The authors thank Adi Sasson for the technical assistance and Helen Guez for the critical reading of the manuscript. This work was supported by European Research Council starting grant no. 336204.

Experiments were conducted according to protocols approved by the Committee on Animal Research at Tel Aviv University.
1. Isolation of Pancreatic Tissue from Mice
<ol>
	<li>For adult mice:
	<ol>
		<li>Prepare the digestion buffer: 0.4 mg/mL collagenase P and 0.1 ng/mL DNase I dissolved in Hanks&#39; Balanced Salt Solution (HBSS). Freshly prepare 5 mL of buffer per mouse in 15-mL conical tubes and keep them on ice until use.</li>
		<li>Euthanize the mice according to institutional guideline.</li>
		<li>Dissect each mouse to remove the pancreas (for instruction, please see Reference 18); place it in a culture dish containing HBSS. It is possible to perform this stage under a stereomicroscope, and to increase digestion efficiency, cut the tissue into 2 - 4 pieces.</li>
		<li>Place the pancreatic tissue into a tube containing digestive buffer (prepared in step 1.1.1). Keep the tubes on ice until all mice are dissected and pancreatic tissues collected.</li>
		<li>Repeat steps 1.1.2 - 1.1.4 with the remaining mice.</li>
	</ol>
	</li>
	<li>For embryos and neonatal mice:
	<ol>
		<li>Prepare the digestion buffer: 0.4 mg/mL collagenase P and 0.1 ng/mL DNase I dissolved in HBSS. For embryos and pups at postnatal day 7 (p7) or younger, freshly prepare 1.5 - 2 mL of buffer per mouse in a 15-mL conical tube. For p7 or older pups, prepare 3 - 4 mL of buffer per mouse in a 15-mL conical tube. Keep on ice until use.</li>
		<li>Euthanize the mice according to institutional guideline. For embryos, remove all embryos from their mother&#39;s uterus and place them in a 10-mm culture dish containing PBS. Dissect one embryo at a time.</li>
		<li>Lay the mouse on its back, with its head pointing away from the investigator. Using fine forceps, pull up the abdominal skin and open at the midline to expose the abdominal cavity up to the mouse diaphragm18.</li>
		<li>Using fine forceps, detach the liver from the back abdominal wall. With a continuous motion toward the mouse tail, scoop out the internal organs (including the liver, stomach, spleen, intestines, kidney, and pancreas) and place them in a culture dish containing HBSS.</li>
		<li>Under a stereomicroscope, remove the liver and kidneys to expose the pancreas (Figure 1). Using fine forceps, detach the pancreas from the stomach, duodenum, and finally, from the spleen.</li>
		<li>Place the pancreatic tissue into a tube containing digestive buffer (prepared in step 1.2.1). For p14 or older pups, cut the tissue into 2 pieces to increase the digestion efficiency. Keep the tubes on ice until all mice are dissected and pancreatic tissues collected.</li>
		<li>Repeat steps 1.2.2 - 1.2.6 with the remaining mice.</li>
	</ol>
	</li>
</ol>
2. Pancreas Digestion
<ol>
	<li>Incubate the tubes containing the pancreatic tissue (in digestion buffer) in a heating block at 37 &#176;C for 30 min with agitation at 700 rpm. After 15 min, manually shake the tubes by inverting them 3 - 4 times and place them back in the heating block. 
	NOTE: If using a heating block without agitation capabilities, invert the tubes every 5 - 10 min. Make sure that the tissue is properly digested. If not, cut the tissue into smaller pieces before incubation or increase the agitation.</li>
	<li>To stop the tissue digestion, place the tubes on ice and add 10 mL of cold HBSS to each tube. Centrifuge the tubes at 4 &#176;C and 300 x g for 5 min and aspirate the supernatant.</li>
	<li>Re-suspension:
	<ol>
		<li>For adult mice and p14 or older pups, re-suspend the pellet with 6 mL of PBS and strain it through a 70-&#181;m cell strainer placed on top of a new 15-mL conical collection polypropylene tube. To ensure maximal cell recovery, wash the original tube with an additional 6 mL of PBS and strain it through the cell strainer onto the collection tube.</li>
		<li>For embryos and pups younger than p14, re-suspend the pellet with 2 mL of PBS and strain it through a 35-&#181;m cell strainer placed on top of a 5-mL round-bottom polystyrene collection tube (FACS tube). To ensure maximal cell recovery, wash the original tube with an additional 2 mL of PBS and strain it through the cell strainer onto the collection tube.</li>
	</ol>
	</li>
	<li>Centrifuge the tubes at 4 &#176;C and 300 x g for 5 min and aspirate the supernatant. Remove the liquid carefully, as cells are loosely attached to the polystyrene tube.</li>
</ol>
3. Preparing Labeled Single Cells
<ol>
	<li>Buffer preparations: For cell isolation by FACS, prepare sorting buffer by mixing PBS (without calcium chloride and magnesium chloride), 5% fetal bovine serum (FBS), and 5 mM EDTA. For flow cytometry analysis, prepare analysis buffer by supplementing sorting buffer with 0.05% sodium azide. Both buffers may be stored at 4-8 &#176;C for up to 2 months.</li>
	<li>Re-suspend cells in sorting or analysis buffer. Re-suspend each pancreas isolated from embryos and pups younger than p7 in 1 mL, from pups between p8 and one month old in 1.5 mL, and from mice older than one month in 3 mL. Strain the cells through a 35-&#181;m cell strainer placed on top of a round-bottom polystyrene tube (FACS tube).</li>
	<li>For staining controls, take out 50- to 100-&#181;L aliquots from the samples made in the previous step (not more than 5% of the total sample volume) and place them into new FACS tubes; include a tube for each fluorophore used, including DAPI and fluorescent proteins, as well as for an unstained control. 
	NOTE: When using transgenic mice with cells expressing a fluorescent protein, or when cell number is limited, include a non-transgenic tissue as a staining control. If cells expressing a fluorescent protein are used without further staining, proceed to step 3.8.</li>
	<li>Spin-down the cells at 300 x g for 5 min at 4 &#176;C and aspirate the supernatant.</li>
	<li>For blocking, re-suspend the cells with blocking solution (100 &#181;L sorting or analysis buffer supplemented with 1 &#181;L of goat IgG) and incubate for 30 min on ice.</li>
	<li>To stain cell surface markers, prepare a mixture that includes all desired fluorophore-conjugated antibodies in a volume of 100 &#181;L per sample . Prepare 2x antibody dilutions in sorting or analysis buffer (i.e., dilute the antibody to obtain double the required concentration; if a final dilution of 1:200 is desired, dilute the antibody 1:100). Without washing the blocking solution, add 100 &#181;L of the mixture to the sample cells to achieve a final staining volume of 200 &#181;L. Incubate for 30-60 min on ice and in the dark.</li>
	<li>To set the analysis or sorting parameters (see steps 4.3 and 5.2), prepare additional tubes that contain only one of the antibodies used (staining control). Prepare 2x antibody dilutions in sorting or analysis buffer (as described in step 3.6). Make sure to include a single staining control dilution for each fluorophore used, as well as an unstained control. Without washing the blocking solution, add 100 &#181;L of antibody mixes to the cells (prepared in step 3.3) to achieve a final staining volume of 200 &#181;L. Incubate for 30 - 60 min on ice and in the dark.</li>
	<li>Wash by filling each tube with analysis or sorting buffer to a maximal volume of 4 mL. Optionally, re-strain the cells through a 35-&#181;m cell strainer (as described in step 3.2).</li>
	<li>Centrifuge at 300 x g for 5 min at 4 &#176;C and remove the supernatant carefully.</li>
	<li>Re-suspend the samples in analysis or sorting buffer. Re-suspend the cells isolated from embryos in 500 &#181;L, from pups younger than one month in 1 mL, from 1 - 3 months old in 2 mL, and from mice older than 3 months in 3 mL. Staining controls may be re-suspended in 300 &#181;L of buffer.</li>
	<li>Add 200 ng/mL of DAPI to re-suspended cells to identify the dead cells. Make sure to include a tube containing unstained cells without DAPI for cytometer settings. Proceed to cell sorting (step 4) or analysis (step 5).</li>
</ol>
4. Cell Sorting
<ol>
	<li>Preparations:
	<ol>
		<li>For cell sorting prior to RNA extraction, coat a 1.5-mL collecting tube with RNase inhibitor immediately before sorting. To this end, add 1 mL of sorting buffer, containing 0.01 U/mL RNase inhibitor, to a sterile 1.5-mL collection tube. After 5 min, vortex the tube and remove the liquid.</li>
		<li>For cell sorting prior to cell culture, add 3 mL of sterile culturing media (Dulbecco&#39;s Modified Eagle Medium (DMEM) supplemented with 20% FBS, 1% L-glutamine, and 1% penicillin-streptomycin) into a sterile 15-mL collection tube.</li>
	</ol>
	</li>
	<li>Before loading a tube into a FACS sorter, vortex it briefly to re-suspend the cells. Keep the remaining tubes on ice.</li>
	<li>Start by analyzing the staining controls to determine the sorting parameters (e.g., voltage and compensation) and sorting gates (e.g., total cell population, live DAPI-negative cells, and cell populations to be sorted).</li>
	<li>Once the sorting parameters and gates are set up, load the samples and initiate cell sorting into the collection tubes. 
	NOTE: Sorting conditions are highly dependent on the instrument. We use a nozzle width of 100 &#181;m, a pressure of 23.1 psi, and a maximal sorting speed of 5.</li>
	<li>Proceed to RNA extraction or the culturing of sorted cells. 
	NOTE: For RNA extraction, centrifuge the cells at 2,000 x g for 5 min and remove the excess liquid before continuing with a standard extraction protocol. For culturing cells, if the cells were sorted under non-sterile conditions, wash them twice by filling the tube with culturing medium and centrifuging it at 300 x g for 7 min before culturing in order to minimize their contamination.</li>
</ol>
5. Cell Analysis by Flow Cytometry
<ol>
	<li>Before loading each tube into the cytometer, vortex it briefly to re-suspend the cells. Keep the remaining tubes on ice.</li>
	<li>Start by analyzing the unstained and single-stained samples in order to determine the analysis parameters (e.g., voltage and compensation).</li>
	<li>Once the analysis parameters are set up, load each sample, including the staining control, and record the results. Analyze the obtained results using flow cytometry analysis software.</li>
</ol>

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The authors have nothing to disclose.

Here, we describe a method to isolate and analyze cells of the pancreatic microenvironment. This method can be used to isolate mesenchymal cells from embryonic and adult pancreatic tissue. In addition, we successfully used this protocol to isolate endothelial cells from the adult and neonatal pancreas5,17. However, it may not be suitable for obtaining a reproducible single-cell suspension of pancreatic epithelial cells (alternative protocols are described in References 18, 23, and 24). Using this method, fluorescently-labeled cells, either expressing fluorescent proteins or immunostained for surface markers, can be purified by FACS or analyzed by flow cytometry. RNA can be extracted from purified cells to profile their gene expression pattern. Alternatively, purified cells can be cultured to establish a cell line for subsequent proteomic analysis. This method will enable the characterization of factors expressed by the pancreas microenvironment, which govern its organogenesis, physiology, and pathophysiology.
The pancreatic mesenchyme supports tissue organogenesis by promoting the proliferation of precursors and differentiated cells5,9. These cells were shown to support the expansion of human embryonic stem cell (hESC)-derived pancreatic progenitors17,25,26. Therefore, delineating the identity of embryonic mesenchymal factors would facilitate current efforts to generate insulin-producing beta cells from hESCs and induced pluripotent stem cells (iPSCs) as a potential cure to diabetes. Mouse genetic studies allowed the identification of growth factors, such as Fgf10, that are produced by the mesenchyme to promote pancreatic epithelium expansion during the early stages of pancreas development3,9. With the aim of identifying additional factors expressed in the embryonic mesenchyme, we isolated these cells using laser-captured microdissection, extracted their RNA, and performed gene expression analysis26. However, in addition to being labor-intense, this method relies on identifying cells based on their morphological features, which restricts its use to developmental stages prior to the branching of the epithelium into the surrounding mesenchyme (i.e., e12.5). To characterize mesenchymal cells at later developmental stages, we employed the method described here5,17.
We used this method to analyze surface marker expression by neonatal pancreatic mesenchyme5. In addition, mesenchymal cells were isolated from embryonic and neonatal pancreatic tissue of Nkx3.2-Cre;R26-EYFP mice, based on their fluorescent labeling in this mouse line, and were cultured to establish cell lines17. The proteomic analysis of these cells allowed for the identification of factors secreted by the pancreatic mesenchyme with the ability to promote hESC-derived pancreatic progenitors17. We further used this cell isolation method to purify mesenchymal cells from adult pancreatic tissues for RNA extraction and gene expression analysis17. Therefore, this method can be used to identify genes and proteins expressed by the pancreatic mesenchyme, with the ability to support pancreatic cell development.
Pancreatic mesenchymal cells were further shown to play a role in pancreas tumorigenesis. PDAC is characterized by the formation of a fibroblast-rich desmoplastic stroma comprised of fibroblasts, immune cells, and ECM27. While the stroma was thought to promote the development of many types of cancer, it was shown to restrain PDAC progression15,16,28. This suggests that components of the pancreatic stroma secrete factors that inhibit tumorigenesis. Furthermore, changes in stroma cellular composition as well as in cell phenotype can underlie their effect on epithelial cells15,16,28. The method described here can therefore assist in characterizing the different cell types that make up a PDAC stroma as compared to healthy pancreatic tissue. It would further allow the purification of the different stromal cell types to characterize potential changes in their gene expression profiles during PDAC progression. However, due to changes in pancreatic ECM composition during tumorigenesis27, adjustments of the tissue digestion parameters, such as the inclusion of additional collagenase types or increasing the incubation time, may be required.

Energy homeostasis and food digestion in mammals depend on proper pancreatic function. The adult pancreas is comprised of two main cellular compartments: the exocrine and the endocrine. Exocrine cells, including the acinar cells that produce and secrete digestive enzymes and the duct cells that transport these enzymes to the gut, encompass more than 80% of the total pancreatic mass1. Endocrine cells, which include insulin-producing beta cells and glucagon-producing alpha cells, are organized in the islets of Langerhans that are embedded in the exocrine tissue and secrete hormones to regulate blood glucose levels2.
Pancreatic cells acquire their differentiated fate through a highly-regulated, multistep process3. Evidence suggests that extrinsic cues provided by neuronal, endothelial, and mesenchymal cells guide pancreatic cell differentiation and proliferation in the embryo3,4,5. One example is the requirement of the aorta for the specification of early pancreatic precursors6. Later in development, endothelial cells were shown to play a central role in the development of both pancreatic endocrine and exocrine cells and to promote beta-cell differentiation4,6,7. Mesenchymal cells were shown to support the survival and expansion of common pancreatic progenitors, mainly through the secretion of the growth factor Fgf108,9. We have further shown that these cells support the proliferation of endocrine and exocrine precursors, as well as of differentiated cells (including acinar and beta cells) in the embryonic pancreas5. Recently, mesenchymal cells were further shown to regulate endocrine cells differentiation10.
In the adult, beta-cell function and mass were shown to depend on cells in their microenvironment, including neuronal, immune, and endothelial cells, as well as pericytes11,12,13. During injury, endothelial cells were shown to recruit immune cells to the pancreas to promote beta-cell replication13. Endothelial cells were further shown to produce extracellular matrix (ECM) components to support insulin expression and beta-cell function14. We recently demonstrated the requirement of islet pericytes for beta-cell function11. Lastly, cells of the pancreatic stroma were shown to regulate the progression of pancreatic ductal adenocarcinoma (PDAC)15,16. However, the identity of extrinsic cues that guide pancreas development, function, and tumorigenesis are largely unknown.
Identifying cues provided by cells of the pancreas microenvironment requires characterizing the genes and proteins expressed by these cells. This depends on isolating these cells from the pancreas in order to perform gene expression and proteomic analyses and/or on establishing cell lines. Here, we propose a method to isolate mesenchymal cells of the pancreas microenvironment by utilizing tissue enzymatic digestion and fluorescence-activated cell sorting (FACS) of either immunofluorescently-labeled cells or cells expressing fluorescent proteins. This protocol was successfully performed to isolate and analyze yellow fluorescent protein (YFP)-expressing mesenchymal cells of the embryonic, neonatal, and adult pancreas5,17.

<table border="0" cellpadding="0" cellspacing="0" width="766">
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	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:243px;">Collagenase P</td>
			<td style="width:167px;">Roche</td>
			<td style="width:191px;">11213865001</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">DNase</td>
			<td style="width:167px;">Sigma-Aldrich</td>
			<td style="width:191px;">D5025-15KU</td>
			<td>The effective units should be at least 2000 unitz/ml protein</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Hanks&#8217; Balanced Salt solution (HBSS)</td>
			<td style="width:167px;">Sigma-Aldrich</td>
			<td style="width:191px;">H6648</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Fetal Bovine Serum (FBS)</td>
			<td style="width:167px;">Biological Industries</td>
			<td style="width:191px;">04-127-1A</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:243px;">EDTA</td>
			<td style="width:167px;">Biological Industries</td>
			<td style="width:191px;">01-862-1A</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Sodium Azide</td>
			<td style="width:167px;">Sigma-Aldrich</td>
			<td style="width:191px;">S2002</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:243px;">Goat IgG serum</td>
			<td style="width:167px;">Sigma-Aldrich</td>
			<td style="width:191px;">G9023</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">DAPI</td>
			<td style="width:167px;">Sigma-Aldrich</td>
			<td style="width:191px;">D9542</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">RNAse inhibitor</td>
			<td style="width:167px;">Invitrogen</td>
			<td style="width:191px;">N8080119</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Dulbecco&#39;s Modified Eagle Medium (DMEM)</td>
			<td style="width:167px;">Invitrogen</td>
			<td style="width:191px;">11965092</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">L-Glutamine</td>
			<td style="width:167px;">Biological Industries</td>
			<td style="width:191px;">03-020-1B</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Penicillin-streptomycin</td>
			<td style="width:167px;">Biological Industries</td>
			<td style="width:191px;">03-031-1B</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:243px;">Dulbecco&#8217;s Phosphate Buffered Saline (PBS)</td>
			<td style="width:167px;">Sigma-Aldrich</td>
			<td style="width:191px;">D8537</td>
			<td>Without Calcium Chloride and Magnesium Chloride</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:243px;"></td>
			<td style="width:167px;"></td>
			<td style="width:191px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:243px;"></td>
			<td style="width:167px;"></td>
			<td style="width:191px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:243px;">1.5 ml tubes</td>
			<td style="width:167px;">Sarstedt</td>
			<td style="width:191px;">72 690</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:243px;">15 ml conical tube</td>
			<td style="width:167px;">Corning</td>
			<td style="width:191px;">430052</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:243px;">Round Bottom Polystyrene 5 ml tube&#160;</td>
			<td style="width:167px;">Corning</td>
			<td style="width:191px;">352008</td>
			<td>FACS tube&#39;. Make sure tube is compatible with the flow cytomter to be used, as there are slight differences in required tubes between brands</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">5ml tube with 35 &#956;m cell strainer Snap Cap</td>
			<td style="width:167px;">Corning</td>
			<td style="width:191px;">352235</td>
			<td>FACS tube&#39;&#160;&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">70 &#956;m cell strainer&#160;</td>
			<td style="width:167px;">Miltenyi Biotec</td>
			<td style="width:191px;">130-098-462</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:243px;"></td>
			<td style="width:167px;"></td>
			<td style="width:191px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:243px;">Heating block with agitation&#160;</td>
			<td style="width:167px;">Eppendorf</td>
			<td style="width:191px;">ThermoMixer C</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:243px;">Centrifuge</td>
			<td style="width:167px;">ThermoFisher</td>
			<td style="width:191px;">Heraeus Megafuge 40R</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:243px;">Steromicroscope</td>
			<td style="width:167px;">Nikon</td>
			<td style="width:191px;">SMZ 745</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:243px;">Cell sorter</td>
			<td style="width:167px;">BD Biosciences</td>
			<td style="width:191px;">FACSAria IIu</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:243px;">flow cytometer</td>
			<td style="width:167px;">Beckman Coulter</td>
			<td style="width:191px;">Gallios&#160;</td>
			<td></td>
		</tr>
	</tbody>
</table>

isolating and analyzing cells of the pancreas mesenchyme by flow cytometry

The pancreas is comprised of epithelial cells that are required for food digestion and blood glucose regulation. Cells of the pancreas microenvironment, including endothelial, neuronal, and mesenchymal cells were shown to regulate cell differentiation and proliferation in the embryonic pancreas. In the adult, the function and mass of insulin-producing cells were shown to depend on cells in their microenvironment, including pericyte, immune, endothelial, and neuronal cells. Lastly, changes in the pancreas microenvironment were shown to regulate pancreas tumorigenesis. However, the cues underlying these processes are not fully defined. Therefore, characterizing the different cell types that comprise the pancreas microenvironment and profiling their gene expression are crucial to delineate the tissue development and function under normal and diseased states. Here, we describe a method that allows for the isolation of mesenchymal cells from the pancreas of embryonic, neonatal, and adult mice. This method utilizes the enzymatic digestion of mouse pancreatic tissue and the subsequent fluorescence-activated cell sorting (FACS) or flow-cytometric analysis of labeled cells. Cells can be labeled by either immunostaining for surface markers or by the expression of fluorescent proteins. Cell isolation can facilitate the characterization of genes and proteins expressed in cells of the pancreas mesenchyme. This protocol was successful in isolating and culturing highly enriched mesenchymal cell populations from the embryonic, neonatal, and adult mouse pancreas.

The pancreatic mesenchyme is required during development and adulthood. The method described here allows the isolation of mesenchymal cells from the embryonic, neonatal, and adult pancreas. Mesenchymal cells, but no other cell types, express yellow fluorescent protein (YFP) in the pancreas of Nkx3.2-Cre;R26R-YFP mice5,11,17,19. During development, Nkx3.2 (also known as BapX1) is expressed by embryonic pancreatic, stomach, and gut mesenchyme, as well as in a subset of skeletal somites19,20,21. This gene was expressed in the pancreatic mesenchyme from e9.5 until e11.5, allowing gene expression under the control of Nkx3.2-Cre from e9.55,19,20. Based on this labeling, cells can be purified from bulk pancreatic tissue using flow cytometry. Figure 2 shows a flow-cytometry analysis of single cells from embryonic, neonatal, and adult pancreatic tissues, isolated as described here. Whereas non-transgenic pancreatic tissues did not contain fluorescent cells, Nkx3.2-Cre;R26R-YFP pancreatic tissue from all analyzed ages contains a distinct YFP-labeled cell population (Figure 2; marked with gates).
Following the method described here, cells expressing fluorescent proteins can be either purified or analyzed by flow cytometry, with or without additional immunostaining. For example, after sorting based on fluorescent labeling, mesenchymal cells can be cultured to establish a cell line (for at least five passages), as shown in Figure 3A. Note the fibrocytic morphology of the cultured cells, typical to mesenchymal cells. In addition, this system was used to analyze gene expression by sorted cells. To this end, RNA was extracted from sorted mesenchymal cells to synthesize cDNA, and gene expression levels were analyzed by qPCR. Such analysis revealed that sorted cells express the pan-mesenchymal marker vimentin (Figure 3B). Lastly, surface marker expression by pancreatic cells can be analyzed by flow-cytometry. For example, we isolated cells from the pancreatic tissue of Nkx3.2-Cre;R26R-YFP adult mice using the method described here and stained them with the cell surface glycoprotein CD9, which was reported to be expressed by fibroblasts22. As shown in Figure 3C, all fluorescently-labeled cells in the Nkx3.2-Cre;R26R-YFP pancreas express CD9.
<img alt="Figure 1" src="/files/ftp_upload/55344/55344fig1.jpg" /> 
Figure 1: Embryonic and neonatal pancreatic tissue. Isolated whole gastrointestinal tract, including the stomach, spleen, intestine, and pancreas, of an e15.5 embryo (A) and a p4 pup (B). The pancreatic tissue is demarcated with a blue line. <a href="http://cloudflare.jove.com/files/ftp_upload/55344/55344fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" src="/files/ftp_upload/55344/55344fig2.jpg" /> 
Figure 2: Mesenchymal cells are fluorescently labeled in Nkx3.2-Cre;R26R-YFP pancreatic tissue. Flow-cytometry analysis of pancreatic cells isolated from non-transgenic (left panels) and Nkx3.2-Cre;R26R-YFP transgenic (right panels) mice at various ages: embryonic (A), neonatal (B), and adult (C). Cells were analyzed for side scatter (y-axis) and yellow fluorescence (x-axis). Gates (marked with &#34;D&#34;) indicated the presence of a YFP+ cell population in transgenic mice but not in non-transgenic controls. <a href="http://cloudflare.jove.com/files/ftp_upload/55344/55344fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" src="/files/ftp_upload/55344/55344fig3.jpg" /> 
Figure 3: Analyses of isolated pancreatic cells. (A) Cells sorted from the pancreatic tissue of Nkx3.2-Cre;R26R-YFP neonatal mice (as described in Figure 2B) were cultured to establish a cell line. Cultured cells were imaged for fluorescence (green; right and left panels) and phase contrast (gray; right panel). (B) Bar diagram showing Vimentin1 (Vim1) expression levels by YFP+-sorted cells from the pancreatic tissue of Nkx3.2-Cre;R26R-YFP adult mice (as described in Figure 1C; green) as compared to unsorted pancreatic tissue (black). RNA was extracted and gene expression was analyzed by qPCR; expression was normalized to Cyclophilin. N = 4. ***P &#60; 0.001. Data represent the mean &#177; SD. (C) Flow-cytometry analysis of dispersed pancreatic cells from Nkx3.2-Cre;R26R-YFP adult mice immuno-stained with allophycocyanin (APC)-conjugated anti-CD9 antibody and analyzed for APC (y-axis) and yellow fluorescence (x-axis). <a href="http://cloudflare.jove.com/files/ftp_upload/55344/55344fig3large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about Isolating and Analyzing Cells of the Pancreas Mesenchyme by Flow Cytometry at JoVE.com

Isolating and Analyzing Cells of the Pancreas Mesenchyme by Flow Cytometry

Here, we describe a method for the isolation of cells in the pancreas microenvironment from embryonic, neonatal and adult mouse tissue, focusing on the isolation of mesenchymal cells. This method allows profiling of cell gene expression and protein secretion in order to elucidate the extrinsic signals that regulate pancreas development, function, and tumorigenesis.

The pancreas is comprised of epithelial cells that are required for food digestion and blood glucose regulation. Cells of the pancreas microenvironment, ...

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Developmental Biology

12.1K Views.  Sackler Faculty of Medicine, Tel Aviv University. Here, we describe a method for the isolation of cells in the pancreas microenvironment from embryonic, neonatal and adult mouse tissue, focusing on the isolation of mesenchymal cells. This method allows profiling of cell gene expression and protein secretion in order to elucidate the extrinsic signals that regulate pancreas development, function, and tumorigenesis.

Video: Isolating and Analyzing Cells of the Pancreas Mesenchyme by Flow Cytometry

Step-specific Sorting of Mouse Spermatids by Flow Cytometry

The differentiation of mouse spermatids is one critical process for the production of a functional male gamete with an intact genome to be transmitted to the next generation. So far, molecular studies of this morphological transition have been hampered by the lack of a method allowing adequate separation of these important steps of spermatid differentiation for subsequent analyses. Earlier attempts at proper gating of these cells using flow cytometry may have been difficult because of a peculiar increase in DNA fluorescence in spermatids undergoing chromatin remodeling. Based on this observation, we provide details of a simple flow cytometry scheme, allowing reproducible purification of four populations of mouse spermatids fixed with ethanol, each representing a different state in the nuclear remodeling process. Population enrichment is confirmed using step-specific markers and morphological criterions. The purified spermatids can be used for genomic and proteomic analyses.

We describe a sorting strategy for mouse spermatids using flow cytometry. Spermatids are sorted into four highly pure populations, including round (spermiogenesis steps 1-9), early elongating (spermiogenesis steps 10-12), late elongating (spermiogenesis steps 13-14) and elongated spermatids (spermiogenesis steps 15-16). DNA staining, size and granulosity are used as selection parameters.

The differentiation of mouse spermatids is one critical process for the production of a functional male gamete with an intact genome to be transmitted to ...

Isolating Hair Follicle Stem Cells and Epidermal Keratinocytes from Dorsal Mouse Skin

The hair follicle (HF) is an ideal system for studying the biology and regulation of adult stem cells (SCs). This dynamic mini organ is replenished by distinct pools of SCs, which are located in the permanent portion of the HF, a region known as the bulge. These multipotent bulge SCs were initially identified as slow cycling label retaining cells; however, their isolation has been made feasible after identification of specific cell markers, such as CD34 and keratin 15 (K15). Here, we describe a robust method for isolating bulge SCs and epidermal keratinocytes from mouse HFs utilizing fluorescence activated cell-sorting (FACS) technology. Isolated hair follicle SCs (HFSCs) can be utilized in various in vivo grafting models and are a valuable in vitro model for studying the mechanisms that govern multipotency, quiescence and activation.

An ideal model for studying adult stem cell biology is the mouse hair follicle. Here we present a protocol for isolating different populations of hair follicles stem cells and epidermal keratinocytes, employing enzymatic digestion of mouse dorsal skin followed by FACS analysis.

The hair follicle (HF) is an ideal system for studying the biology and regulation of adult stem cells (SCs). This dynamic mini organ is replenished by ...

In Vitro Colony Assays for Characterizing Tri-potent Progenitor Cells Isolated from the Adult Murine Pancreas

Stem and progenitor cells from the adult pancreas could be a potential source of therapeutic beta-like cells for treating patients with type 1 diabetes. However, it is still unknown whether stem and progenitor cells exist in the adult pancreas. Research strategies using cre-lox lineage-tracing in adult mice have yielded results that either support or refute the idea that beta cells can be generated from the ducts, the presumed location where adult pancreatic progenitors may reside. These in vivo cre-lox lineage-tracing methods, however, cannot answer the questions of self-renewal and multi-lineage differentiation-two criteria necessary to define a stem cell. To begin addressing this technical gap, we devised 3-dimensional colony assays for pancreatic progenitors. Soon after our initial publication, other laboratories independently developed a similar, but not identical, method called the organoid assay. Compared to the organoid assay, our method employs methylcellulose, which forms viscous solutions that allow the inclusion of extracellular matrix proteins at low concentrations. The methylcellulose-containing assays permit easier detection and analyses of progenitor cells at the single-cell level, which are critical when progenitors constitute a small sub-population, as is the case for many adult organ stem cells. Together, results from several laboratories demonstrate in vitro self-renewal and multi-lineage differentiation of pancreatic progenitor-like cells from mice. The current protocols describe two methylcellulose-based colony assays to characterize mouse pancreatic progenitors; one contains a commercial preparation of murine extracellular matrix proteins and the other an artificial extracellular matrix protein known as a laminin hydrogel. The techniques shown here are 1) dissociation of the pancreas and sorting of CD133+Sox9/EGFP+ ductal cells from adult mice, 2) single cell manipulation of the sorted cells, 3) single colony analyses using microfluidic qRT-PCR and whole-mount immunostaining, and 4) dissociation of primary colonies into single-cell suspensions and re-plating into secondary colony assays to assess self-renewal or differentiation.

In Vitro Colony Assays for Characterizing Tri-potent Progenitor Cells Isolated from the Adult Murine Pancreas

In vitro colony assays to detect self-renewal and differentiation of progenitor cells isolated from adult murine pancreas are devised. In these assays, pancreatic progenitors give rise to cell colonies in 3-dimensional space in methylcellulose-containing semi-solid medium. Protocols for handling single cells and characterization of individual colonies are described.

Stem and progenitor cells from the adult pancreas could be a potential source of therapeutic beta-like cells for treating patients with type 1 diabetes. ...

Identification Of Erythromyeloid Progenitors And Their Progeny In The Mouse Embryo By Flow Cytometry

Macrophages are professional phagocytes from the innate arm of the immune system. In steady-state, sessile macrophages are found in adult tissues where they act as front line sentinels of infection and tissue damage. While other immune cells are continuously renewed from hematopoietic stem and progenitor cells (HSPC) located in the bone marrow, a lineage of macrophages, known as resident macrophages, have been shown to be self-maintained in tissues without input from bone marrow HSPCs. This lineage is exemplified by microglia in the brain, Kupffer cells in the liver and Langerhans cells in the epidermis among others. The intestinal and colon lamina propria are the only adult tissues devoid of HSPC-independent resident macrophages. Recent investigations have identified that resident macrophages originate from the extra-embryonic yolk sac hematopoiesis from progenitor(s) distinct from fetal hematopoietic stem cells (HSC). Among yolk sac definitive hematopoiesis, erythromyeloid progenitors (EMP) give rise both to erythroid and myeloid cells, in particular resident macrophages. EMP are only generated within the yolk sac between E8.5 and E10.5 days of development and they migrate to the fetal liver as early as circulation is connected, where they expand and differentiate until at least E16.5. Their progeny includes erythrocytes, macrophages, neutrophils and mast cells but only EMP-derived macrophages persist until adulthood in tissues. The transient nature of EMP emergence and the temporal overlap with HSC generation renders the analysis of these progenitors difficult. We have established a tamoxifen-inducible fate mapping protocol based on expression of the macrophage cytokine receptor Csf1r promoter to characterize EMP and EMP-derived cells in vivo by flow cytometry.

While infiltrating macrophages are continuously recruited to adult tissues from circulating precursors, resident macrophages seed their tissue during development, where they are maintained without further input from progenitors. The progenitors for resident macrophages were recently identified. Here, we present methods for the genetic fate mapping of the resident macrophage progenitors.

Macrophages are professional phagocytes from the innate arm of the immune system. In steady-state, sessile macrophages are found in adult tissues where ...

A Standardized Approach for Multispecies Purification of Mammalian Male Germ Cells by Mechanical Tissue Dissociation and Flow Cytometry

Fluorescence-activated cell sorting (FACS) has been one of the methods of choice to isolate enriched populations of mammalian testicular germ cells. Currently, it allows the discrimination of up to 9 murine germ cell populations with high yield and purity. This high-resolution in discrimination and purification is possible due to unique changes in chromatin structure and quantity throughout spermatogenesis. These patterns can be captured by flow cytometry of male germ cells stained with fluorescent DNA-binding dyes such as Hoechst-33342 (Hoechst). Herein is a detailed description of a recently developed protocol to isolate mammalian testicular germ cells. Briefly, single cell suspensions are generated from testicular tissue by mechanical dissociation, double stained with Hoechst and propidium iodide (PI) and processed by flow cytometry. A serial gating strategy, including the selection of live cells (PI negative) with different DNA content (Hoechst intensity), is used during FACS sorting to discriminate up to 5 germ cell types. These include, with corresponding average purities (determined by microscopy evaluation): spermatogonia (66%), primary (71%) and secondary (85%) spermatocytes, and spermatids (90%), further separated into round (93%) and elongating (87%) subpopulations. Execution of the entire workflow is straightforward, allows the isolation of 4 cell types simultaneously with the appropriate FACS machine, and can be performed in less than 2 h. As reduced processing time is crucial to preserve the physiology of ex vivo cells, this method is ideal for downstream high-throughput studies of male germ cell biology. Moreover, a standardized protocol for multispecies purification of mammalian germ cells eliminates methodological sources of variables and allows a single set of reagents to be used for different animal models.

This work describes the standardization of a method to obtain purified germ cell populations from testicular tissue of different mammalian species. It is a straightforward protocol that combines mechanical testis dissociation, staining with Hoechst-33342 and propidium iodide, and FACS sorting, with wide applications in comparative studies of male reproductive biology.

Fluorescence-activated cell sorting (FACS) has been one of the methods of choice to isolate enriched populations of mammalian testicular germ cells. ...

Identification of Skeletal Muscle Satellite Cells by Immunofluorescence with Pax7 and Laminin Antibodies

Immunofluorescence is an effective method that helps to identify different cell types on tissue sections. In order to study the desired cell population, antibodies for specific cell markers are applied on tissue sections. In adult skeletal muscle, satellite cells (SCs) are stem cells that contribute to muscle repair and regeneration. Therefore, it is important to visualize and trace the satellite cell population under different physiological conditions. In resting skeletal muscle, SCs reside between the basal lamina and myofiber plasma membrane. A commonly used marker for identifying SCs on the myofibers or in cell culture is the paired box protein Pax7. In this article, an optimized Pax7 immunofluorescence protocol on skeletal muscle sections is presented that minimizes non-specific staining and background. Another antibody that recognizes a protein (laminin) of the basal lamina was also added to help identify SCs. Similar protocols can also be used to perform double or triple labeling with Pax7 and antibodies for additional proteins of interest.

The precise identification of satellite cells is essential for studying their functions under various physiological and pathological conditions. This article presents a protocol to identify satellite cells on adult skeletal muscle sections by immunofluorescence-based staining.

Immunofluorescence is an effective method that helps to identify different cell types on tissue sections. In order to study the desired cell population, ...

Computational Analysis of the Caenorhabditis elegans Germline to Study the Distribution of Nuclei, Proteins, and the Cytoskeleton

The Caenorhabditis elegans (C. elegans) germline is used to study several biologically important processes including stem cell development, apoptosis, and chromosome dynamics. While the germline is an excellent model, the analysis is often two dimensional due to the time and labor required for three-dimensional analysis. Major readouts in such studies are the number/position of nuclei and protein distribution within the germline. Here, we present a method to perform automated analysis of the germline using confocal microscopy and computational approaches to determine the number and position of nuclei in each region of the germline. Our method also analyzes germline protein distribution that enables the three-dimensional examination of protein expression in different genetic backgrounds. Further, our study shows variations in cytoskeletal architecture in distinct regions of the germline that may accommodate specific spatial developmental requirements. Finally, our method enables automated counting of the sperm in the spermatheca of each germline. Taken together, our method enables rapid and reproducible phenotypic analysis of the C. elegans germline.

Computational Analysis of the Caenorhabditis elegans Germline to Study the Distribution of Nuclei, Proteins, and the Cytoskeleton

We present an automated method for three-dimensional reconstruction of the Caenorhabditis elegans germline. Our method determines the number and position of each nucleus within the germline and analyses germline protein distribution and cytoskeletal structure.

The Caenorhabditis elegans (C. elegans) germline is used to study several biologically important processes including stem cell development, apoptosis, and ...

Use of Hematopoietic Stem Cell Transplantation to Assess the Origin of Myelodysplastic Syndrome

Myelodysplastic syndromes (MDS) are a diverse group of hematopoietic stem cell disorders that are defined by ineffective hematopoiesis, peripheral blood cytopenias, dysplasia, and a propensity for transformation to acute leukemia. NUP98-HOXD13 (NHD13) transgenic mice recapitulate human MDS in terms of peripheral blood cytopenias, dysplasia, and transformation to acute leukemia. We previously demonstrated that MDS could be transferred from a genetically engineered mouse with MDS to wild-type recipients by transplanting MDS bone marrow nucleated cells (BMNC). To more clearly understand the MDS cell of origin, we have developed approaches to transplant specific, immunophenotypically defined hematopoietic subsets. In this article, we describe the process of isolating and transplanting specific populations of hematopoietic stem and progenitor cells. Following transplantation, we describe approaches to assess the efficiency of transplantation and persistence of the donor MDS cells.

We describe the use of hematopoietic stem cell transplantation (HSCT) to assess the malignant potential of genetically engineered hematopoietic cells. HSCT is useful for evaluating various malignant hematopoietic cells in vivo as well as generating a large cohort of mice with myelodysplastic syndromes (MDS) or leukemia to evaluate novel therapies.

Myelodysplastic syndromes (MDS) are a diverse group of hematopoietic stem cell disorders that are defined by ineffective hematopoiesis, peripheral blood ...

Real-time Live-cell Flow Cytometry to Investigate Calcium Influx, Pore Formation, and Phagocytosis by P2X7 Receptors in Adult Neural Progenitor Cells

Live-cell flow cytometry is increasingly used among cell biologists to quantify biological processes in a living cell culture. This protocol describes a method whereby live-cell flow cytometry is extended upon to analyze the multiple functions of P2X7 receptor activation in real-time. Using a time module installed on a flow cytometer, live-cell functionality can be assessed and plotted over a given time period to explore the kinetics of calcium influx, transmembrane pore formation, and phagocytosis. This simple method is advantageous as all three canonical functions of the P2X7 receptor can be assessed using one machine, and the gathered data plotted over time provides information on the entire live-cell population rather than single-cell recordings often obtained using technically challenging patch-clamp methods. Calcium influx experiments use a calcium indicator dye, while P2X7 pore formation assays rely on ethidium bromide being allowed to pass through the transmembrane pore formed upon high agonist concentrations. Yellow-green (YG) latex beads are utilized to measure phagocytosis. Specific agonists and antagonists are applied to investigate the effects of P2X7 receptor activity. Individually, these methods can be modified to provide quantitative data on any number of calcium channels and purinergic and scavenger receptors. Taken together, they highlight how the use of real-time live-cell flow cytometry is a rapid, cost-effective, reproducible, and quantifiable method to investigate P2X7 receptor function.

Providing single-cell sensitivity, real-time flow cytometry is uniquely suited to quantify multimodal receptor functions of live cultures. Using adult neural progenitor cells, the P2X7 receptor function was assessed via calcium influx detected by calcium indicator dye, transmembrane pore formation by ethidium bromide uptake, and phagocytosis using fluorescent latex beads.

Live-cell flow cytometry is increasingly used among cell biologists to quantify biological processes in a living cell culture. This protocol describes a ...

In Vitro Generation of Somite Derivatives from Human Induced Pluripotent Stem Cells

In response to signals such as WNTs, bone morphogenetic proteins (BMPs), and sonic hedgehog (SHH) secreted from surrounding tissues, somites (SMs) give rise to multiple cell types, including the myotome (MYO), sclerotome (SCL), dermatome (D), and syndetome (SYN), which in turn develop into skeletal muscle, axial skeleton, dorsal dermis, and axial tendon/ligament, respectively. Therefore, the generation of SMs and their derivatives from human induced pluripotent stem cells (iPSCs) is critical to obtain pluripotent stem cells (PSCs) for application in regenerative medicine and for disease research in the field of orthopedic surgery. Although the induction protocols for MYO and SCL from PSCs have been previously reported by several researchers, no study has yet demonstrated the induction of SYN and D from iPSCs. Therefore, efficient induction of fully competent SMs remains a major challenge. Here, we recapitulate human SM patterning with human iPSCs in vitro by mimicking the signaling environment during chick/mouse SM development, and report on methods of systematic induction of SM derivatives (MYO, SCL, D, and SYN) from human iPSCs under chemically defined conditions through the presomitic mesoderm (PSM) and SM states. Knowledge regarding chick/mouse&#160;SM development was successfully applied to the induction of SMs with human iPSCs. This method could be a novel tool for studying human somitogenesis and patterning without the use of embryos and for cell-based therapy and disease modeling.

We present here a protocol for the differentiation of human induced pluripotent stem cells into each somite derivative (myotome, sclerotome, dermatome, and syndetome) in chemically defined conditions, which has applications in future disease modeling and cell-based therapies in orthopedic surgery.

In response to signals such as WNTs, bone morphogenetic proteins (BMPs), and sonic hedgehog (SHH) secreted from surrounding tissues, somites (SMs) give ...