We thank the previous and the current team members who have helped develop this method, including Jean-Marc Doisne, Norman Shreeve, Iva Filipovic, and Anita Qualls. This research was funded by the Wellcome trust [Grant number 200841/Z/16/Z ] and the Medical Research Council (MR/P001092/1). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.&#160;

All animal experiments described in this paper were conducted according to the Animals (Scientific Procedures) Act 1986 under PP2363781 issued by the UK Home Office. The protocol below consists of several sections starting from mice husbandry and finishing with staining for FACS analysis. Figure 3 reflects the main steps of the protocol. The materials used in the protocol are listed in the Table of Materials.
1. General mice husbandry, mating, and dissection
<ol>
	<li>Keep 7-14 week old female mice under specific pathogen-free (SPF) conditions and group-housed (typically 4-6 females according to cage size and animal weight), for 10-14 days to trigger the Lee-Boot effect, which results in estrus synchronization17.</li>
	<li>Keep the stud males in SPF conditions, single-housed, and rested for at least 48 h between each mating (time for sperm regeneration). It is preferable to use experienced proven 3-4 month old stud males as they are typically more performant than the young ones.</li>
	<li>To increase the likelihood of females becoming pregnant, introduce soiled bedding from a male&#39;s cage in the female cage 3 days prior to mating. This triggers the Whitten effect18 by exposure to male urine pheromones, and results in synchronized estrus as well as enhanced receptivity for mating.</li>
	<li>On Day 0 (D0), set up the mice for mating using one stud male per two females; consider a plug rate of approximately 20%-25%. 
	NOTE: Mating will likely occur at night since mice are nocturnal animals.</li>
	<li>In the morning following mating (D0.5), check for the presence of a vaginal plug, which is an indicator of copulation (Figure 4). The vaginal plug is an aggregate of the male ejaculate and typically persists for up to 8-24 h after mating. Check the plugs early morning.</li>
	<li>Consolidate the plugged females in a new cage and earmark them. Return the males to their cages for resting.</li>
	<li>At D9.5 or 10.5-after mating, prepare 5 mL tubes with 1 mL sterile HBSS 1x (with Mg2+ and Ca2+) for tissue collection and place them on ice.</li>
	<li>Proceed to animal euthanasia by cervical dislocation, followed by exsanguination to confirm death.</li>
	<li>Work in a sterile environment if the downstream application requires to do so. Directly after euthanasia, wipe the mouse body with 70% ethanol and proceed to dissection under a laminar flux cabinet with sterile instruments.</li>
	<li>Dissect the pregnant uterus free of mesometrial fat (Figure 5) and place the whole uterus in a prepared and appropriately labeled 5 mL tube. Keep the tubes on ice.</li>
</ol>
2. Mechanical and enzymatic digestion of the uterus
<ol>
	<li>To prepare the enzymatic digestion solution, mix 3 mL per uterus of sterile HBSS 1x with 30 &#181;g/mL of DNAse and 0.1 W&#252;nsch unit (WU)/mL of Liberase DH or 0.52 WU/mL of Liberase TM. Put the solution in a water bath at 37 &#176;C. 
	NOTE: Both Liberase TM and Liberase DH can be used. The choice of one over the other must be guided by their potential effect on epitopes recognized by antibodies used for subsequent flow cytometry analysis. 
	CAUTION: If using lyophilized enzymes, work under the hood.</li>
	<li>Prepare 20 mL of 5 mM EDTA in PBS (no Ca2+/Mg2+). Place half the solution at 37 &#176;C in a water bath and the other half on ice.</li>
	<li>Under a laminar flux cabinet, gently remove the fat surrounding the pregnant uterus with sterile instruments in a sterile Petri dish. Do not allow the tissue to dry.</li>
	<li>Dissect each implantation site with sterile instruments to remove the fetuses (seahorse-shaped translucid structure, around 1 mm in length) (Figure 6A). Discard the fetuses.</li>
	<li>Return the uterus to their original collection 5 mL tube and mince the tissue using scissors directly in the 5 mL tube and collection medium. Keep the tubes on ice all the time between the procedures.</li>
	<li>Place the 5 mL tubes containing the minced tissue in a water bath at 37 &#176;C.</li>
	<li>Add 3 mL of warm enzymatic digestion mix to each sample so that the total volume of liquid in the tube is 4 mL (1 mL of collection medium with the minced uterus and 3 mL of enzymatic digestion solution). Incubate the 5 mL tubes for 30 min at 37 &#176;C with agitation to enhance enzymatic digestion activity.</li>
	<li>Vortex the 5 mL tubes and place them on ice to inhibit the action of enzymes. Then, subsequently, transfer the contents into properly labeled 15 mL centrifuge tubes.</li>
	<li>Flush everything out of the 5 mL tubes into the 15 mL centrifuge tubes using 10 mL of ice-cold 5 mM EDTA PBS solution.</li>
	<li>Centrifuge the 15 mL centrifuge tubes containing the digested tissues for 10 min at 400 x g.</li>
	<li>Discard the supernatant, gently flick the pellet, and then resuspend it in 10 mL of warm (37 &#176;C) 5 mM EDTA PBS solution.</li>
	<li>Incubate the samples in the 15 mL centrifuge tubes at 37 &#176;C with agitation for 15 min to remove the left-over digestion medium and reduce the cell clumping.</li>
	<li>Vortex the samples on high for 10 s to further facilitate tissue dissociation.</li>
</ol>
3. Processing of the uterus into a single cell suspension
<ol>
	<li>Using the plunger of a sterile 1 mL syringe, force the digested tissue through a 70 &#181;m strainer onto a properly labeled and sterile 50 mL centrifuge tube to remove the cell clumps and the undissociated tissue.</li>
	<li>Wash the strainer several times with a total of 10 mL of cold PBS to collect all the cells.</li>
	<li>Spin the 50 mL centrifuge tube for 10 min at 400 x g. 
	NOTE: Perform the further steps using Option A or Option B. Option A allows better enrichment of the lymphocytes with less debris and stromal cell contamination than Option B. However, Option B gives a higher immune cell yield due to less cell loss and less variability of cell yield between samples. Option B is also easier to perform technically. Therefore, depending on preference, proceed with Option A or Option B.
	<ol>
		<li>The steps for Option A are as follows.
		<ol>
			<li>Label one sterile 15 mL centrifuge tube per sample containing 5 mL of 80% (v/v) isotonic Percoll diluted in PBS.</li>
			<li>After the spin, discard the supernatant from the 50 mL centrifuge tube. Use a pipet boy to resuspend each pellet in 8 mL of 40% (v/v) isotonic Percoll in PBS.</li>
			<li>Use a pipet boy on slow speed to carefully overlay the pellet resuspended in the 40% Percoll solution onto 80% Percoll solution. Pipette slowly and continuously; hold the 15 mL tube at an angle of 45&#176; (Figure 6B).</li>
			<li>Without disturbing the overlay, centrifuge the 15 mL centrifuge tubes for 20 min at 850 x g, at room temperature (medium acceleration and minimum break).</li>
			<li>Carefully remove the tubes from the centrifuge without disturbing the Percoll layers (Figure 6C).</li>
			<li>Without disturbing the ring of leukocytes at the interface of the two Percoll solutions, use a sterile Pasteur Pipette to discard all except for approximately 0.5-1 mL of the top Percoll layer.</li>
			<li>While trying to suck a minimum amount of Percoll solution (up to 4-5 mL total), carefully collect the ring of leukocytes and transfer the cells into a new labeled 15 mL centrifuge tube.</li>
			<li>Top up each sample with 10 mL of sterile RMPI-1640 medium supplemented with 10% of heat-inactivated FBS.</li>
			<li>Centrifuge for 5 min at 500 x g at 4 &#176;C.</li>
			<li>Discard the supernatant and proceed to RBC lysis.</li>
		</ol>
		</li>
		<li>The steps for Option B are as follows.
		<ol>
			<li>Label one sterile 15 mL centrifuge tube per sample.</li>
			<li>After the spin, discard the supernatant from the 50 mL centrifuge tube. Use a pipet boy to resuspend each pellet with 8 mL of 35% (v/v) isotonic Percoll in RPMI-1640 medium.</li>
			<li>Transfer the samples into 15 mL centrifuge tubes.</li>
			<li>Centrifuge the samples at 940 x g for 10 min at room temperature with medium acceleration and minimum break.</li>
			<li>Aspirate the supernatant carefully using an aspirator or pipette boy (not by inverting the tube).</li>
			<li>Resuspend the pellet in 14 mL of RPMI-1640 medium supplemented with 10% heat-inactivated FBS and then centrifuge the sample at 500 x g for 5 min at 4 &#176;C.</li>
			<li>Discard the supernatant by aspiration and proceed to RBC lysis.</li>
		</ol>
		</li>
	</ol>
	</li>
</ol>
4.RBC lysis
<ol>
	<li>To lyse the RBCs, resuspend the samples in 3 mL of 1x RBC lysing solution and incubate for 3 min at room temperature.</li>
	<li>Add 10 mL of PBS into the samples to stop the reaction.</li>
	<li>Centrifuge the tubes at 400 x g for 5 min and discard the supernatant.</li>
	<li>Add 10 mL of PBS and repeat step 4.3.</li>
	<li>Resuspend each pellet in 1 mL of RPMI-1640 medium supplemented with 10% of heat-inactivated FBS.</li>
	<li>Pass the samples through sterile 70 &#181;m cell strainers.</li>
	<li>Perform the cell count using trypan blue and a Neubauer Chamber as per the manufacturer&#39;s instructions.</li>
	<li>Adjust the concentration of the cell suspension to 1-2 million cells in 100 &#181;L of PBS or medium.</li>
</ol>
5. Panel design strategy and controls
NOTE: The panel described in this paper is suitable for the discrimination of uILC1, trNK, and cNK cells and was designed to be used on a 5-laser BD LSRFortessa. Minor modifications can be made to study different cell populations and use alternative fluorochromes. It is recommended to check the configuration of the instrument, using titrated antibodies for optimal separation, consulting the manufacturer&#39;s brightness index and using the brightest dyes for low expressing antigens such as NKp46, and following general guidelines19. It is recommended to include a Fluorescence Minus One (FMO) control for NKp46.
6. Innate lymphoid cell staining for FACS phenotyping
<ol>
	<li>Transfer 1-2 million cells per well into a round-bottom 96-well plate.</li>
	<li>Spin the plate at 400 x g for 3 min at 4 &#176;C and discard the supernatant by flicking it into a sink.</li>
	<li>Resuspend the cell pellets into 100 &#181;L of PBS (protein and azide-free) using a multi-channel pipette. 
	NOTE: Ensure that the PBS contains no sodium azide, no Tris, or any proteins for the subsequent step.</li>
	<li>Repeat step 6.2.</li>
	<li>Resuspend cells in 50 &#181;L of fixable viability dye diluted in PBS (protein and azide-free) (1:1,000). Incubate the cells at room temperature for 30 min in the dark. 
	NOTE: Ensure that the PBS contains no sodium azide, no Tris, or any proteins such as FBS or BSA as this may result in decreased staining intensity of dead cells and/or increased background staining for the live cells. 
	CAUTION: If viability dye is powdered, use under the hood.</li>
	<li>Add 150 &#181;L of PBS, resuspend the cells with a multi-channel pipette, and then repeat step 6.2.</li>
	<li>Resuspend the cells in 25 &#181;L of FACS Buffer (PBS supplemented with 1% BSA or 2% FBS) containing Fc receptor blocking reagent. Incubate the cells for 5 min at 4 &#176;C.</li>
	<li>Add 25 &#181;L of a surface antibody cocktail. 
	NOTE: Always titrate antibodies and optimize the antibody panel prior to the experiment.</li>
	<li>Incubate the samples at room temperature for 20 min in the dark.</li>
	<li>Add 150 &#181;L of FACS Buffer to each well, mix thoroughly, and then repeat step 6.2.</li>
	<li>Repeat step 6.10. 
	NOTE: Perform further steps using Option A or Option B. Use option A to stain the cells with surface markers. Use option B to study the intracellular markers by flow cytometry.
	<ol>
		<li>The steps for Option A are as follows.
		<ol>
			<li>Resuspend the samples in 100 &#181;L of 4% paraformaldehyde (PFA) per well and incubate for 20 min at room temperature. 
			CAUTION: Use PFA under the hood. Please refer to the safety sheet for discarding PFA waste/objects that have come into contact with PFA (e.g., pipettes) safely.</li>
			<li>Repeat step 6.2, twice. 
			CAUTION: Do not discard by flicking into the sink here as it contains PFA. Aspirate with a pipette and discard the waste as per the safety sheet.</li>
			<li>Resuspend the samples in 200 &#181;L of PBS.</li>
			<li>Transfer the samples into labeled FACS tubes and top up with 100 &#181;L of PBS. Keep the tubes on ice or in a fridge until processing with FACS analysis. Acquire the samples on a flow cytometer within 24 h.</li>
		</ol>
		</li>
		<li>The steps for Option B are as follows.
		<ol>
			<li>Resuspend the samples in 100 &#181;L of fixation / permeabilization solution per well (containing paraformaldehyde) and incubate for 20 min at 4 &#176;C. 
			CAUTION: Use PFA under the hood. Please refer to the safety sheet for discarding PFA waste/objects that have come into contact with PFA (e.g., pipettes) safely.</li>
			<li>Repeat step 6.2. 
			CAUTION: Do not discard by flicking into the sink here as it contains PFA. Aspirate with a pipette and discard the waste as per the safety sheet.</li>
			<li>Add 200 &#181;L of 1x permeabilization / washing buffer, mix well, and then repeat step 6.2.</li>
			<li>Repeat step 6.11.2.3.</li>
			<li>Resuspend the fixed and permeabilized cells in 50 &#181;L of 1x permeabilization/washing&#160;buffer containing antibodies mix for intracellular staining.</li>
			<li>Incubate the samples at 4 &#176;C for 30 min in the dark.</li>
			<li>Add 200 &#181;L of 1x permeabilization / washing solution, mix well, and then repeat step 6.2.</li>
			<li>Repeat step 6.11.2.7.</li>
			<li>Resuspend the samples in 200 &#181;L of PBS.</li>
			<li>Transfer the samples into labeled FACS tubes and top up with 100 &#181;L of PBS. Keep the tubes on ice or in a fridge until processing with FACS analysis. Acquire the samples on a flow cytometer within 24 h. 
			NOTE: After performing this protocol, the decidual cell suspension is ready for FACS analysis. It is recommended to record as many events as possible per sample; at least 1,000-3,000 events of a parental population have to be obtained to achieve reliable results.</li>
		</ol>
		</li>
	</ol>
	</li>
</ol>

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The authors have nothing to disclose and no conflicts of interest.

The method contains several critical steps discussed hereafter. The first critical step is to obtain multiple synchronous pregnancies as the relative frequency of leukocyte populations changes through pregnancy. Having multiple dams at the same gestational day allows for either biological repeats in the same experiments or pooling lymphocytes from individual dams to obtain larger numbers required for downstream applications. Timed mating allows the researcher to pinpoint conception within a 24 h period. Although mice live for around 2.5 years, they will be of reproductive age from 4-7 weeks until 6-8 months old. As younger mice usually produce smaller pups, female mice are generally not mated until they are between 6-8 weeks, and male mice until they are between 8-10 weeks. Given that estrus lasts about 15 h in mice and occurs every 4-5 days, the typical mating rate (revealed by a vaginal plug, see Figure 4) is around 25%. It is therefore important to use mice in estrus and plan sufficient numbers to obtain the required number of dams for a given experiment. The estrus cycle phase can be determined by vaginal smear cytology22. The plug rate can be improved by resting males 48 h prior to mating and by taking advantage of the Whitten effect18. Alternatively, one can administer pregnant mare serum, which mimics the effect of the endogenous follicle-stimulating hormone, inducing oocyte maturation and, 42-50 h later, human chorionic gonadotropin, which mimics the effect of the endogenous luteinizing hormone, inducing ovulation. This hormonal treatment bypasses the requirement for estrus and makes virtually all treated females receptive.
A second critical step is to ensure the quality of the FACS staining. Antibodies used in flow cytometry must always be titrated and used at the optimal concentration, and it is necessary to check that the enzymatic digestion does not cleave crucial antigenic epitopes. To assess whether an enzyme will cleave an epitope, one could stain two fractions of the same sample in parallel, one undergoing enzymatic and the other mechanical digestion. Similarly, the use of appropriate controls and single stains is crucial to obtain reliable data. For rare events, beads can be used to generate single stain samples. It is recommended not to use beads for setting up voltages but rather a population of cells containing lymphocytes and other leukocytes, such as splenocytes. If beads are used, it is necessary to titrate antibodies for bead staining, so the fluorescence intensity of stained beads will be comparable to the fluorescence intensity of cells. In case of difficulty separating positive from negative cells for a particular marker, an FMO control can also be used to facilitate the gating for a specific marker. In the case of intracellular markers, an isotype control&#160;must be used as intracellular staining might result in residual unbound antibodies, which may still be present within cells after the washing steps and therefore increase the background signal. It is recommended to run the samples within 24 h of fixing the cells to obtain the best results in phenotyping by FACS analysis, as autofluorescence increases significantly over time and fluorescence intensity of some antibodies might decline over time.
Another crucial factor to consider is the downstream application of the single-cell suspension obtained with the protocol. For functional assays, it is essential to work in sterile conditions. Similarly, for subsequent omics studies, it is important to work in sterile and RNase, DNase and protease-free.
The protocol presented here focuses on phenotyping group 1 ILCs but can be adapted for phenotyping other cell types by modifying the antibody panel. It is recommended that all antibodies are tested against digested and non-digested cell suspension to detect the loss/alteration of surface epitopes by the enzymatic treatment. Similarly, different enzymes can be used to digest the tissue and increase cell yield, but its effect on crucial antigenic epitopes must be carefully studied. While NKp46 is a good marker for splenic NK cells and works in all strains of laboratory mice, the expression of NKp46 on uNK cells in C57BL/6 mice is considerably lower than on spleen NK cells. It is best to stain for both NK1.1 and NKp46 simultaneously. If multiple organs are to be compared directly, it is recommended to treat all samples equally, even if the enzymatic digestion is not required for tissues such as the spleen or the bone marrow. Although the method presented here is applicable to the non-pregnant uterus, the lymphocyte ring isolation by a two-phase Percoll gradient will be challenging, and the yield of isolated cells may be too low for reliable FACS analysis and therefore will require pooling together cells isolated from the uterus of individual, non-pregnant mice23.
There are limitations to the protocol to consider for the interpretation of the data. As it is the case for all tissues, circulating lymphocytes coming from the blood will be isolated alongside tissue-resident cells. If the exclusion of circulating lymphocytes is essential for data interpretation, intravital staining can be performed to label circulating cells. Furthermore, a second limitation to the protocol is that some cells will be lost as not all cells can be extracted from the tissue. The most common problems and their troubleshooting are presented in Table 2.
Historically, the study of cells in tissues has relied on histological examination of tissue sections. Sandra Peel&#39;s excellent review24 summarizes the work done over more than 100 years until the late &#39;80s. Descriptions of cells later known as uNK cells indeed appear in manuscripts published more than half a century before lymphocytes were even discovered. So, before the discovery of NK cells in 1975, and the uNK cells have been indicated as maternal glycogen cells or granulated metrial gland cells. Anne Croy has made major contributions in the field25 and kindly taught the team the dissection she had optimized3, and that is used currently. Although it is instrumental in describing the morphology and tissue location of uNK cells, classical histological examination is limited to the detection of only a few markers on the cells of interest. In 2008, a flow cytometry-based method to simultaneously detect multiple markers on uterine lymphocytes was described26. This is essentially the method that has been described in this paper. More recent technologies such as spatial transcriptomics and imaging by mass cytometry combine the power of histology and flow-cytometry, allowing both the simultaneous detection of multiple genes or proteins, respectively, and the preservation of the normal tissue architecture.
The applications of the method described here are multiple and include FACS phenotyping, functional assay (such as ELISPOT, degranulation or cytotoxic assays), cell sorting, and subsequent transcriptomics or proteomics. Further applications that could be developed based on this method include the culture and expansion of decidual NK cells after cell sorting or enrichment by negative depletion. Currently, there is no protocol to culture and expand mouse uNK cells and preserve their viability and functionality for an extended period, in a similar fashion to human NK cells that can be cultivated and expanded for 7-14 days by addition of IL-2 or a combination IL-12 and IL-15. The optimization of such a method for mouse uNK cells would provide more flexibility when performing functional assays and allow for multiple conditions to be tested with a higher cell number. On the other hand, culture conditions are known to modify the unique phenotype of lymphocytes and potentially their function too.

Described here is a simple method to obtain a high yield of uterine innate lymphocytes from individual pregnant uterus. This method preserves protein surface expression and functionality of uterine innate lymphocytes and it is suitable for subsequent applications such as FACS phenotyping, RNAseq, proteomics or functional assays. Here, the focus is on the phenotyping of group 1 uILCs by flow cytometry.
The uterus is composed of three layers: the endometrium, myometrium, and perimetrium (Figure 1). The endometrium is the mucosa, lining the lumen of the uterus. Progesterone, produced by the corpus luteum, converts the endometrium into decidua. The myometrium is composed of two layers of smooth muscle that make up the uterine wall. The perimetrium is the serosa that wraps the uterus and connects it to the peritoneum through the broad ligament called mesometrium. In a cross-section of the uterus, the part opposite to the lumen is called the mesometrial side, while the part close to the lumen is called the anti-mesometrial side. A variety of maternal leukocytes populate the endometrium and the decidua, including several types of cells, where the innate immune cells represent the vast majority of cells. Innate lymphoid cells (ILCs), macrophages, dendritic cells (DC), as well as CD4+ and CD8+ T lymphocytes, regulatory T cells (Tregs), and rare B cells, may all play important roles in the regulation of the uterine environment throughout pregnancy1,2. ILCs in the uterus are found not only in the mucosa, but also in the myometrium in mice. Including all three groups of ILCs, the uterus is indeed the organ most densely populated by group 1 ILCs. With the structural transformation of uterine tissues throughout gestation, the number and proportion of uterine leukocytes also change (see Figure 2A for an example of variations in the percentage of group 1 uILC subsets)3,4.
When mice are referred to in this paper, the C57BL/6 strain of inbred laboratory mice is meant. Outbred mice (e.g., NMRI mice) are often used in reproductive research because of their high reproductive rate. However, the use of inbred strains is necessary to generate consistent results, and the immunologist&#39;s favorite genetic background is C57BL/6, also known as B6.
Approximately 30% of uterine leukocytes in B6 dams at mid-gestation are g1 uILCs, which are defined by flow cytometry as viable CD45+CD3-CD19-NK1.1+NKp46+ cells (Figure 2B): pro-angiogenic tissue-resident NK (trNK), IFN-g producing conventional NK (cNK), and uILC14,5. The percentage of uNK cells is even higher in humans, reaching about 70% in the first trimester6. There are more similarities than differences between human and mouse uNK and uILC7,8. Although it is important to keep the differences in mind, it is useful to integrate information available on the two species. When one combines information obtained from investigating uILC in humans and laboratory rodents, it is clear that NK cells assist in homeostatic changes essential for the biology of the uterus, including maintenance of arterial integrity9 and spiral artery remodeling10, as well as trophoblast invasion11,12. They also play specific roles in the defense against pathogens13,14. In mice and rats, besides filling the decidua around the implantation site, NK cells accumulate between the two muscle layers of the myometrium of dams in a transient structure known as the Mesometrial Lymphoid Aggregate of pregnancy (MLAp)15 (Figure 1B), also known in the past as the metrial gland, the function of which is yet to be discovered.
Described here is a detailed protocol of the method used in the laboratory to isolate lymphocytes from the uterus of pregnant mice using a combination of mechanical disaggregation and enzymatic digestion. As the whole uterus is used in the method, lymphocytes isolated from the uterus during gestation are a mixture of decidual and myometrial cells. Further dissection of the decidua from the uterine wall and its MLAp is possible, and it has been described before16. The method described here was developed to obtain uterine lymphocytes while preserving protein surface expression, cellular functionality, and viability. The outcome is a single cell suspension with minimal residual cellular debris and a yield typically ranging from 1-5 million cells at mid-gestation (10.5 days) for a pregnant uterus. The applications of this method encompass phenotyping by flow cytometry, cell sorting for subsequent transcriptomic or proteomic studies, functional studies such as intracellular cytokine production, degranulation, ELISPOT or cytotoxic assays. The protocol presented here focuses on identifying group 1 ILCs but can be adapted for other cell types such as other ILCs, T cells, B cells, DC, or macrophages with minor modifications of the antibody panel used for FACS analysis. The protocol can also be used to isolate cells from other tissues and for pooled non-pregnant uteri.

<table><tbody><tr><td>70 &amp;micro;m cell strainers</td><td>Falcon</td><td>352350</td><td></td></tr><tr><td>BSA</td><td>Sigma</td><td>A9647-100G</td><td></td></tr><tr><td>CD19 antibody</td><td>BD</td><td>562701</td><td></td></tr><tr><td>CD3 antibody</td><td>BD</td><td>562600</td><td></td></tr><tr><td>CD45 antibody</td><td>BioLegend</td><td>103108</td><td></td></tr><tr><td>CD49a antibody</td><td>BD</td><td>740262</td><td></td></tr><tr><td>DNase I</td><td>Roche (Sigma)</td><td>10104159001</td><td></td></tr><tr><td>EOMES antibody</td><td>eBioscience</td><td>12-4875-82</td><td></td></tr><tr><td>Fc block Trustain fcx</td><td>BioLegend</td><td>101320</td><td></td></tr><tr><td>Fetal Bovine Serum</td><td>Gibco</td><td>10217-106</td><td></td></tr><tr><td>Fix/Perm buffer (part of BD Cytofix/Cytoperm Fixation/Permeabilization Kit)</td><td>BD</td><td>554714</td><td></td></tr><tr><td>HBSS, calcium, magnesium, no phenol red</td><td>Gibco</td><td>14025092</td><td></td></tr><tr><td>Liberase DH</td><td>Roche (Sigma)</td><td>5401089001</td><td></td></tr><tr><td>Lysis buffer Pharmlyse</td><td>BD</td><td>555899</td><td></td></tr><tr><td>NK1.1 antibody</td><td>BioLegend</td><td>108739</td><td></td></tr><tr><td>NKp46&amp;nbsp; antibody</td><td>BioLegend</td><td>137608</td><td></td></tr><tr><td>Paraformaldehyde 16% Solution (methanol-free)</td><td>Agar Scientific</td><td>AGR1026</td><td></td></tr><tr><td>PBS 10x</td><td>Gibco</td><td>14030-048</td><td></td></tr><tr><td>PBS 1x (no Ca2+ or Mg2+)</td><td>Thermo Scientific</td><td>14190144</td><td></td></tr><tr><td>Percoll</td><td>VWR international</td><td>17-0891-01</td><td></td></tr><tr><td>Phosphate buffered saline</td><td>Sigma-Aldrich</td><td>P5368-10PAK</td><td></td></tr><tr><td>Pre-Separation filters</td><td>Miltenyi</td><td>130-095-823</td><td></td></tr><tr><td>RMPI-1640 medium + GlutaMAX</td><td>Gibco</td><td>61870-010</td><td></td></tr><tr><td>UltraPure 0.5M EDTA, pH 8.0</td><td>Thermo Scientific</td><td>15575020</td><td></td></tr><tr><td>Zombie Violet Fixable Viability dye</td><td>BioLegend</td><td>423113</td><td></td></tr></tbody></table>

isolation of uterine innate lymphoid cells for analysis by flow cytometry

Described here is a simple method to isolate and phenotype mouse group 1 uterine innate lymphoid cells (g1 uILCs) from individual pregnant uterus by flow cytometry. The protocol describes how to set up time mating to obtain multiple synchronous dams, the mechanical and enzymatic digestion of the pregnant uterus, the staining of single-cell suspensions, and a FACS strategy to phenotype and discriminate g1 uILCs. Although this method inevitably loses the spatial information of cellular distribution within the tissue, the protocol has been successfully applied to determine uILC heterogeneity, their response to maternal and foetal factors affecting pregnancy, their gene expression profile, and their functions.

Watch this Scientific Journal Video about Isolation of Uterine Innate Lymphoid Cells for Analysis by Flow Cytometry at JoVE.com

Isolation of Uterine Innate Lymphoid Cells for Analysis by Flow Cytometry

This is a method to isolate uterine lymphoid cells from both pregnant and non-pregnant mice. This method can be used for multiple downstream applications such as FACS phenotyping, cell sorting, functional assays, RNA-seq, and proteomics. The protocol here demonstrates how to phenotype group 1 uterine innate lymphoid cells by flow cytometry.

Described here is a simple method to isolate and phenotype mouse group 1 uterine innate lymphoid cells (g1 uILCs) from individual pregnant uterus by flow ...

isolation-uterine-innate-lymphoid-cells-for-analysis-flow

Universidad San Sebastian

Research

JoVE Journal

Immunology and Infection

4.7K Views.  University of Cambridge School of Clinical Medicine. Onze methode maakt het mogelijk om de samenstelling en functionele kenmerken van verschillende subpopulaties van lymfocyten in het baarmoederweefsel van zwangere en niet-drachtige dieren te beoordelen. Dit protocol zorgt voor isolatie van baarmoederlymfocyten met behoud van oppervlakte-expressie van eiwit, cel levensvatbaarheid en functionaliteit. Daarom is het geschikt voor een reeks volgende toepassingen.Verwijdering van foetussen aan het begin van het experiment en leukocytenverzame...

Video: Isolation of Uterine Innate Lymphoid Cells for Analysis by Flow Cytometry

Isolation of Lymphocytes from Mouse Genital Tract Mucosa

Mucosal surfaces, including in the gastrointestinal, urogenital, and respiratory tracts, provide portals of entry for pathogens, such as viruses and bacteria 1. Mucosae are also inductive sites in the host to generate immunity against pathogens, such as the Peyers patches in the intestinal tract and the nasal-associated lymphoreticular tissue in the respiratory tract. This unique feature brings mucosal immunity as a crucial player of the host defense system. Many studies have been focused on gastrointestinal and respiratory mucosal sites. However, there has been little investigation of reproductive mucosal sites. The genital tract mucosa is the primary infection site for sexually transmitted diseases (STD), including bacterial and viral infections. STDs are one of the most critical health challenges facing the world today. Centers for Disease Control and Prevention estimates that there are 19 million new infectious every year in the United States. STDs cost the U.S. health care system $17 billion every year 2, and cost individuals even more in immediate and life-long health consequences. In order to confront this challenge, a greater understanding of reproductive mucosal immunity is needed and isolating lymphocytes is an essential component of these studies. Here, we present a method to reproducibly isolate lymphocytes from murine female genital tracts for immunological studies that can be modified for adaption to other species. The method described below is based on one mouse.&#x2003;

An efficient way to isolate lymphocytes from mouse genital tract is described. This method takes advantage of enzyme digestion and Percoll gradient separation to allow efficient isolation. This technique is also adaptable to for use in other species

Mucosal surfaces, including in the gastrointestinal, urogenital, and respiratory tracts, provide portals of entry for pathogens, such as viruses and ...

Isolation and Th17 Differentiation of Na&iuml;ve CD4 T Lymphocytes

Th17 cells are a distinct subset of T cells that have been found to produce interleukin 17 (IL-17), and differ in function from the other T cell subsets including Th1, Th2, and regulatory T cells. Th17 cells have emerged as a central culprit in overzealous inflammatory immune responses associated with many autoimmune disorders. In this method we purify T lymphocytes from the spleen and lymph nodes of C57BL/6 mice, and stimulate purified CD4+ T cells under control and Th17-inducing environments. The Th17-inducing environment includes stimulation in the presence of anti-CD3 and anti-CD28 antibodies, IL-6, and TGF-&#946;. After incubation for at least 72 hours and for up to five days at 37 &#176;C, cells are subsequently analyzed for the capability to produce IL-17 through flow cytometry, qPCR, and ELISAs. Th17 differentiated CD4+CD25- T cells can be utilized to further elucidate the role that Th17 cells play in the onset and progression of autoimmunity and host defense. Moreover, Th17 differentiation of CD4+CD25- lymphocytes from distinct murine knockout/disease models can contribute to our understanding of cell fate plasticity.

Isolation and Th17 Differentiation of Na&#239;ve CD4 T Lymphocytes

With effector functions distinct from other T cell subsets, Th17 cells have been centrally implicated in inflammatory autoimmunity. This in vitro Th17 differentiation protocol provides a means to determine whether na&#239;ve CD4+ T lymphocytes can differentiate into Th17 cells, and to further examine their role in autoimmunity and host response.

Th17 cells are a distinct subset of T cells that have been found to produce interleukin 17 (IL-17), and differ in function from the other T cell subsets ...

Isolation of Murine Lymph Node Stromal Cells

Secondary lymphoid organs including lymph nodes are composed of stromal cells that provide a structural environment for homeostasis, activation and differentiation of lymphocytes. Various stromal cell subsets have been identified by the expression of the adhesion molecule CD31 and glycoprotein podoplanin (gp38), T zone reticular cells or fibroblastic reticular cells, lymphatic endothelial cells, blood endothelial cells and FRC-like pericytes within the double negative cell population. For all populations different functions are described including, separation and lining of different compartments, attraction of and interaction with different cell types, filtration of the draining fluidics and contraction of the lymphatic vessels. In the last years, different groups have described an additional role of stromal cells in orchestrating and regulating cytotoxic T cell responses potentially dangerous for the host. 
Lymph nodes are complex structures with many different cell types and therefore require a appropriate procedure for isolation of the desired cell populations. Currently, protocols for the isolation of lymph node stromal cells rely on enzymatic digestion with varying incubation times; however, stromal cells and their surface molecules are sensitive to these enzymes, which results in loss of surface marker expression and cell death. Here a short enzymatic digestion protocol combined with automated mechanical disruption to obtain viable single cells suspension of lymph node stromal cells maintaining their surface molecule expression is proposed.

Isolation of lymph node stromal cells is a multistep procedure including enzymatic digestion and mechanical disaggregation to obtain fibroblastic reticular cells, lymphatic and blood endothelial cells. In the described procedure, a short digestion is combined with automated mechanical disaggregation to minimize surface marker degradation of viable lymph node stromal cells.

Secondary lymphoid organs including lymph nodes are composed of stromal cells that provide a structural environment for homeostasis, activation and ...

Collection, Isolation, and Flow Cytometric Analysis of Human Endocervical Samples

Despite the public health importance of mucosal pathogens (including HIV), relatively little is known about mucosal immunity, particularly at the female genital tract (FGT). Because heterosexual transmission now represents the dominant mechanism of HIV transmission, and given the continual spread of sexually transmitted infections (STIs), it is critical to understand the interplay between host and pathogen at the genital mucosa. The substantial gaps in knowledge around FGT immunity are partially due to the difficulty in successfully collecting and processing mucosal samples. In order to facilitate studies with sufficient sample size, collection techniques must be minimally invasive and efficient. To this end, a protocol for the collection of cervical cytobrush samples and subsequent isolation of cervical mononuclear cells (CMC) has been optimized. Using ex vivo flow cytometry-based immunophenotyping, it is possible to accurately and reliably quantify CMC lymphocyte/monocyte population frequencies and phenotypes. This technique can be coupled with the collection of cervical-vaginal lavage (CVL), which contains soluble immune mediators including cytokines, chemokines and anti-proteases, all of which can be used to determine the anti- or pro-inflammatory environment in the vagina.

The use of cytobrush sampling to collect lymphocytes and monocytes from the endocervix is a minimally invasive technique that provides samples for analysis of female genital tract immunity. In this protocol, we describe the collection of cytobrush samples and immune cell isolation for flow cytometry assays.

Despite the public health importance of mucosal pathogens (including HIV), relatively little is known about mucosal immunity, particularly at the female ...

Medicine

Isolation of Infiltrating Leukocytes from Mouse Skin Using Enzymatic Digest and Gradient Separation

Dissociating murine skin into a single cell suspension is essential for downstream cellular analysis such as the characterization of infiltrating immune cells in rodent models of skin inflammation. Here, we describe a protocol for the digestion of mouse skin in a nutrient-rich solution with collagenase D, followed by separation of hematopoietic cells using a discontinuous density gradient. Cells thus obtained can be used for in vitro studies, in vivo transfer, and other downstream cellular and molecular analyses including flow cytometry. This protocol is an effective and economical alternative to expensive mechanical dissociators, specialized separation columns, and harsher trypsin- and dispase-based digestion methods, which may compromise cellular viability or density of surface proteins relevant for phenotypic characterization or cellular function. As shown here in our representative data, this protocol produced highly viable cells, contained specific immune cell subsets, and had no effect on integrity of common surface marker proteins used in flow cytometric analysis.

This protocol describes enzymatic digestion of mouse skin in nutrient-rich medium followed by gradient separation to isolate leukocytes. Cells thus derived can be used for diverse downstream applications. This is an effective, economical, and improved alternative to tissue dissociation machines and harsher trypsin and dispase-based tissue digestion protocols.

Dissociating murine skin into a single cell suspension is essential for downstream cellular analysis such as the characterization of infiltrating immune ...

Isolation and Flow Cytometric Characterization of Murine Small Intestinal Lymphocytes

The intestines &#8212; which contain the largest number of immune cells of any organ in the body &#8212; are constantly exposed to foreign antigens, both microbial and dietary. Given an increasing understanding that these luminal antigens help shape the immune response and that education of immune cells within the intestine is critical for a number of systemic diseases, there has been increased interest in characterizing the intestinal immune system. However, many published protocols are arduous and time-consuming. We present here a simplified protocol for the isolation of lymphocytes from the small-intestinal lamina propria, intraepithelial layer, and Peyer&#39;s patches that is rapid, reproducible, and does not require laborious Percoll gradients. Although the protocol focuses on the small intestine, it is also suitable for analysis of the colon. Moreover, we highlight some aspects that may need additional optimization depending on the specific scientific question. This approach results in the isolation of large numbers of viable lymphocytes that can subsequently be used for flow cytometric analysis or alternate means of characterization.

There is growing interest in the quantitative characterization of intestinal lymphocytes owing to increasing recognition that these cells play a critical role in a variety of intestinal and systemic diseases. In this protocol, we describe how to isolate single cell populations from different small-intestinal compartments for subsequent flow cytometric characterization.

The intestines &#8212; which contain the largest number of immune cells of any organ in the body &#8212; are constantly exposed to foreign antigens, both ...

Isolation and Flow Cytometric Analysis of Human Endocervical Gamma Delta T Cells

The female reproductive tract (FRT) mucosal immune system serves as the first line of defense. Better knowledge of the genital mucosa is therefore essential for understanding pathogenicity of different pathogens including HIV. Gamma delta (GD) T cells are the prototype of &#39;unconventional&#39; T cells and represent a relatively small subset of T cells defined by their expression of heterodimeric T-cell receptors (TCRs) composed of gamma and delta chains. This sets them apart from the classical and much better known CD4+ helper T cells and CD8+ cytotoxic T cells that are defined by alpha-beta TCRs. GD T cells often show tissue-specific localization and are enriched in epithelium. GD T cells orchestrate immune responses in inflammation, tumor surveillance, infectious disease, and autoimmunity.
Here, we present a method to reproducibly isolate and analyze human endocervical intraepithelial GD T lymphocytes. We have used endocervical cytobrush samples from women participating in the Women&#39;s Interagency HIV Infection Study (WIHS). Knowledge about GD T cells interactions during conditions in which there is an insult to the vaginal mucosal could be applied to any clinical study in which mucosal vulnerability is addressed, including the development of vaginal microbicides.In addition, knowledge about mucosal GD T cell responses has potential for application of GD T cell-based immune therapy in treating infectious diseases.

We describe here an isolation method to obtain human endocervical intraepithelial lymphocytes for the analysis of intraepithelial gamma delta T cells. This protocol can be extended for the purification of endocervical gamma delta T cells by magnetic beads or by cell sorting.

The female reproductive tract (FRT) mucosal immune system serves as the first line of defense. Better knowledge of the genital mucosa is therefore ...

Isolation of Dendritic Cells from the Human Female Reproductive Tract for Phenotypical and Functional Studies

The characterization of the human dendritic cells (DCs) resident in mucosal tissues is challenging due to the difficulty in obtaining samples, and the low numbers of DCs present per tissue. Yet, as the phenotype and function of DCs is modified by the tissue environment, it is necessary to analyze tissue resident DC populations, since blood derived DCs incompletely reflect the complexities of DCs in tissues. Here we present a protocol to isolate DCs from the human female reproductive tract (FRT) using hysterectomy specimens that allows both phenotypical and functional analyses. The protocol consists of tissue digestion to generate a single cell mixed cell suspension, followed by positive magnetic bead selection. Our tissue digestion protocol does not cleave surface markers, which allows phenotypical and functional analysis of DCs in the steady state, without overnight incubation or cell activation. This protocol can be adapted for the isolation of other immune cell types or isolation of DCs from other tissues.

We describe here a method to isolate and purify dendritic cells from different anatomical compartments in the human female reproductive tract for the evaluation of their phenotypical and functional characteristics. This method can be adapted to isolate other immune cells or dendritic cells from other mucosal tissues.

The characterization of the human dendritic cells (DCs) resident in mucosal tissues is challenging due to the difficulty in obtaining samples, and the low ...

Isolating Lymphocytes from the Mouse Small Intestinal Immune System

The intestinal immune system plays an essential role in maintaining the barrier function of the gastrointestinal tract by generating tolerant responses to dietary antigens and commensal bacteria while mounting effective immune responses to enteropathogenic microbes. In addition, it has become clear that local intestinal immunity has a profound impact on distant and systemic immunity. Therefore, it is important to study how an intestinal immune response is induced and what the immunologic outcome of the response is. Here, a detailed protocol is described for the isolation of lymphocytes from small intestine inductive sites like the gut-associated lymphoid tissue Peyer&#39;s patches and the draining mesenteric lymph nodes and effector sites like the lamina propria and the intestinal epithelium. This technique ensures isolation of a large numbers of lymphocytes from small intestinal tissues with optimal purity and viability and minimal cross compartmental contamination within acceptable time constraints. The technical capability to isolate lymphocytes and other immune cells from intestinal tissues enables the understanding of immune responses to gastrointestinal infections, cancers, and inflammatory diseases.

Here we describe a detailed protocol for the isolation of lymphocytes from the inductive sites including the gut-associated lymphoid tissue Peyer&#39;s patches and the draining mesenteric lymph nodes, and the effector sites including the lamina propria and the intestinal epithelium of the small intestinal immune system.

The intestinal immune system plays an essential role in maintaining the barrier function of the gastrointestinal tract by generating tolerant responses to ...

Flow Cytometric Analysis for Identification of the Innate and Adaptive Immune Cells of Murine Lung

The respiratory tract is in direct contact with the outside environment and requires a precisely regulated immune system to provide protection while suppressing unwanted reactions to environmental antigens. Lungs host several populations of innate and adaptive immune cells that provide immune surveillance but also mediate protective immune responses. These cells, which keep the healthy pulmonary immune system in balance, also participate in several pathological conditions such as asthma, infections, autoimmune diseases, and cancer. Selective expression of surface and intracellular proteins provides unique immunophenotypic properties to the immune cells of the lung. Consequently, flow cytometry has an instrumental role in the identification of such cell populations during steady-state and pathological conditions. This paper presents a protocol that describes a consistent and reproducible method to identify the immune cells that reside in the lungs of healthy mice under steady-state conditions. However, this protocol can also be used to identify changes in these cell populations in various disease models to help identify disease-specific changes in the lung immune landscape.

In this study, we present an effective and reproducible protocol to isolate the immune populations of the murine respiratory system. We also provide a method for the identification of all innate and adaptive immune cells that reside in the lungs of healthy mice, using a 9-color-based flow cytometry panel.

The respiratory tract is in direct contact with the outside environment and requires a precisely regulated immune system to provide protection while ...

Isolation of Uterine Innate Lymphoid Cells for Analysis by Flow Cytometry

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