This work was supported in part by a DoD Breakthrough Award to AMW (BCRP W81XWH-14-1-0425). KCR was partially supported by intramural fellowships: the Pease Cancer Pre-Doctoral Fellowship and the Mary Galvin Burden Pre-Doctoral Fellowship in Biomedical Sciences and University of California, Riverside, intramural awards: the Graduate Council Fellowship Committee Dissertation Research Grant and the Graduate Division Dissertation Year Program Award. The authors thank Gillian M. Wright and Alyssa M. Kumari for assistance in early troubleshooting of this method.

All animal handling and procedures were approved by the University of California, Riverside institutional animal care and use committee and were in accordance with guidelines from the American Association for Laboratory Animal Care, the United States Department of Agriculture, and the National Institutes of Health. The described method utilized C57BL/6 adult, female mice. All animals were euthanized by decapitation prior to tissue harvesting.
NOTE: An overview of the protocol, which uses a blue dye to assist in efficient dissection and uncoiling of the oviduct, is shown in the first figure (Figure 1).
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/63168/63168fig01.jpg" /> 
Figure 1: Overview of the microdissection method. (A) Left panel shows the intact structure from which most of the ovarian fat pad and remnants of connective tissue surrounding the oviduct have been removed. After this, the addition of toluidine blue helps distinguish the coils of the oviduct (middle panel). Right panel shows structures after the removal of the ovary. (B) An uncoiled oviduct with internal turns for determining where each segment begins and ends. (C) Cartoon of the segmentation used (not drawn to scale). <a href="https://www.jove.com/files/ftp_upload/63168/63168fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
1. Preparation of the dissection surface
<ol>
	<li>Affix a piece of dental wax to a Petri dish with adhesive and let it dry (Figure 2A). Sanitize the dish with 70% ethanol. The surface is ready for dissection.</li>
</ol>
2. Macrodissection of the ovary, oviduct, and uterus
<ol>
	<li>Immobilize the Petri dish containing the dental wax on a cold platform of choice (e.g., an ice pack kept at -20 &#176;C prior to use) under a dissection microscope when ready for dissection (Figure 2A).</li>
	<li>Disinfect the ventral surface of the animal with 70% ethanol. Open the abdominal and pelvic cavity with sterile dissection scissors and move the gastrointestinal tract to one side to locate the dorsal bihornal uterus. Follow each uterine horn rostrally to locate each oviduct and ovary enveloped in the uterine fat pad, found just below the kidney (Figure 2B,C).</li>
	<li>Excise both lateral oviducts with the ovaries and a portion of the distal uterine horn still attached using dissection scissors. Cut each lateral uterine horn with approximately 1-2 cm of the horn still attached to the coiled oviduct and ovary (Figure 2D). Submerge the tissue immediately in 2 mL of cold dissection medium (see Table of materials).</li>
</ol>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/63168/63168fig02.jpg" /> 
Figure 2: Macrodissection of the ovary and the dissection setup. The oviduct is located dorsally in the pelvic cavity at the base of the kidney within the ovarian fat pad (B). Locate the uterine bifurcation in the pelvic cavity (C) and follow the lateral uterine horn to locate the uterus-oviduct-ovary continuum (B). Remove these structures by cutting through one uterine horn and coarse dissection. Place onto the dissecting platform (A) and affix the uterine portion to dental wax with a needle (A and D). <a href="https://www.jove.com/files/ftp_upload/63168/63168fig02large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
NOTE: Leave enough uterine horn intact and attached to the oviduct to allow affixation to the dissection platform (Figure 2D).
<ol start="4">
	<li>Affix the uterine tissue to the dental wax with a sterile 25 G needle to secure tissue for dissection (Figure 2A,D, and Figure 3A). Working under the dissection microscope, clean and dissect away the ovarian fat pad and connective tissue to allow clear visualization of the oviduct (Figure 3B).</li>
</ol>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/63168/63168fig03.jpg" /> 
Figure 3: Step by step oviduct microdissection. Following removal of remnant fat and connective tissue (A,B), add toluidine blue to the tissue (C), and then wash away to facilitate visualization and subsequent removal of the ovary and uncoiling of the tube (D-H). The infundibulum can be found beside the proximal isthmus and uterine-tubal junction (UTJ). Lightly pull the distal end while cutting at the mesosalpinx to uncoil and reveal the endogenous turns of the oviduct (H) to orient for appropriate segmentation. Figure A-C scale bar = 500 &#956;m, D-H scale bar = 400 &#956;m (I) Cartoon of the various segments (not drawn to scale). <a href="https://www.jove.com/files/ftp_upload/63168/63168fig03large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<ol start="5">
	<li>Using a 1 mL syringe, dispense and incubate the oviduct affixed to the uterus in 1-2 drops of sterile 1% toluidine blue dye solution&#160;for 30 s-1 min. Rinse with cold Dulbecco&#39;s phosphate-buffered saline (DPBS) and remove all the liquid (Figure 3C).</li>
	<li>Lightly pull the ovary from the coiled oviduct and cut away at the bursal membrane and broad ligament to remove the ovary from the oviduct without compromising the tubal tissue (Figure 3D,E). 
	&#8203;NOTE: The ovary is not attached to the oviduct but encased in the bursal membrane with the oviduct (Figure 2D) and connected to the lateral side of the uterus via the broad ligament.</li>
</ol>
3. Microdissection and segmentation of the oviduct
<ol>
	<li>Locate the distal, fimbrial end of the oviduct found lateral to the uterine-tubal junction (UTJ). The oviduct coils back on itself; hence the fimbrial end can be located lateral to the proximal end and is an appropriate starting point to orient for uncoiling of the oviduct (Figure 3F,I).
	<ol>
		<li>While gently pulling the tube, cut away at the mesosalpinx (Figure 3I) with spring-form micro-scissors to uncoil the oviduct (Figure 3G).</li>
	</ol>
	</li>
	<li>Once uncoiled, cut the tube to produce the infundibular, ampullary, and isthmic regions (Figure 3H).
	<ol>
		<li>Following excision of the infundibulum (fimbrial end and proximal stalk), excise the ampullary region by cutting after the second prominent turn of the tube (cut between turns two and three, approximately 1 cm in length). Finally, cut the remaining portion to the UTJ, which is the isthmic region (Figure 3H). 
		NOTE: The oviduct will not completely uncoil into a straight structure. The tube will maintain its turns (Figure 3H)3. Based on the subsequent turns following the ampullary region, one may further segment the remaining tube into the ampullary-isthmic junction and isthmus3. Following ampulla excision, cut between turns five and six to obtain the ampullary-isthmic junction; the remaining tube (turn six to the start of the UTJ) is the isthmus3.</li>
	</ol>
	</li>
	<li>Immediately snap freeze dissected tissue segments in liquid nitrogen for RNA isolation or fix and process each segment for oriented embedding and immunohistological analysis.
	<ol>
		<li>Add 200 &#956;L of cold RNA extraction reagent and 1:1 homogenization bead mix (see Table of materials) to the tissue if proceeding for RNA extraction (see step 5.1).</li>
	</ol>
	</li>
</ol>
4. Oviduct dissociation
<ol>
	<li>Continued from step 3.1.1 above) For optimal dissociation of the epithelium, slit open the oviduct in the areas where possible (i.e., infundibulum and ampulla) to expose the luminal epithelium (Figure 4A).</li>
</ol>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/63168/63168fig04.jpg" /> 
Figure 4: Oviduct cell dissociation, part 1. Cartoon showing how to expose the distal epithelium for optimal cell dissociation (A) and an image showing the easiest way to use the 1 mm2 mesh (B). <a href="https://www.jove.com/files/ftp_upload/63168/63168fig04large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<ol start="1" style="margin-left: 40px;">
	<li>Starting at the fimbrial region, using forceps as leverage, slit the tube longitudinally with spring-form scissors.</li>
</ol>
<ol start="2">
	<li>Mince the slit-open portions and the remaining oviduct into segments (~1-2 mm in size) and add 5 mL of warm, non-enzymatic dissociation buffer (see Table of Materials) and incubate at 37 &#176;C.
	<ol>
		<li>Resuspend the tissue pieces and dissociated cells with a bulb pipettor every 3 min for 9-10 min. Dilute the dissociation buffer 1:1 with cold dissection medium.</li>
	</ol>
	</li>
	<li>Collect the cells by centrifugation (350 x g, 3 min, 4 &#176;C). Resuspend the cells in 2 mL of RBC lysis buffer for 2 min at room temperature, and then dilute 1:1 with cold dissection medium.</li>
	<li>Collect the cells by centrifugation (350 x g, 3 min, 4 &#176;C) and resuspend in 5 mL of cold pronase solution.
	<ol>
		<li>Incubate in pronase digestion medium and resuspend the cell clumps with a bulb pipettor every 3-5 min until a single cell suspension is achieved (~25-30 min). 
		NOTE: This step is best performed in a tissue culture plate or flask to allow constant observation preventing unnecessary overexposure to pronase.</li>
	</ol>
	</li>
	<li>Pass the cells through a sterile macro-mesh (1 mm x 1 mm mesh affixed to a conical tube with a rubber band (Figure 4B)) to remove any remaining undissociated tissue pieces. Collect the cells by centrifugation (350 x g, 3 min, 4 &#176;C) and resuspend them in a cold medium appropriate for downstream analysis (e.g., FACS buffer if proceeding with staining for flow cytometry).</li>
</ol>
5. RNA extraction of oviductal segments
<ol>
	<li>Homogenize snap-frozen samples in 200 &#181;L of RNA extraction reagent in a bead bullet blender tissue homogenizer on level 12 for two intervals (3 min each) at 4 &#176;C using the stainless-steel bead mix. 
	NOTE: To preserve RNA integrity, samples should be immediately moved from snap-frozen state into RNA extraction reagent and not weighed.</li>
	<li>Briefly centrifuge homogenate at 100-200 x g in a tabletop centrifuge for approximately 5 s at room temperature to separate the liquid from the beads. Transfer the supernatant to a fresh tube.</li>
	<li>Add another 200 &#181;L of RNA extraction reagent to the beads to recover more samples, followed by centrifugation (100-200 x g, 5 s, room temperature). Combine the supernatants. 
	NOTE: Use a small pipette tip (most p200 tips are suitable) to prevent bead carryover when removing the supernatant.</li>
	<li>Follow manufacturer&#39;s guidelines to phase separate and precipitate RNA. Representative samples were precipitated overnight at -20 &#176;C with 100% isopropanol (approximately 2:1 volume, isopropanol: recovered aqueous phase).</li>
	<li>Transfer the complete RNA precipitate along with the solution to an RNA-binding spin column and centrifuge for 30 s at 9,500 x g. Purify the RNA on-column as per the manufacturer&#39;s guidelines, and then elute the RNA in 20 &#181;L of nuclease-free water. Assess the quality/quantity on a microvolume spectrophotometer and/or bioanalyzer.</li>
</ol>

<ol>
	<li>Stewart, C. A., et al., Kubiak, J. Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Mouse oviduct developmemt in Mouse Development: From Oocyte to Stem Cells. , 247-262 (2012).</li><li>Ford, M. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Oviduct+epithelial+cells+constitute+two+developmentally+distinct+lineages+that+are+spatially+separated+along+the+distal-proximal+axis.">Oviduct epithelial cells constitute two developmentally distinct lineages that are spatially separated along the distal-proximal axis.</a> Cell Reports. 36 (10), 109677 (2021).</li><li>Harwalkar, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Anatomical+and+cellular+heterogeneity+in+the+mouse+oviduct-its+potential+roles+in+reproduction+and+preimplantation+development.">Anatomical and cellular heterogeneity in the mouse oviduct-its potential roles in reproduction and preimplantation development.</a> Biology of Reproduction. 104 (6), 1249-1261 (2021).</li><li>Agduhr, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Studies+on+the+structure+and+development+of+the+bursa+ovarica+and+the+tuba+uterina+in+the+mouse.">Studies on the structure and development of the bursa ovarica and the tuba uterina in the mouse.</a> Acta Zoologica. 8 (1), 1 (1927).</li><li>Pulkkinen, M. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Oviductal+function+is+critical+for+very+early+human+life.">Oviductal function is critical for very early human life.</a> Annals of Medicine. 27 (3), 307-310 (1995).</li><li>Kindelberger, D. W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Intraepithelial+carcinoma+of+the+fimbria+and+pelvic+serous+carcinoma:+Evidence+for+a+causal+relationship.">Intraepithelial carcinoma of the fimbria and pelvic serous carcinoma: Evidence for a causal relationship.</a> American Journal of Surgical Pathology. 31 (2), 161-169 (2007).</li><li>Ghosh, A., Syed, S. M., Tanwar, P. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vivo+genetic+cell+lineage+tracing+reveals+that+oviductal+secretory+cells+self-renew+and+give+rise+to+ciliated+cells.">In vivo genetic cell lineage tracing reveals that oviductal secretory cells self-renew and give rise to ciliated cells.</a> Development. 144 (17), 3031-3041 (2017).</li><li>Lee, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+candidate+precursor+to+serous+carcinoma+that+originates+in+the+distal+fallopian+tube.">A candidate precursor to serous carcinoma that originates in the distal fallopian tube.</a> Journal of Pathology. 211 (1), 26-35 (2007).</li><li>Kim, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-grade+serous+ovarian+cancer+arises+from+fallopian+tube+in+a+mouse+model.">High-grade serous ovarian cancer arises from fallopian tube in a mouse model.</a> Proceedings of the National Academy of Sciences of the United States of America. 109 (10), 3921-3926 (2012).</li><li>Perets, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transformation+of+the+fallopian+tube+secretory+epithelium+leads+to+high-grade+serous+ovarian+cancer+in+Brca;Tp53;Pten+models.">Transformation of the fallopian tube secretory epithelium leads to high-grade serous ovarian cancer in Brca;Tp53;Pten models.</a> Cancer Cell. 24 (6), 751-765 (2013).</li><li>Sherman-Baust, C. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+genetically+engineered+ovarian+cancer+mouse+model+based+on+fallopian+tube+transformation+mimics+human+high-grade+serous+carcinoma+development.">A genetically engineered ovarian cancer mouse model based on fallopian tube transformation mimics human high-grade serous carcinoma development.</a> Journal of Pathology. 233 (3), 228-237 (2014).</li><li>Zhai, Y. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-grade+serous+carcinomas+arise+in+the+mouse+oviduct+via+defects+linked+to+the+human+disease.">High-grade serous carcinomas arise in the mouse oviduct via defects linked to the human disease.</a> Journal of Pathology. 243 (1), 16-25 (2017).</li><li>Karthikeyan, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Prolactin+signaling+drives+tumorigenesis+in+human+high+grade+serous+ovarian+cancer+cells+and+in+a+spontaneous+fallopian+tube+derived+model.">Prolactin signaling drives tumorigenesis in human high grade serous ovarian cancer cells and in a spontaneous fallopian tube derived model.</a> Cancer Letters. 433, 221-231 (2018).</li><li>Shao, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Differences+in+prolactin+receptor+(PRLR)+in+mouse+and+human+fallopian+tubes:+Evidence+for+multiple+regulatory+mechanisms+controlling+PRLR+isoform+expression+in+mice.">Differences in prolactin receptor (PRLR) in mouse and human fallopian tubes: Evidence for multiple regulatory mechanisms controlling PRLR isoform expression in mice.</a> Biology of Reproduction. 79 (4), 748-757 (2008).</li><li>Alwosaibai, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PAX2+maintains+the+differentiation+of+mouse+oviductal+epithelium+and+inhibits+the+transition+to+a+stem+cell-like+state.">PAX2 maintains the differentiation of mouse oviductal epithelium and inhibits the transition to a stem cell-like state.</a> Oncotarget. 8 (44), 76881-76897 (2017).</li><li>Peri, L. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+novel+class+of+interstitial+cells+in+the+mouse+and+monkey+female+reproductive+tracts.">A novel class of interstitial cells in the mouse and monkey female reproductive tracts.</a> Biology of Reproduction. 92 (4), 102 (2015).</li><li>L&#245;hmussaar, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Assessing+the+origin+of+high-grade+serous+ovarian+cancer+using+CRISPR-modification+of+mouse+organoids.">Assessing the origin of high-grade serous ovarian cancer using CRISPR-modification of mouse organoids.</a> Nature Communications. 11 (1), 2660 (2020).</li><li>Chen, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+air-liquid+interphase+approach+for+modeling+the+early+embryo-maternal+contact+zone.">An air-liquid interphase approach for modeling the early embryo-maternal contact zone.</a> Scientific Reports. 7, 42298 (2017).</li><li>Desjardins, P., Conklin, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=NanoDrop+microvolume+quantitation+of+nucleic+acids.">NanoDrop microvolume quantitation of nucleic acids.</a> Journal of Visualized Experiments: JoVE. (45), e2565 (2010).</li><li>Schroeder, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+RIN:+an+RNA+integrity+number+for+assigning+integrity+values+to+RNA+measurements.">The RIN: an RNA integrity number for assigning integrity values to RNA measurements.</a> BMC Molecular Biology. 7, 3 (2006).</li><li>McGlade, E. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cell-type+specific+analysis+of+physiological+action+of+estrogen+in+mouse+oviducts.">Cell-type specific analysis of physiological action of estrogen in mouse oviducts.</a> The FASEB Journal. 35 (5), 21563 (2021).</li></ol>

The authors have nothing to disclose.

The three segments of the oviduct are histologically, morphologically, and functionally distinct1,2,3. The epithelium varies greatly from one end of the oviduct to the other. Ciliated cells dominate at the fimbrial/infundibular end, while secretory cells dominate in the isthmic region1. While this overall gradient has been recognized for some time, recent work has uncovered more distinctions among the ovi...

The murine oviduct is similar in function and morphology to the human fallopian tube1. Both consist of a pseudostratified ciliated epithelium, consisting of two historically described epithelial resident cells: ciliated cells and secretory cells1,2. The oviduct has three classically recognized segments: the infundibulum, the ampulla, and the isthmus. In a recent study, Harwalkar et al.3 investigated oviduct morphology and gene expression leading to the expansion of the categorization of resident epithelial cells to seven distinct populations. In addition, they established the ampullary-isthmus junction as a distinct segment of the oviduct3. The method described herein, which focuses on the infundibulum, ampulla, and isthmus, could easily be extended to include the ampullary-isthmic junction as well2,3. The infundibular region contains the ostium, or opening of the oviduct, and includes the fimbrial region as well as the proximal stalk. Moving toward the uterus, next is the ampulla, and then the isthmus. Ciliated cells are most prominent in the distal end of the region, proximal to the ovary, or infundibulum, while secretory cells are most prominent in the proximal end or isthmus segment1. Unlike the human fallopian tube, the murine oviduct is a coiled structure supported by the mesosalpinx, an extension of the broad ligament peritoneum1,4. In addition, the mouse oviduct is encased in a bursal sac that increases the likelihood of oocyte transfer into the oviduct4. The ampulla is identified as the location of fertilization, from which developing embryos pass into the isthmus before entering the uterus5. Tubal segments are 200-400 &#956;m in diameter and the longer ampullary and isthmus regions are approximately 0.5-1.0 cm in length4. The oviduct distends during the estrous cycle and the ampulla and infundibulum are more distensible than the isthmus1.
Over proliferation of cells, especially secretory cells, characterize precursor lesions to serous tumors found in the pelvic cavity6. These precursor serous intraepithelial lesions arise in the oviduct epithelium solely in the fimbrial region; it is unknown why lesion formation is restricted to this region where normally the predominant cell type is ciliated, not secretory2,7,8. The regionality in terms of normal physiological function, as well as heightened interest in the oviductal origin of ovarian cancer9,10,11,12,13, underscores the importance of separate evaluation of the oviduct segments.
The method described here details the collection of separate oviductal segments for subsequent downstream analyses of segment-specific gene expression and function of dissociated cells. Traditionally, many tissues are processed for whole RNA extraction following either the phenol: chloroform method or an on-column complete extraction method; however, we found that RNA quality was maintained while producing sufficient yield with the described combination method. Utilizing this method, very small functional segments of the oviduct can be processed for downstream analyses rather than investigating the oviduct as a whole, which can mask results representative of the different segments14.
Dissociated murine oviductal cells have rarely been investigated by flow cytometry, most likely due to the limiting cell yield from this tissue. One approach to overcome this problem has been to dissociate cells, grow them in culture, and then stimulate re-differentiation in vitro to obtain appropriate cell numbers for downstream cell analysis15,16,17,18. A limitation to this approach is the time ex vivo and altered microenvironment in culture, both of which likely change gene expression. There is also an assumption that morphological re-differentiation has the same transcriptional and proteomic signature as was present in the intact animal. The current dissociation method was designed to achieve the highest number of epithelial cells in a heterogenous oviductal cell population while maintaining single cell differentiation. Further, the mostly non-enzymatic approach likely limits the loss of cell surface proteins.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>0.5 mm Stainless steel bead mix</td>
			<td>Next Advance</td>
			<td>SSB05</td>
			<td>Mix 1:1 with 1.4 mm SSB14B, sterilized</td>
		</tr>
		<tr>
			<td>1.4 mm Stainless steel bead mix</td>
			<td>Next Advance</td>
			<td>SSB14B</td>
			<td>Mix 1:1 with 0.5 mm SSB05, sterilized</td>
		</tr>
		<tr>
			<td>1X Dulbecco&#39;s Phosphate Buffered Saline A, pH 7.4 (DPBS)</td>
			<td>Gibco</td>
			<td>21600-010</td>
			<td>Cold, sterile</td>
		</tr>
		<tr>
			<td>25G needle</td>
			<td>BD</td>
			<td>305122</td>
			<td></td>
		</tr>
		<tr>
			<td>60 mm sterile petri dishes</td>
			<td>Corning</td>
			<td>430166</td>
			<td></td>
		</tr>
		<tr>
			<td>70 &#956;m cell meshes</td>
			<td>Fisherbrand</td>
			<td>22-636-548</td>
			<td></td>
		</tr>
		<tr>
			<td>Agilent Eukaryote Total RNA 6000 Pico Chip kit</td>
			<td>Agilent 2100 Bioanalyzer</td>
			<td>5067-1513</td>
			<td></td>
		</tr>
		<tr>
			<td>Bead Bullet Blender Tissue Homogenizer</td>
			<td>Next Advance</td>
			<td>BBY24M</td>
			<td></td>
		</tr>
		<tr>
			<td>Bioanlyzer</td>
			<td>Agilent 2100 Bioanalyzer</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Bovine serum albumin</td>
			<td>Sigma Aldrich</td>
			<td>A7906</td>
			<td></td>
		</tr>
		<tr>
			<td>Cold plate/pack/surface of choice</td>
			<td>N/A</td>
			<td>N/A</td>
			<td>Kept at -20C for dissection</td>
		</tr>
		<tr>
			<td>Dental wax</td>
			<td>Polysciences Inc.</td>
			<td>403</td>
			<td></td>
		</tr>
		<tr>
			<td>Dulbecco&#8217;s Modified Eagle&#8217;s Medium (DMEM)/ Ham&#8217;s F12</td>
			<td>Corning</td>
			<td>10-090-CV</td>
			<td>Prepare dissection medium: DMEM/ Ham&#8217;s F12, 10% FBS, 25 mM Hepes, 1% Pen-Strep</td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum</td>
			<td>Corning</td>
			<td>35-015CV</td>
			<td></td>
		</tr>
		<tr>
			<td>Fine point forceps of choice</td>
			<td>N/A</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycine</td>
			<td>Sigma Aldrich</td>
			<td>G712b</td>
			<td>Immunocytochemical validation images</td>
		</tr>
		<tr>
			<td>Goat anti-mouse IgG Alexa Fluor 555</td>
			<td>Invitrogen</td>
			<td>A-21422</td>
			<td>Immunocytochemical validation images</td>
		</tr>
		<tr>
			<td>Goat anti-rabbit IgG Alexa Fluor 488</td>
			<td>Invitrogen</td>
			<td>A-11001</td>
			<td>Immunocytochemical validation images</td>
		</tr>
		<tr>
			<td>Hepes</td>
			<td>Sigma Aldrich</td>
			<td>H-3784</td>
			<td></td>
		</tr>
		<tr>
			<td>Hoescht 33342</td>
			<td>Cell Signaling Technologies</td>
			<td>4082S</td>
			<td>Immunocytochemical validation images</td>
		</tr>
		<tr>
			<td>Inverted compound microscope</td>
			<td>Keyence BZ-X700</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Mouse anti-mouse Occludin</td>
			<td>Invitrogen</td>
			<td>33-1500</td>
			<td>Immunocytochemical validation images</td>
		</tr>
		<tr>
			<td>Non-enzymatic dissociation buffer</td>
			<td>N/A</td>
			<td></td>
			<td>5 mM EDTA, 1 g/L glucose, 0.4% BSA, 1X DPBS</td>
		</tr>
		<tr>
			<td>Nylon macro-mesh 1 mm x 1 mm</td>
			<td>Thomas Scientific</td>
			<td>1210U04</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraformaldehyde</td>
			<td>Sigma Aldrich</td>
			<td>P-6148</td>
			<td>Immunocytochemical validation images</td>
		</tr>
		<tr>
			<td>Pen-Strep</td>
			<td>MP Biomedicals</td>
			<td>10220-718</td>
			<td></td>
		</tr>
		<tr>
			<td>Prolong Gold Antifade Reagent</td>
			<td>Cell Signaling Technologies</td>
			<td>9071S</td>
			<td>Immunocytochemical validation images: antifade mounting medium</td>
		</tr>
		<tr>
			<td>Pronase</td>
			<td>Sigma Aldrich</td>
			<td>10165921001</td>
			<td>Prepare pronase digestion medium: 0.15% Pronase in DMEM/Ham&#39;s F12, sterile</td>
		</tr>
		<tr>
			<td>Propidium Iodide</td>
			<td>Roche</td>
			<td>11 348 639 001</td>
			<td>Viability validation images</td>
		</tr>
		<tr>
			<td>Rabbit anti-mouse Acetylated-Tubulin</td>
			<td>Abcam</td>
			<td>ab179484</td>
			<td>Immunocytochemical validation images</td>
		</tr>
		<tr>
			<td>RBC lysis buffer</td>
			<td>BD Biosciences</td>
			<td>555899</td>
			<td></td>
		</tr>
		<tr>
			<td>RNeasy Mini Kit</td>
			<td>Qiagen</td>
			<td>74134</td>
			<td>Utilized for on-column purification in text.</td>
		</tr>
		<tr>
			<td>Spring form microdissection scissors</td>
			<td>Roboz Surgical</td>
			<td>RS-5610</td>
			<td></td>
		</tr>
		<tr>
			<td>Sterile 3 mL bulb pipettors</td>
			<td>Globe Scientific</td>
			<td>137135</td>
			<td></td>
		</tr>
		<tr>
			<td>Toluidine blue</td>
			<td>Alfa Aesar</td>
			<td>J66015</td>
			<td>Prepare toluidine blue solution: 1% in 1X DPBS, sterile</td>
		</tr>
		<tr>
			<td>Tris-Buffered Saline-Tween (TBST)</td>
			<td>N/A</td>
			<td>N/A</td>
			<td>Immunocytochemical validation images; 0.1 N NaCl, 10 mM Tris-Cl pH 7.5, 1% Tween 20</td>
		</tr>
		<tr>
			<td>Triton-X-100</td>
			<td>Mallinckrodt Inc.</td>
			<td>3555</td>
			<td>Immunocytochemical validation images</td>
		</tr>
		<tr>
			<td>Trizol RNA Extraction Reagent</td>
			<td>Invitrogen</td>
			<td>15596026</td>
			<td>Referred to as RNA extraction reagent. Nucelase-free water, chloroform and isoproponal are required in supplement of performing Trizol extraction per manufacturer&#39;s guidelines</td>
		</tr>
	</tbody>
</table>

microdissection and dissociation of the murine oviduct: individual segment identification and single cell isolation

Mouse model systems are unmatched for the analysis of disease processes because of their genetic manipulability and the low cost of experimental treatments. However, because of their small body size, some structures, such as the oviduct with a diameter of 200-400 &#956;m, have proven to be relatively difficult to study except by immunohistochemistry. Recently, immunohistochemical studies have uncovered more complex differences in oviduct segments than were previously recognized; thus, the oviduct is divided into four functional segments with different ratios of seven distinct epithelial cell types. The different embryological origins and ratios of the epithelial cell types likely make the four functional regions differentially susceptible to disease. For example, precursor lesions to serous intraepithelial carcinomas arise from the infundibulum in mouse models and from the corresponding fimbrial region in the human fallopian tube. The protocol described here details a method for microdissection to subdivide the oviduct in such a way to yield a sufficient amount and purity of RNA necessary for downstream analysis such as reverse transcription-quantitative PCR (RT-qPCR) and RNA sequencing (RNAseq). Also described is a mostly non-enzymatic tissue dissociation method appropriate for flow cytometry or single cell RNAseq analysis of fully differentiated oviductal cells. The methods described will facilitate further research utilizing the murine oviduct in the field of reproduction, fertility, cancer, and immunology.

The described dissociation protocol yields 100,000-120,000 cells per mouse with pooling of both oviducts. The method is gentle enough to leave multi-ciliated cell borders intact, allowing for a distinction between multi-ciliated cells and secretory cells, and verifying that the digestion method is gentle enough to prevent de-differentiation. Representative immunofluorescence images in Figure 5 show small cell clumps following step 4.2.1, fixed for 3 min in 4% paraformaldehyde (PFA)/ DPBS, wa...

Watch this Scientific Journal Video about Microdissection and Dissociation of the Murine Oviduct: Individual Segment Identification and Single Cell Isolation at JoVE.com

Microdissection and Dissociation of the Murine Oviduct: Individual Segment Identification and Single Cell Isolation

A method for microdissection of the mouse oviduct that allows collection of the individual segments while maintaining RNA integrity is presented. In addition, non-enzymatic oviductal cell dissociation procedure is described. The methods are appropriate for subsequent gene and protein analysis of the functionally different oviductal segments and dissociated oviductal cells.

Mouse model systems are unmatched for the analysis of disease processes because of their genetic manipulability and the low cost of experimental ...

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Research

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Developmental Biology

3.6K Views.  University of California, Riverside. A method for microdissection of the mouse oviduct that allows collection of the individual segments while maintaining RNA integrity is presented. In addition, non-enzymatic oviductal cell dissociation procedure is described. The methods are appropriate for subsequent gene and protein analysis of the functionally different oviductal segments and dissociated oviductal cells.

Video: Microdissection and Dissociation of the Murine Oviduct: Individual Segment Identification and Single Cell Isolation

Murine Dermal Fibroblast Isolation by FACS

Fibroblasts are the principle cell type responsible for secreting extracellular matrix and are a critical component of many organs and tissues. Fibroblast physiology and pathology underlie a spectrum of clinical entities, including fibroses in multiple organs, hypertrophic scarring following burns, loss of cardiac function following ischemia, and the formation of cancer stroma. However, fibroblasts remain a poorly characterized type of cell, largely due to their inherent heterogeneity. Existing methods for the isolation of fibroblasts require time in cell culture that profoundly influences cell phenotype and behavior. Consequently, many studies investigating fibroblast biology rely upon in vitro manipulation and do not accurately capture fibroblast behavior in vivo. To overcome this problem, we developed a FACS-based protocol for the isolation of fibroblasts from the dorsal skin of adult mice that does not require cell culture, thereby preserving the physiologic transcriptional and proteomic profile of each cell. Our strategy allows for exclusion of non-mesenchymal lineages via a lineage negative gate (Lin-) rather than a positive selection strategy to avoid pre-selection or enrichment of a subpopulation of fibroblasts expressing specific surface markers and be as inclusive as possible across this heterogeneous cell type.

Fibroblast behavior underlies a spectrum of clinical entities, but they remain poorly characterized, largely due to their inherent heterogeneity. Traditional fibroblast research relies upon in vitro manipulation, masking in vivo fibroblast behavior. We describe a FACS-based protocol for the isolation of mouse skin fibroblasts that does not require cell culture.

Fibroblasts are the principle cell type responsible for secreting extracellular matrix and are a critical component of many organs and tissues. Fibroblast ...

Isolation and Characterization of Single Cells from Zebrafish Embryos

The zebrafish (Danio rerio) is a powerful model organism to study vertebrate development. Though many aspects of zebrafish embryonic development have been described at the morphological level, little is known about the molecular basis of cellular changes that occur as the organism develops. With recent advancements in microfluidics and multiplexing technologies, it is now possible to characterize gene expression in single cells. This allows for investigation of heterogeneity between individual cells of specific cell populations to identify and classify cell subtypes, characterize intermediate states that occur during cell differentiation, and explore differential cellular responses to stimuli. This study describes a protocol to isolate viable, single cells from zebrafish embryos for high throughput multiplexing assays. This method may be rapidly applied to any zebrafish embryonic cell type with fluorescent markers. An extension of this method may also be used in combination with high throughput sequencing technologies to fully characterize the transcriptome of single cells. As proof of principle, the relative abundance of cardiac differentiation markers was assessed in isolated, single cells derived from nkx2.5 positive cardiac progenitors. By evaluation of gene expression at the single cell level and at a single time point, the data support a model in which cardiac progenitors coexist with differentiating progeny. The method and work flow described here is broadly applicable to the zebrafish research community, requiring only a labeled transgenic fish line and access to microfluidics technologies.

This protocol describes a method for isolating single cells from zebrafish embryos, enriching for cells of interest, capturing zebrafish cells in microfluidic based single cell multiplex systems, and assessing gene expression from single cells.

The zebrafish (Danio rerio) is a powerful model organism to study vertebrate development. Though many aspects of zebrafish embryonic development have been ...

Isolation of Murine Embryonic Hemogenic Endothelial Cells

The specification of hemogenic endothelial cells from embryonic vascular endothelium occurs during brief developmental periods within distinct tissues, and is necessary for the emergence of definitive HSPC from the murine extra embryonic yolk sac, placenta, umbilical vessels, and the embryonic aorta-gonad-mesonephros (AGM) region. The transient nature and small size of this cell population renders its reproducible isolation for careful quantification and experimental applications technically difficult. We have established a fluorescence-activated cell sorting (FACS)-based protocol for simultaneous isolation of hemogenic endothelial cells and HSPC during their peak generation times in the yolk sac and AGM. We demonstrate methods for dissection of yolk sac and AGM tissues from mouse embryos, and we present optimized tissue digestion and antibody conjugation conditions for maximal cell survival prior to identification and retrieval via FACS. Representative FACS analysis plots are shown that identify the hemogenic endothelial cell and HSPC phenotypes, and describe a methylcellulose-based assay for evaluating their blood forming potential on a clonal level.

Hematopoietic stem and progenitor cells (HSPC) derive from specialized (hemogenic) endothelial cells during development, yet little is known about the process by which some endothelial cells specify to become blood forming. We demonstrate a flow-cytometry based method allowing simultaneous isolation of hemogenic endothelial cells and HSPC from murine embryonic tissues.

The specification of hemogenic endothelial cells from embryonic vascular endothelium occurs during brief developmental periods within distinct tissues, ...

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 ...

Cell Dissociation from the Tongue Epithelium and Mesenchyme/Connective Tissue of Embryonic-Day 12.5 and 8-Week-Old Mice

Cell dissociation has been an essential procedure for studies at the individual-cell level and/or at a cell-population level (e.g.,&#160;single cell RNA sequencing and primary cell culture). Yielding viable, healthy cells in large quantities is critical, and the optimal conditions to do so are tissue dependent. Cell populations in the tongue epithelium and underlying mesenchyme/connective tissue are heterogeneous and tissue structures vary in different regions and at different developmental stages. We have tested protocols for isolating cells from the mouse tongue epithelium and mesenchyme/connective tissue in the early developmental [embryonic day 12.5 (E12.5)] and young adult (8-week) stages. A clean separation between the epithelium and underlying mesenchyme/connective tissue was easy to accomplish. However, to further process and isolate cells, yielding viable healthy cells in large quantities, and careful selection of enzymatic digestion buffer, incubation time, and centrifugation speed and time are critical. Incubation of separated epithelium or underlying mesenchyme/connective tissue in 0.25% Trypsin-EDTA for 30 min at 37 &#176;C, followed by centrifugation at 200 x g for 8 min resulted in a high yield of cells at a high viability rate (&#62;90%) regardless of the mouse stages and tongue regions. Moreover, we found that both dissociated epithelial and mesenchymal/connective tissue cells from embryonic and adult tongues could survive in the cell culture-based medium for at least 3 h without a significant decrease of cell viability. The protocols will be useful for studies that require the preparation of isolated cells from mouse tongues at early developmental (E12.5) and young adult (8-week) stages requiring cell dissociation from different tissue compartments.

We have developed a generalized protocol to dissociate a large quantity of high-quality single cells from the epithelium and mesenchyme/connective tissue of embryonic and adult mouse tongues.

Cell dissociation has been an essential procedure for studies at the individual-cell level and/or at a cell-population level (e.g.,&#160;single cell RNA ...

Identification and Isolation of Burst-Forming Unit and Colony-Forming Unit Erythroid Progenitors from Mouse Tissue by Flow Cytometry

Early erythroid progenitors were originally defined by their colony-forming potential in vitro and classified into burst-forming and colony-forming &#34;units&#34; known as BFU-e and CFU-e. Until recently, methods for the direct prospective and complete isolation of pure BFU-e and CFU-e progenitors from freshly isolated adult mouse bone marrow were not available. To address this gap, a single-cell RNA-seq (scRNAseq) dataset of mouse bone marrow was analyzed for the expression of genes coding for cell surface markers. This analysis was combined with cell fate assays, allowing the development of a novel flow cytometric approach that identifies and allows the isolation of complete and pure subsets of BFU-e and CFU-e progenitors in mouse bone marrow or spleen. This approach also identifies other progenitor subsets, including subsets enriched for basophil/mast cell and megakaryocytic potentials. The method consists of labeling fresh bone marrow or spleen cells with antibodies directed at Kit and CD55. Progenitors that express both these markers are then subdivided into five principal populations. Population 1 (P1 or CFU-e, Kit+ CD55+ CD49fmed/low CD105med/high CD71med/high) contains all of the CFU-e progenitors and may be further subdivided into P1-low (CD71med CD150high) and P1-hi (CD71high CD150low), corresponding to early and late CFU-e, respectively; Population 2 (P2 or BFU-e, Kit+ CD55+ CD49fmed/low CD105med/high CD71low CD150high) contains all of the BFU-e progenitors; Population P3 (P3, Kit+ CD55+ CD49fmed/high CD105med/low CD150low CD41low) is enriched for basophil/mast cell progenitors; Population 4 (P4, Kit+ CD55+ CD49fmed/high CD105med/low CD150high CD41+) is enriched for megakaryocytic progenitors; and Population 5 (P5, Kit+ CD55+ CD49fmed/high CD105med/low CD150high CD41-) contains progenitors with erythroid, basophil/mast cell, and megakaryocytic potential (EBMP) and erythroid/ megakaryocytic/ basophil-biased multipotential progenitors (MPPs). This novel approach allows greater precision when analyzing erythroid and other hematopoietic progenitors and also allows for reference to transcriptome information for each flow cytometrically defined population.

Here, we describe a novel flow cytometric method for prospective isolation of early burst-forming unit erythroid (BFU-e) and colony-forming unit erythroid (CFU-e) progenitors directly from fresh mouse bone marrow and spleen. This protocol, developed based on single-cell transcriptomic data, is the first to isolate all the tissue's erythroid progenitors with high purity.

Early erythroid progenitors were originally defined by their colony-forming potential in vitro and classified into burst-forming and colony-forming ...

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

Gut Isolation from Zebrafish Larvae for Single-cell RNA Sequencing

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

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

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

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

Single Cell and Nuclei Extraction from Human Brain Organoids

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

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

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

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

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

Isolation and Genotyping of Gastrulating Mouse Embryo for Single-Cell Sequencing

Single-Cell RNA Sequencing of Mutant Whole Mouse Embryos: From the Epiblast to the End of Gastrulation

Over the last decade, single-cell approaches have become the gold standard for studying gene expression dynamics, cell heterogeneity, and cell states within samples. Before single-cell advances, the feasibility of capturing the dynamic cellular landscape and rapid cell transitions during early development was limited. In this paper, a robust pipeline was designed to perform single-cell and nuclei analysis on mouse embryos from embryonic day E6.5 to E8, corresponding to the onset and completion of gastrulation. Gastrulation is a fundamental process during development that establishes the three germinal layers: mesoderm, ectoderm, and endoderm, which are essential for organogenesis. Extensive literature is available on single-cell omics applied to wild-type perigastrulating embryos. However, single-cell analysis of mutant embryos is still scarce and often limited to FACS-sorted populations. This is partially due to the technical constraints associated with the need for genotyping, timed pregnancies, the count of embryos with desired genotypes per pregnancy, and the number of cells per embryo at these stages. Here, a methodology is presented designed to overcome these limitations. This method establishes breeding and timed pregnancy guidelines to achieve a higher chance of synchronized pregnancies with desired genotypes. Optimization steps in the embryo isolation process coupled with a same-day genotyping protocol (3 h) allow for microdroplet-based single-cell to be performed on the same day, ensuring the high viability of cells and robust results. This method further includes guidelines for optimal nuclei isolations from embryos. Thus, these approaches increase the feasibility of single-cell approaches of mutant embryos at the gastrulation stage. We anticipate that this method will facilitate the analysis of how mutations shape the cellular landscape of the gastrula.

Author Spotlight: A Pipeline to Analyze Lineage-Specific Mutant Embryos at Single-Cell Resolution

This paper establishes a pipeline for high-quality single-cell and nuclei suspensions of gastrulating mouse embryos for sequencing of single cells and nuclei.

Over the last decade, single-cell approaches have become the gold standard for studying gene expression dynamics, cell heterogeneity, and cell states ...