introduce genetic modifications, which permits the testing of gene functions. However, the introduction of such modifications is laborious and expensive. This paper describes a fast and cost-efficient approach to genetically modify cell populations within the ventricle-like structures of primate cerebral organoids, a subtype of brain organoids. This method combines a modified protocol for the reliable generation of cerebral organoids from human-, chimpanzee-, rhesus macaque-, and common marmoset-derived induced pluripotent stem cells (iPSCs) with a microinjection and electroporation approach. This provides an effective tool for the study of neurodevelopmental and evolutionary processes that can also be applied for disease modeling.

Author Spotlight: Targeted Microinjection and Electroporation of Primate Cerebral Organoids for Genetic Modification  

The electroporation of primate cerebral organoids provides a precise and efficient approach to introduce transient genetic modification(s) into different progenitor types and neurons in a model system close to primate (patho)physiological neocortex development. This allows the study of neurodevelopmental and evolutionary processes and can also be applied for disease modeling.

The cerebral cortex is the outermost brain structure and is responsible for the processing of sensory input and motor output; it is seen as the seat of ...

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

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  

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 ...

Processing Gut Cells from Zebrafish Larvae for Single-Cell RNA Sequencing

Gut Isolation from Zebrafish Larvae for Single-cell RNA Sequencing

The gastrointestinal (GI) tract performs a range of functions essential for life. Congenital defects affecting its development can lead to enteric neuromuscular disorders, highlighting the importance to understand the molecular mechanisms underlying GI development and dysfunction. In this study, we present a method for gut isolation from zebrafish larvae at 5 days post fertilization to obtain live,&#160;viable cells which can be used for single-cell RNA sequencing (scRNA-seq) analysis. This protocol is based on the manual dissection of the zebrafish intestine, followed by enzymatic dissociation with papain. Subsequently, cells are submitted to fluorescence-activated cell sorting, and viable cells are collected for scRNA-seq. With this method, we were able to successfully identify different intestinal cell types, including epithelial, stromal, blood, muscle, and immune cells, as well as enteric neurons and glia. Therefore, we consider it to be a valuable resource for studying the composition of the GI tract in health and disease, using the zebrafish.

Author Spotlight: Isolating and Analyzing Intestinal Cells of Zebrafish Larvae for Investigating Transcriptomic Aspects of Gastrointestinal Development 

Here, we describe a method for gut isolation from zebrafish larvae at 5 days post fertilization, for single-cell RNA sequencing analysis.

The gastrointestinal (GI) tract performs a range of functions essential for life. Congenital defects affecting its development can lead to enteric ...

High-Quality Nuclei from iPSC-Derived Hematopoietic Cells for Multiomics Studies

Nuclear Isolation from Cryopreserved In Vitro Derived Blood Cells

Induced pluripotent stem cell (iPSC)-based models are excellent platforms to understand blood development, and iPSC-derived blood cells have translational utility as clinical testing reagents and transfusable cell therapeutics. The advent and expansion of multiomics analysis, including but not limited to single nucleus RNA sequencing (snRNAseq) and Assay for Transposase-Accessible Chromatin sequencing (snATACseq), offers the potential to revolutionize our understanding of cell development. This includes developmental biology using in vitro hematopoietic models. However, it can be technically challenging to isolate intact nuclei from cultured or primary cells. Different cell types often require tailored nuclear preparations depending on cellular rigidity and content. These technical difficulties can limit data quality and act as a barrier to investigators interested in pursuing multiomics studies. Specimen cryopreservation is often necessary due to limitations with cell collection and/or processing, and frozen samples can present additional technical challenges for intact nuclear isolation. In this manuscript, we provide a detailed method to isolate high-quality nuclei from iPSC-derived cells at different stages of in vitro hematopoietic development for use in single-nucleus multiomics workflows. We have focused the method development on the isolation of nuclei from iPSC-derived adherent stromal/endothelial cells and non-adherent hematopoietic progenitor cells, as these represent very different cell types with regard to structural and cellular identity. The described troubleshooting steps limited nuclear clumping and debris, allowing the recovery of nuclei in sufficient quantity and quality for downstream analyses. Similar methods may be adapted to isolate nuclei from other cryopreserved cell types.

Author Spotlight: Advancing In Vitro Blood Cell Production with Single-Cell Multiomics and Functional Genomics

We describe a protocol for extracting high-quality nuclei from cryopreserved induced pluripotent stem cell-derived stromal/endothelial and blood cell types to support single-nucleus next-generation sequencing analyses. Producing high-quality, intact nuclei is imperative for multiomics experiments but can be a barrier to entry in the field for some laboratories.

Induced pluripotent stem cell (iPSC)-based models are excellent platforms to understand blood development, and iPSC-derived blood cells have translational ...

Single Cell and Nuclei Extraction from Human Brain Organoids

Generation and Downstream Analysis of Single-Cell and Single-Nuclei Transcriptomes in Brain Organoids

Over the past decade, single-cell transcriptomics has significantly evolved and become a standard laboratory method for simultaneous analysis of gene expression profiles of individual cells, allowing the capture of cellular diversity. In order to overcome limitations posed by difficult-to-isolate cell types, an alternative approach aiming at recovering single nuclei instead of intact cells can be utilized for sequencing, making transcriptome profiling of individual cells universally applicable. These techniques have become a cornerstone in the study of brain organoids, establishing them as models of the developing human brain. Leveraging the potential of single-cell and single-nucleus transcriptomics in brain organoid research, this protocol presents a step-by-step guide encompassing key procedures such as organoid dissociation, single-cell or nuclei isolation, library preparation&#160;and sequencing. By implementing these alternative approaches, researchers can obtain high-quality datasets, enabling the identification of neuronal and non-neuronal cell types, gene expression profiles, and cell lineage trajectories. This facilitates comprehensive investigations into cellular processes and molecular mechanisms shaping brain development.

Author Spotlight: Integrating Organoid Models with Single-Cell and Spatial Transcriptomics Technologies

Here, we introduce a comprehensive protocol for the generation and downstream analysis of human brain organoids using single-cell and single-nucleus RNA sequencing.

Over the past decade, single-cell transcriptomics has significantly evolved and become a standard laboratory method for simultaneous analysis of gene ...