The authors acknowledge U19 AI157984, U01 DK103168, U19 AI144297, P30 DK56338, P01 AI057788, U19 AI116497 grants and NASA Cooperative Agreement Notice/TRISH NNX16AO69A.

The organoid lines used here were obtained from the Texas Medical Center Digestive Disease Center GEMS Core. Briefly, to initially establish organoid lines, donor tissue samples were washed and enzymatically digested to release the intestinal crypts. Crypts were embedded in a basement membrane and cultured in a medium. The Institutional Review Board at Baylor College of Medicine approved the study protocol to obtain tissue samples from which organoid lines were established, and informed consent was obtained from all donors to establish organoid lines from the donated tissue.
1. Passaging of 3D HIOs to expand for differentiation
<ol>
	<li>Remove and discard medium from wells of organoids grown in 24-well plates (around the solid basement membrane) with a P1000 pipet. Add 300 &#181;L of 0.05% Trypsin-EDTA to the well and mechanically break up organoids by pipetting with a P1000 pipet up and down 5x.</li>
	<li>Incubate plate at 37 &#176;C for 4 min. Add 500 &#181;L of complete media without growth factors (CMGF- medium) with 10% FBS to each well (Table 1). Use a P1000 pipet and pipet CMGF medium and HIO mixture, 10x back and forth in the well. Transfer the entire volume into a 15 mL tube. Combine passage from multiple wells into the same 15 mL tube. Do not combine more than 10 wells per tube.</li>
	<li>Spin down cells at 4 &#176;C using a swing rotor centrifuge at 100 x g for 5 min. Remove all the medium, keeping the pellet at the bottom of the tube. Keep the tube on ice.</li>
	<li>Calculate the amount of basement membrane needed for the number of HIO plated, and&#160;resuspend the HIO pellet in 30 &#181;L/well of basement membrane using cold P200 pipet tips. Pipette the HIO basement membrane mixture as a droplet into the center of a 24-well plate using cold P200 pipet tips.</li>
	<li>Transfer the plate to a 37&#160;&#176;C incubator. Let the basement membrane solidify for 5-10 min, then add 500 &#181;L of room temperature complete medium containing WNT, R-spondin, noggin, EGF, and ROCK inhibitor (WRNE+Y; Table 1) to each well and culture in a 37&#160;&#176;C incubator. Refresh culture with WRNE+Y every other day for 7 days. 
	NOTE: A healthy HIO will be cystic in shape with a shiny budding epithelium (Figure 2). Cells in the middle of the cyst cannot be visualized. An unhealthy HIO will look dull and have a thick epithelium with a solid middle. The most important characteristic is the shiny appearance.</li>
</ol>
2. HIO differentiation: 3D format
<ol>
	<li>Use one well of 3D HIOs for 3 wells of 3D differentiated HIOs 1 week after culturing.</li>
	<li>Remove media from wells. Disperse basement membrane and HIOs using a P1000 pipet and add cold 500 &#181;L of CMGF- per well and pipet up and down at least 5x. Spin down HIOs at 4 &#176;C using a swing rotor centrifuge at 100 x g for 5 min. Remove all the medium keeping the pellet at the bottom of the tube.</li>
	<li>Add 30 &#181;L of basement membrane per well of HIOs being plated. Pipette the 30 &#181;L droplet of basement membrane with HIOs into a well of a 24-well plate. Incubate at 37 &#176;C for 10 min. Add 500 &#181;L of WRNE+Y/Diff (50/50) media.</li>
	<li>Switch the medium to differentiation medium after 24 h for 3 additional days, refreshing the medium every other day. Prepare 3 wells per sample to pool to reduce technical variability.</li>
</ol>
3. HIO differentiation: Monolayer format
<ol>
	<li>Coat the&#160;membrane cell culture inserts or wells of a 96-well plate with 100 &#181;L/well of human placental collagen IV (1mg/ml in 100mM acetic acid) diluted in cold H2O (1:30). Incubate at 37 &#176;C for a minimum of 1.5 h or maximum overnight. For membrane cell culture insert, add sterile H2O in the plate space to humidify the plate; for 96-well plate, add sterile H2O in the unused wells.</li>
	<li>Collect 3D HIOs cultured in WRNE for 7 days by removing the media and recovering the basement membrane and cells by adding 500 &#181;L/well of cold 0.5 mM EDTA (0.5 M EDTA diluted 1:1000 in sterile PBS). Use a P1000 pipet to pipet organoids and solution up and down 5x and transfer to a 15 mL microcentrifuge tube. Do not pool more than 10 wells of organoids per tube. Centrifuge for 5 min at 300 x g in a swinging bucket rotor at 4&#160;&#176;C. 
	NOTE: To prepare 3 wells on a 96-well plate, use 1 well of 3D HIOs. To prepare 1 membrane cell culture insert, use 1 well of 3D HIOs (seeding density of single cells is approximately 1-2 x 105 cells/well for 96-well plate, 2.5-3 x 105 cells/well for membrane cell culture insert).</li>
	<li>Remove 500 &#181;L of media, leaving the pellet at the bottom of the tube. Dissociate the HIOs by adding 500 &#181;L of 0.05% Trypsin/0.5 mM EDTA and incubating for 4-5 min at 37&#160;&#176;C. Vigorously pipette up and down for ~50x using a P1000. Avoid making bubbles by pipetting against the side of the tube.</li>
	<li>Inactivate the trypsin by adding 1 mL of CMGF- containing 10% FBS. Filter out large clumps of undigested cells by wetting a 40 &#181;m cell strainer with 1 mL of CMGF- containing 10% FBS and adding the cells to the top of the cell strainer. Use gravity to allow the cells to pass through the strainer and discard the cell strainer containing cell clumps.</li>
	<li>Collect the cells by centrifugation for 5 min at 400 x g in a swinging bucket rotor at room temperature.</li>
	<li>Remove the liquid from the collagen-coated membrane cell culture insert or from the 96-well plate. Resuspend the HIO pellet in 100 &#181;L/well of WRNE containing 10 &#181;M Y-27632, then pipette into the upper compartment of the membrane cell culture insert or into the 96-well plate. For membrane cell culture insert, add 600 &#181;L of WRNE containing 10 &#181;M Y-27632 into the lower compartment of the well.</li>
	<li>Remove the medium after 24 h from both the upper and lower part of the membrane cell culture insert or from the 96-well plate&#160;and replace with differentiation medium for 5 days. Prepare 3 wells per sample to pool to reduce technical variability.</li>
</ol>
4. Preparation of single cell suspensions from differentiated 3D HIOs for single cell transcriptomics
<ol>
	<li>Place enzymatic cell digestion reagent at 37 &#176;C in a CO2 incubator&#160;to thaw and warm 30 min prior to initiation of 3D HIO digestion. Check the HIOs using a bright field microscope at 10x to ensure cell health.</li>
	<li>Remove the media from the wells and add 500 &#181;L of cold cell recovery solution to the wells. Pipette up and down a few times to liberate the cells from the basement membrane using a P1000 pipette and standard pipette tips. Transfer the cell suspension to a 1.5 mL microcentrifuge tube. 
	NOTE: The use of replicate wells ensures adequate cell numbers and reduces well-to-well variation. Do not combine wells before step 4.7 below.</li>
	<li>Incubate the tubes of cells on ice for 10 min, pipetting up and down every 5 min. Collect the cells by centrifugation for 3 min at 400 x g at 4 &#176;C.</li>
	<li>Remove the liquid from the tube, taking care not to disturb the cell pellet. Resuspend the cells in 500 &#181;L of pre-warmed enzymatic cell digestion reagent. Pipette up and down with a P1000 at least 10x.</li>
	<li>Incubate the HIOs for 30 min at 37 &#176;C in a CO2 incubator. Every 10 min, pipette the entire volume 10x using a P1000 pipette to help dissociate the cells. Avoid introducing air bubbles into the cell suspension.</li>
	<li>Pellet the cells for 3 min at 400 x g at 4 &#176;C. Remove the supernatant, resuspend the cells in 1 mL of differentiation media, and store on ice. 
	NOTE: From this point on, the HIOs must always be kept on ice.</li>
	<li>Pipette the cells up and down 50x rapidly using a P1000 to ensure HIOs are dissociated into single cells. Take care not to introduce air bubbles at this step, as it will cause cell loss.</li>
	<li>Filter the entire volume through a 70 &#181;m tip strainer using a P1000 pipette tip. Use a 1.5 mL microcentrifuge tube to collect the eluate. 
	NOTE: The filter tip will not become clogged if digestion time is sufficient. Use multiple filter tips if the filter becomes clogged; do not force the volume through the filter.</li>
	<li>Repeat step 4.8 with a 40 &#181;m tip strainer. Store samples on ice.</li>
	<li>Count viable single cells on a cell counting chamber using trypan blue exclusion by adding 5 &#181;L of 0.4% trypan blue to 5 &#181;L of cell suspension. Dilute the sample as needed to 1000 cells/&#181;L. If the cell density is less than 1000 cells/&#181;L, pellet cells for 2 min at 400 x g at 4 &#176;C, remove the original media, and resuspend in cell culture media. This protocol typically yields 5 x 105-1 x 106 cells. 
	NOTE: Preparation of a high-quality suspension (90% viable and 90% single cells) is essential for high quality single-cell data. However, experience indicates viability as low as 75% can be accepted in cases where treatment, such as infection or small molecule application, impact viability.</li>
	<li>Prepare DNA libraries for single cell transcriptional profiling platforms according to the manufacturer&#39;s protocols. Process the data according to best practice protocols for scRNAseq data analysis13,14.</li>
</ol>
5. Preparation of single cell suspensions from HIOs differentiated on membrane cell culture insert
<ol>
	<li>Place enzymatic cell digestion reagent at 37 &#176;C in a CO2 incubator to thaw and warm 30 min prior to initiation of HIO membrane cell culture insert digestion. Divide the pre-warmed enzymatic cell digestion reagent into 200 &#181;L aliquots in 1.5 mL microcentrifuge tubes, 1 tube per membrane cell culture insert. Keep the tubes in the 37 &#176;C incubator until ready for use.</li>
	<li>Prepare PBS-EDTA by adding 5 &#181;L of 0.5 M EDTA to 5 mL of PBS. Aliquot 500 &#181;L of PBS-EDTA into a 24-well plate, 1 well per membrane cell culture insert.</li>
	<li>Wash the cells with PBS-EDTA: transfer the membrane cell culture inserts from wells containing growth media to the wells containing PBS-EDTA. Remove the cell culture media from the apical side and replace it with 100 &#181;L of PBS-EDTA. Take care not to disturb the cell layer.</li>
	<li>Immediately discard the PBS-EDTA added to the apical side of the membrane cell culture inserts. Remove the membrane cell culture insert from the well, blot it by gently touching the edge to a paper towel, and then invert it on the benchtop. Use a sharp scalpel blade to remove the membrane from the insert by cutting around the inner circumference of the membrane. Work quickly to prevent drying.</li>
	<li>Use forceps to transfer the membrane to the pre-warmed 1.5 mL microcentrifuge tube filled with enzymatic cell digestion reagent and ensure the membrane is completely submerged. Repeat for all additional membrane cell culture inserts. 
	NOTE: Increasing the volume of the enzymatic cell digestion reagent to 500 &#181;L may aid in dissociating dense monolayers.</li>
	<li>Dissociate the cells by incubating tubes with membranes at 37 &#176;C in a CO2 incubator. Mix by gently pipetting the entire volume 5x with a 200 &#181;L pipette every 10 min for a total of 30 min. Avoid bubbles and suction of the membrane to preserve viability.</li>
	<li>Transfer a small aliquot of cells (1-2 &#181;L) to a glass slide every 10 min to assess dissociation by qualitatively assessing the percent of single cells. It may take up to 50 min with additional pipetting to achieve 80%-90% single cells, depending on the HIO type. Gently scrape the membrane with a pipette tip during mixing steps to encourage dissociation, particularly for hard to dissociate cells, however scraping may impact viability.</li>
	<li>Combine 3 replicate wells per condition in a single 1.5 mL microcentrifuge tube (600 &#181;L total). Add 400 &#181;L of cell culture media (diff) + 10 &#181;M ROCKi (1 mL total volume). Mix gently by pipetting. 
	NOTE: The use of replicate wells ensures adequate cell numbers and reduces well-to-well variation. Wells should be pooled at this step.</li>
	<li>Filter the entire volume through a 70 &#181;m tip strainer using a 1 mL pipette tip. Collect the flow through in a fresh 1.5 mL microcentrifuge tube. 
	NOTE: The filter tip will not become clogged if digestion time is sufficient. Use multiple filter tips if the filter becomes clogged; do not force the volume through.</li>
	<li>Repeat step 5.9 with a 40 &#181;m tip strainer. Store samples on ice.</li>
	<li>Count viable single cells on a cell counting chamber using trypan blue exclusion by adding 5 &#181;L of 0.4% trypan blue to 5 &#181;L of cell suspension. Dilute sample as needed to 1000 cells/ &#181;L. If the cell density is less than 1000 cells/ &#181;L, spin 2 min at 400 x g at 4 &#176;C to pellet the cells, remove the original media, and resuspend in WRNE+Y at the desired cell density. This protocol typically yields 4 x 105 - 6 x 105 cells. 
	NOTE: Preparation of high-quality suspension (90% viable and 90% single cells) is essential for high quality single-cell data. However, experience indicates viability as low as 75% can be accepted in cases where treatment, such as infection or small molecule application, impact viability.</li>
	<li>Prepare DNA libraries for the single cell transcriptional profiling platforms according to the manufacturer&#39;s protocols. Process the data according to best practice protocols for scRNAseq data analysis13,14.</li>
</ol>
6. Preparation of single cell suspensions from HIOs differentiated as 96-well monolayers
<ol>
	<li>Place enzymatic cell digestion reagent at 37 &#176;C in a CO2 incubator to thaw and warm 30 min prior to initiation of monolayer HIO digestion.</li>
	<li>Prepare PBS-EDTA by adding 5 &#181;L of 0.5 M EDTA to 5 mL of PBS. Discard the cell culture media from the 96-well plate and replace it with 100 &#181;L of PBS-EDTA. Take care not to disturb the cell layer.</li>
	<li>Dissociate the cells: Discard the PBS-EDTA and add 100 &#181;L of warm enzymatic cell digestion reagent to each well. Place the plate in the 37 &#176;C in a 5% CO2 incubator and mix by gently pipetting the entire volume 5x with a 200 &#181;L pipette tip every 10 min for 20-30 min. Avoid bubbles to preserve viability. 
	NOTE: Increasing the volume of enzymatic cell digestion reagent to 500 &#181;L may aid in dissociating dense monolayers.</li>
	<li>Transfer a small aliquot of cells (1-2 &#181;L) to a glass slide every 10 min to assess dissociation. It may take up to 50 min to achieve 80%-90% single cells, depending on the HIO type. Gently scrape the plate with a pipette tip during mixing steps to encourage dissociation, particularly for hard to dissociate cells; however, scraping may impact viability.</li>
	<li>Combine 3 replicate wells per condition in a single 1.5 mL microcentrifuge tube (300 &#181;L total). Add 700 &#181;L of cell culture media (diff) + 10 uM ROCKi (1 mL total volume). Mix gently by pipetting. 
	NOTE: The use of replicate grown wells ensures adequate cell numbers and reduces well-to-well variation.</li>
	<li>Filter the entire volume through a 70 &#181;m tip strainer using a 1 mL pipette tip. Collect the flow through in a fresh 1.5 mL microcentrifuge tube. 
	NOTE: The filter tip will not become clogged if enzymatic cell digestion reagent digestion time is sufficient. Use multiple filter tips if the filter becomes clogged; do not force the volume through.</li>
	<li>Repeat step 6.6 with a 40 &#181;m tip strainer. Store samples on ice.</li>
	<li>Count viable single cells on a cell counting chamber using trypan blue exclusion by adding 5 &#181;L of 0.4% trypan blue to 5 &#181;L of cell suspension. Dilute as needed to 1000 cells/&#181;L. If the cell density is less than 1000 cells/&#181;L, spin 2 min at 400 x g 4 &#176;C to pellet the cells, remove the original media, and resuspend in cell culture media + ROCKi at the desired cell density. This protocol typically yields 2 x 105 - 6 x 105 cells. 
	NOTE: Preparation of high-quality suspension (90% viable and 90% single cells) is essential for high quality single-cell data. However, experience indicates viability as low as 75% can be accepted in cases where treatment, such as infection or small molecule application, impact viability.</li>
	<li>Prepare DNA libraries according to the single cell transcriptional profiling platform manufacturer&#39;s protocols. Process the data according to best practice protocols for scRNAseq data analysis13,14.</li>
</ol>

Integrating Single-Cell Transcriptomics with Human Intestinal Organoids

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	<li>Sato, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Long-term+expansion+of+epithelial+organoids+from+human+colon,+adenoma,+adenocarcinoma,+and+Barrett's+epithelium.">Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett's epithelium.</a> Gastroenterology. 141 (5), 1762-1772 (2011).</li><li>Blutt, S. 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=Gastrointestinal+microphysiological+systems.">Gastrointestinal microphysiological systems.</a> Exp Biol Med. 242 (16), 1633-1642 (2017).</li><li>VanDussen, K. 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=Development+of+an+enhanced+human+gastrointestinal+epithelial+culture+system+to+facilitate+patient-based+assays.">Development of an enhanced human gastrointestinal epithelial culture system to facilitate patient-based assays.</a> Gut. 64 (6), 911-920 (2015).</li><li>Elmentaite, 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=Cells+of+the+human+intestinal+tract+mapped+across+space+and+time.">Cells of the human intestinal tract mapped across space and time.</a> Nature. 597 (7875), 250-255 (2021).</li><li>Hickey, J. 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=Organization+of+the+human+intestine+at+single-cell+resolution.">Organization of the human intestine at single-cell resolution.</a> Nature. 619 (7970), 572-584 (2023).</li><li>Burclaff, 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=A+proximal-to-distal+survey+of+healthy+adult+human+small+intestine+and+colon+epithelium+by+single-cell+transcriptomics.">A proximal-to-distal survey of healthy adult human small intestine and colon epithelium by single-cell transcriptomics.</a> Cell Mol Gastroenterol Hepatol. 13 (5), 1554-1589 (2022).</li><li>Triana, 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=Single-cell+transcriptomics+reveals+immune+response+of+intestinal+cell+types+to+viral+infection.">Single-cell transcriptomics reveals immune response of intestinal cell types to viral infection.</a> Mol Syst Biol. 17 (7), e9833 (2021).</li><li>Triana, 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=Single-cell+analyses+reveal+SARS-CoV-2+interference+with+intrinsic+immune+response+in+the+human+gut.">Single-cell analyses reveal SARS-CoV-2 interference with intrinsic immune response in the human gut.</a> Mol Syst Biol. 17 (4), e10232 (2021).</li><li>Fujii, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Human+intestinal+organoids+maintain+self-renewal+capacity+and+cellular+diversity+in+niche-inspired+culture+condition.">Human intestinal organoids maintain self-renewal capacity and cellular diversity in niche-inspired culture condition.</a> Cell Stem Cell. 23 (6), 787-793 (2021).</li><li>Beumer, 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=BMP+gradient+along+the+intestinal+villus+axis+controls+zonated+enterocyte+and+goblet+cell+states.">BMP gradient along the intestinal villus axis controls zonated enterocyte and goblet cell states.</a> Cell Rep. 38 (9), 110438 (2022).</li><li>Beumer, 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-resolution+mRNA+and+secretome+atlas+of+human+enteroendocrine+cells.">High-resolution mRNA and secretome atlas of human enteroendocrine cells.</a> Cell. 182 (4), 1062-1064 (2020).</li><li>Busslinger, G. 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The authors have no conflicts of interest.

Using single cell genomics platforms, complex biological systems, such as tissue derived HIO cultures that model the intestinal epithelium, can be broken down to yield individual cellular contributions to overall biological response4,5,6. Cellular heterogeneity and rare cell populations can also be identified and interrogated. Cellular input needs to be optimized to maximize output using single cell transcriptomic-based platform...

The small intestinal epithelium has two distinct zones: the crypt that houses the intestinal stem cell (ISC) and the villus, which is comprised of differentiated cells of the secretory and absorptive lineages. Adding to this complexity is the regional specificity of the epithelium that provides unique functional properties between the regions of the small intestine. Pioneering work established culture conditions in which both the human small intestinal crypt and villus zones can be generated ex vivo from surgical tissues or tissue biopsies1. These cultures are bridging the gap between animal studies and clinical trials and are revealing previously unrecognized cell biology, biochemistry, and physiology of the gastrointestinal tract. The HIOs are propagated as 3D spherical structures using a media with growth factors that promote stem cell viability and extracellular support matrices. These conditions result in a crypt-like HIO model that consists mostly of progenitors and stem cells. Removal of the growth factors promotes ISC differentiation (villus-like model) and production of mature intestinal epithelial cells (goblet, enteroendocrine, tuft, enterocyte) in appropriate ratios along with cell proliferation and differentiation, polarization, barrier integrity, regional specific features, and appropriate physiological responses2. HIO cultures are genetically stable and can be propagated indefinitely in their crypt-like state. Easy access to the apical surface of these cultures is provided by culture conditions that allow growth in a monolayer format3. HIOs also allow considerations of host individual variability such as genetics, age, sex, ethnicity, and disease status to be included in biological analyses. Analytic and functional assessment tools are identical to those used in approaches centered on transformed cell lines and include a variety of molecular techniques such as flow cytometry, microscopy, transcriptomics, proteomics, and metabolomics.
Single cell transcriptomics is revolutionizing our understanding of the biology and physiology of the small intestine by providing insight into the individual contributions of each cell type to a biological process. Pioneering work using this technology has provided a landscape of the cell types present in the native human intestine4,5,6. Single cell transcriptional profiling platforms allow exploration of the transcriptional landscape of individual cells, allowing cell heterogeneity to come to the forefront of scientific exploration. In some single cell transcriptional profiling platforms, microfluidic partitioning and barcoding are used to generate cDNA libraries from cellular polyadenylated mRNAs obtained from up to 10,000 cells per sample. On this platform, droplets containing single cells, barcoded oligonucleotides, reverse transcription reagents, and oil form a reaction vesicle that results in all cDNAs from a single cell having the same barcode. The barcoded cDNAs can then be efficiently sequenced using next generation sequencing. Data generated can be handled through software and visualization tools, which convert the barcoded sequences into visualization maps and single cell transcriptional profiles. Cell populations can be identified using publicly available databases of human small intestinal epithelium4,5,6. Although many studies have utilized this platform to interrogate murine intestinal organoids at the single cell level, the analysis of single cell transcriptional responses of HIOs has lagged behind7,8,9,10,11,12.
Here, we provide a step-by-step guide to isolating viable cells from small intestinal HIOs for processing on single cell transcriptional profiling platforms (Figure 1). We provide culturing and differentiation guidelines along with media components that have been optimized for epithelial differentiation. We outline cell recovery methods for three different culture formats: three dimensional (3D) and monolayer cultures either on plastic or on membrane cell culture inserts. We provide sample clustering data obtained using open-source software to derive differentially expressed genes in each cluster.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>[Leu15]-Gastrin I</td>
			<td>Sigma-Aldrich</td>
			<td>G9145</td>
			<td>10 nM</td>
		</tr>
		<tr>
			<td>0.05% Trypsin-EDTA</td>
			<td>Invitrogen</td>
			<td>25300054</td>
			<td></td>
		</tr>
		<tr>
			<td>0.4% Trypan blue</td>
			<td>Millipore-Sigma</td>
			<td>T8154</td>
			<td></td>
		</tr>
		<tr>
			<td>0.5 M EDTA</td>
			<td>Corning</td>
			<td>46-034-CI</td>
			<td></td>
		</tr>
		<tr>
			<td>1x PBS Ca- Mg-</td>
			<td>Corning</td>
			<td>21-040-CM</td>
			<td></td>
		</tr>
		<tr>
			<td>24 mm Transwell</td>
			<td>Costar</td>
			<td>3412</td>
			<td></td>
		</tr>
		<tr>
			<td>24 well Nunclon delta surface tissue culture dish</td>
			<td>Thermo Scientific</td>
			<td>142475</td>
			<td></td>
		</tr>
		<tr>
			<td>40 &#181;m cell strainer</td>
			<td>Falcon</td>
			<td>352340</td>
			<td></td>
		</tr>
		<tr>
			<td>40 &#181;m Flowmi tip strainer</td>
			<td>SP Bel-Art Labware</td>
			<td>H13680-0040</td>
			<td></td>
		</tr>
		<tr>
			<td>70 &#181;m Flowmi tip strainer</td>
			<td>SP Bel-Art Labware</td>
			<td>H13680-0070</td>
			<td></td>
		</tr>
		<tr>
			<td>96 well plate</td>
			<td>Corning</td>
			<td>3595</td>
			<td></td>
		</tr>
		<tr>
			<td>A-83-01</td>
			<td>Tocris</td>
			<td>2939</td>
			<td>500 nM</td>
		</tr>
		<tr>
			<td>Accutase</td>
			<td>StemCell Technologies</td>
			<td>7920</td>
			<td></td>
		</tr>
		<tr>
			<td>Advanced DMEM/F12</td>
			<td>Invitrogen</td>
			<td>12634-028</td>
			<td></td>
		</tr>
		<tr>
			<td>B27 supplement</td>
			<td>Invitrogen</td>
			<td>17504-044</td>
			<td>1X</td>
		</tr>
		<tr>
			<td>Chromium Next GEM Single Cell 3&#8217; GEM, Library &#38; Gel Bead Kit v3.1</td>
			<td>10x Genomics</td>
			<td>PN-1000128</td>
			<td></td>
		</tr>
		<tr>
			<td>Collagen IV</td>
			<td>Sigma-Aldrich</td>
			<td>C5533-5MG</td>
			<td>33 &#181;g/mL</td>
		</tr>
		<tr>
			<td>Corning Cell Recovery Solution&#160;</td>
			<td>VWR</td>
			<td>354253</td>
			<td></td>
		</tr>
		<tr>
			<td>DPBS (Mg2-, Ca2-)</td>
			<td>Invitrogen</td>
			<td>14190-136</td>
			<td>1X</td>
		</tr>
		<tr>
			<td>GlutaMAX-I</td>
			<td>Invitrogen</td>
			<td>35050-061</td>
			<td>2 mM</td>
		</tr>
		<tr>
			<td>HEPES 1M</td>
			<td>Invitrogen</td>
			<td>15630-080</td>
			<td>10 mM</td>
		</tr>
		<tr>
			<td>L-WRN conditioned media</td>
			<td>ATCC</td>
			<td>CRL-3276</td>
			<td></td>
		</tr>
		<tr>
			<td>Matrigel, GFR, phenol free</td>
			<td>Corning</td>
			<td>356231</td>
			<td></td>
		</tr>
		<tr>
			<td>mouse recombinant EGF</td>
			<td>Invitrogen</td>
			<td>PMG8043</td>
			<td>50 ng/mL</td>
		</tr>
		<tr>
			<td>N2 supplement</td>
			<td>Invitrogen</td>
			<td>17502-048</td>
			<td>1X</td>
		</tr>
		<tr>
			<td>N-Acetylcysteine</td>
			<td>Sigma-Aldrich</td>
			<td>A9165-5G</td>
			<td>500 &#181;M</td>
		</tr>
		<tr>
			<td>Nicotinamide</td>
			<td>Sigma-Aldrich</td>
			<td>N0636</td>
			<td>10 mM</td>
		</tr>
		<tr>
			<td>SB202190</td>
			<td>Sigma-Aldrich</td>
			<td>S7067</td>
			<td>10 &#181;M</td>
		</tr>
		<tr>
			<td>Transwell</td>
			<td>Corning</td>
			<td>3413</td>
			<td></td>
		</tr>
		<tr>
			<td>Y27632</td>
			<td>Stem Cell Technologies</td>
			<td>72308</td>
			<td>10 &#181;M</td>
		</tr>
	</tbody>
</table>

using human intestinal organoids to understand the small intestine epithelium at the single cell transcriptional level

Single cell transcriptomics has revolutionized our understanding of the cell biology of the human body. State-of-the-art human small intestinal organoid cultures provide ex vivo model systems that bridge the gap between animal models and clinical studies. The application of single cell transcriptomics to human intestinal organoid (HIO) models is revealing previously unrecognized cell biology, biochemistry, and physiology of the GI tract. The advanced single cell transcriptomics platforms use microfluidic partitioning and barcoding to generate cDNA libraries. These barcoded cDNAs can be easily sequenced by next generation sequencing platforms and used by various visualization tools to generate maps. Here, we describe methods to culture and differentiate human small intestinal HIOs in different formats and procedures for isolating viable cells from these formats that are suitable for use in single-cell transcriptional profiling platforms. These protocols and procedures facilitate the use of small intestinal HIOs to obtain an increased understanding of the cellular response of human intestinal epithelium at the transcriptional level in the context of a variety of different environments.

Single-cell suspensions were pooled from 2-3 wells of membrane cell culture insert, monolayer, and 3D HIOs to ensure sufficient cell yield and reduce well-to-well variation. Single cell libraries were prepared using reagents specific to the single cell transcriptional profiling platform. and sequenced with paired end reads on a next generation sequencing platform, 30,000 reads/cell. Reads were mapped, counted, and analyzed using analytical tools for single cell genomics. Low-quality cells with more than 20% mitochondrial...

Author Spotlight: Integrating Single-Cell Transcriptomics with Organoid Cultures for Advanced Research and Therapeutic Insights

The protocol combines human intestinal organoid technology with single cell transcriptomic analysis to provide significant insight into previously unexplored intestinal biology.

Using Human Intestinal Organoids to Understand the Small Intestine Epithelium at the Single Cell Transcriptional Level

Single cell transcriptomics has revolutionized our understanding of the cell biology of the human body. State-of-the-art human small intestinal organoid ...

using-human-intestinal-organoids-to-understand-small-intestine

Research

JoVE Journal

Biology

643 Views.  Baylor College of Medicine. The protocol combines human intestinal organoid technology with single cell transcriptomic analysis to provide significant insight into previously unexplored intestinal biology. 

Video: Author Spotlight: Integrating Single-Cell Transcriptomics with Organoid Cultures for Advanced Research and Therapeutic Insights

Method for Measurement of Viral Fusion Kinetics at the Single Particle Level

Membrane fusion is an essential step during entry of enveloped viruses into cells. Conventional fusion assays typically report on a large number of fusion events, making it difficult to quantitatively analyze the sequence of the molecular steps involved. We have developed an in vitro, two-color fluorescence assay to monitor kinetics of single virus particles fusing with a target bilayer on an essentially fluid support.
Influenza viral particles are incubated with a green lipophilic fluorophore to stain the membrane and a red hydrophilic fluorophore to stain the viral interior. We deposit a ganglioside-containing lipid bilayer on the dextran-functionilized glass surface of a flow cell, incubate the viral particles on the planar bilayer and image the fluorescence of a 100 x 100 &mu;m2 area, containing several hundreds of particles, on a CCD camera. By imaging both the red and green fluorescence, we can simultaneously monitor the behavior of the membrane dye (green) and the aqueous content (red) of the particles.
Upon lowering the pH to a value below the fusion pH, the particles will fuse with the membrane. Hemifusion, the merging of the outer leaflet of the viral membrane with the outer leaflet of the target membrane, will be visible as a sudden change in the green fluorescence of a particle. Upon the subsequent fusion of the two remaining distal leaflets a pore will be formed and the red-emitting fluorophore in the viral particle will be released under the target membrane. This event will give rise to a decrease of the red fluorescence of individual particles. Finally, the integrated fluorescence from a pH-sensitive fluorophore that is embedded in the target membrane reports on the exact time of the pH drop.
From the three fluorescence-time traces, all the important events (pH drop, lipid mixing upon hemifusion, content mixing upon pore formation) can now be extracted in a straightforward manner and for every particle individually. By collecting the elapsed times for the various transitions for many individual particles in histograms, we can determine the lifetimes of the corresponding intermediates. Even hidden intermediates that do not have a direct fluorescent observable can be visualized directly from these histograms.

We present an in vitro, two-color fluorescence assay to visualize the fusion of single virus particles with a fluid target bilayer. By labeling viral particles with fluorophores that differentially stain the viral membrane and its interior, we are able to monitor the kinetics of hemifusion and pore formation.

Membrane fusion is an essential step during entry of enveloped viruses into cells. Conventional fusion assays typically report on a large number of fusion ...

Single Cell Transcriptional Profiling of Adult Mouse Cardiomyocytes

While numerous studies have examined gene expression changes from homogenates of heart tissue, this prevents studying the inherent stochastic variation between cells within a tissue. Isolation of pure cardiomyocyte populations through a collagenase perfusion of mouse hearts facilitates the generation of single cell microarrays for whole transcriptome gene expression, or qPCR of specific targets using nanofluidic arrays. We describe here a procedure to examine single cell gene expression profiles of cardiomyocytes isolated from the heart. This paradigm allows for the evaluation of metrics of interest which are not reliant on the mean (for example variance between cells within a tissue) which is not possible when using conventional whole tissue workflows for the evaluation of gene expression (Figure 1). We have achieved robust amplification of the single cell transcriptome yielding micrograms of double stranded cDNA that facilitates the use of microarrays on individual cells. In the procedure we describe the use of NimbleGen arrays which were selected for their ease of use and ability to customize their design. Alternatively, a reverse transcriptase - specific target amplification (RT-STA) reaction, allows for qPCR of hundreds of targets by nanofluidic PCR. Using either of these approaches, it is possible to examine the variability of expression between cells, as well as examining expression profiles of rare cell types from within a tissue. Overall, the single cell gene expression approach allows for the generation of data that can potentially identify idiosyncratic expression profiles that are typically averaged out when examining expression of millions of cells from typical homogenates generated from whole tissues.

Single cell expression profiling allows the detailed gene expression analysis of individual cells. We describe methods for the isolation of cardiomyocytes, and preparing the resulting lysates for either whole transcriptome microarray or qPCR of specific targets.

While numerous studies have examined gene expression changes from homogenates of heart tissue, this prevents studying the inherent stochastic variation ...

Studying Proteolysis of Cyclin B at the Single Cell Level in Whole Cell Populations

Equal distribution of chromosomes between the two daughter cells during cell division is a prerequisite for guaranteeing genetic stability 1. Inaccuracies during chromosome separation are a hallmark of malignancy and associated with progressive disease 2-4. The spindle assembly checkpoint (SAC) is a mitotic surveillance mechanism that holds back cells at metaphase until every single chromosome has established a stable bipolar attachment to the mitotic spindle1. The SAC exerts its function by interference with the activating APC/C subunit Cdc20 to block proteolysis of securin and cyclin B and thus chromosome separation and mitotic exit. Improper attachment of chromosomes prevents silencing of SAC signaling and causes continued inhibition of APC/CCdc20 until the problem is solved to avoid chromosome missegregation, aneuploidy and malignant growths1.
Most studies that addressed the influence of improper chromosomal attachment on APC/C-dependent proteolysis took advantage of spindle disruption using depolymerizing or microtubule-stabilizing drugs to interfere with chromosomal attachment to microtubules. Since interference with microtubule kinetics can affect the transport and localization of critical regulators, these procedures bear a risk of inducing artificial effects 5.
To study how the SAC interferes with APC/C-dependent proteolysis of cyclin B during mitosis in unperturbed cell populations, we established a histone H2-GFP-based system which allowed the simultaneous monitoring of metaphase alignment of mitotic chromosomes and proteolysis of cyclin B 6.
To depict proteolytic profiles, we generated a chimeric cyclin B reporter molecule with a C-terminal SNAP moiety 6 (Figure 1). In a self-labeling reaction, the SNAP-moiety is able to form covalent bonds with alkylguanine-carriers (SNAP substrate) 7,8 (Figure 1). SNAP substrate molecules are readily available and carry a broad spectrum of different fluorochromes. Chimeric cyclin B-SNAP molecules become labeled upon addition of the membrane-permeable SNAP substrate to the growth medium 7 (Figure 1). Following the labeling reaction, the cyclin B-SNAP fluorescence intensity drops in a pulse-chase reaction-like manner and fluorescence intensities reflect levels of cyclin B degradation 6 (Figure 1). Our system facilitates the monitoring of mitotic APC/C-dependent proteolysis in large numbers of cells (or several cell populations) in parallel. Thereby, the system may be a valuable tool to identify agents/small molecules that are able to interfere with proteolytic activity at the metaphase to anaphase transition. Moreover, as synthesis of cyclin B during mitosis has recently been suggested as an important mechanism in fostering a mitotic block in mice and humans by keeping cyclin B expression levels stable 9,10, this system enabled us to analyze cyclin B proteolysis as one element of a balanced equilibrium 6.

Metaphase to anaphase transition is triggered through anaphase-promoting complex (APC/C)-dependent ubiquitination and subsequent destruction of cyclin B. Here, we established a system which, following pulse-chase labeling, allows monitoring cyclin B proteolysis in entire cell populations and facilitates the detection of interference by the mitotic checkpoint.

Equal distribution of chromosomes between the two daughter cells during cell division is a prerequisite for guaranteeing genetic stability 1. Inaccuracies ...

Analyzing Craniofacial Morphogenesis in Zebrafish Using 4D Confocal Microscopy

Time-lapse imaging is a technique that allows for the direct observation of the process of morphogenesis, or the generation of shape. Due to their optical clarity and amenability to genetic manipulation, the zebrafish embryo has become a popular model organism with which to perform time-lapse analysis of morphogenesis in living embryos. Confocal imaging of a live zebrafish embryo requires that a tissue of interest is persistently labeled with a fluorescent marker, such as a transgene or injected dye. The process demands that the embryo is anesthetized and held in place in such a way that healthy development proceeds normally. Parameters for imaging must be set to account for three-dimensional growth and to balance the demands of resolving individual cells while getting quick snapshots of development. Our results demonstrate the ability to perform long-term in vivo imaging of fluorescence-labeled zebrafish embryos and to detect varied tissue behaviors in the cranial neural crest that cause craniofacial abnormalities. Developmental delays caused by anesthesia and mounting are minimal, and embryos are unharmed by the process. Time-lapse imaged embryos can be returned to liquid medium and subsequently imaged or fixed at later points in development. With an increasing abundance of transgenic zebrafish lines and well-characterized fate mapping and transplantation techniques, imaging any desired tissue is possible. As such, time-lapse in vivo imaging combines powerfully with zebrafish genetic methods, including analyses of mutant and microinjected embryos.

Time-lapse confocal imaging is a powerful technique useful for characterizing embryonic development. Here, we describe the methodology and characterize craniofacial morphogenesis in wild-type, as well as pdgfra, smad5, and smo mutant embryos.

Time-lapse imaging is a technique that allows for the direct observation of the process of morphogenesis, or the generation of shape. Due to their optical ...

Analysis of Global RNA Synthesis at the Single Cell Level following Hypoxia

Hypoxia or lowering of the oxygen availability is involved in many physiological and pathological processes. At the molecular level, cells initiate a particular transcriptional program in order to mount an appropriate and coordinated cellular response. The cell possesses several oxygen sensor enzymes that require molecular oxygen as cofactor for their activity. These range from prolyl-hydroxylases to histone demethylases. The majority of studies analyzing cellular responses to hypoxia are based on cellular populations and average studies, and as such single cell analysis of hypoxic cells are seldom performed. Here we describe a method of analysis of global RNA synthesis at the single cell level in hypoxia by using Click-iT RNA imaging kits in an oxygen controlled workstation, followed by microscopy analysis and quantification.&nbsp; Using cancer cells exposed to hypoxia for different lengths of time, RNA is labeled and measured in each cell. This analysis allows the visualization of temporal and cell-to-cell changes in global RNA synthesis following hypoxic stress.

We describe a technique for analysis of global RNA synthesis in hypoxia using imaging. Click-chemistry labeling of RNA has not previously been performed under hypoxia and allows visualization of global RNA changes at the single cell level. This approach complements the existing averaged RNA techniques, allowing direct visualization of cell-to-cell changes in global RNA synthesis.

Hypoxia or lowering of the oxygen availability is involved in many physiological and pathological processes. At the molecular level, cells initiate a ...

Analysis of LINE-1 Retrotransposition at the Single Nucleus Level

Long interspersed nuclear element-1 (Line-1 or L1) accounts for approximately 17% of the DNA present in the human genome. While the majority of L1s are inactive due to 5' truncations, ~80-100 of these elements remain retrotransposition competent and propagate to different locations throughout the genome via RNA intermediates. While older L1s are believed to target AT rich regions of the genome, the chromosomal targets of newer, more active L1s remain poorly defined. Here we describe fluorescence in situ hybridization (FISH) methodology that can be used to track patterns of L1 insertion and rates of ectopic L1 incorporation at the single nucleus level. In these experiments, fluorescein isothiocyanate/cyanine-3 (FITC/CY3) labeled neomycin probes were employed to track L1 retrotransposition in vitro in HepG2 cells stably expressing ectopic L1. This methodology prevents errors in the estimation of rates of retrotransposition posed by toxicity and account for the occurrence of multiple insertions into a single nucleus.

Here we employ FISH methodology to track LINE-1 retrotransposition at the single nuclei level in chromosome spreads of HepG2 cell lines stably expressing synthetic LINE-1.

Long interspersed nuclear element-1 (Line-1 or L1) accounts for approximately 17% of the DNA present in the human genome. While the majority of L1s are ...

CUBIC Protocol Visualizes Protein Expression at Single Cell Resolution in Whole Mount Skin Preparations

The skin is essential for our survival. The outer epidermal layer consists of the interfollicular epidermis, which is a stratified squamous epithelium covering most of our body, and epidermal appendages such as the hair follicles and sweat glands. The epidermis undergoes regeneration throughout life and in response to injury. This is enabled by K14-expressing basal epidermal stem/progenitor cell populations that are tightly regulated by multiple regulatory mechanisms active within the epidermis and between epidermis and dermis. This article describes a simple method to clarify full thickness mouse skin biopsies, and visualize K14 protein expression patterns, Ki67 labeled proliferating cells, Nile Red labeled sebocytes, and DAPI nuclear labeling at single cell resolution in 3D. This method enables accurate assessment and quantification of skin anatomy and pathology, and of abnormal epidermal phenotypes in genetically modified mouse lines. The CUBIC protocol is the best method available to date to investigate molecular and cellular interactions in full thickness skin biopsies at single cell resolution.

This report describes a CUBIC protocol to clarify full thickness mouse skin biopsies, and visualize protein expression patterns, proliferating cells, and sebocytes at the single cell resolution in 3D. This method enables accurate assessment of skin anatomy and pathology, and of abnormal epidermal phenotypes in genetically modified mouse lines.

The skin is essential for our survival. The outer epidermal layer consists of the interfollicular epidermis, which is a stratified squamous epithelium ...

Analysis of Beta-cell Function Using Single-cell Resolution Calcium Imaging in Zebrafish Islets

Pancreatic beta-cells respond to increasing blood glucose concentrations by secreting the hormone insulin. The dysfunction of beta-cells leads to hyperglycemia and severe, life-threatening consequences. Understanding how the beta-cells operate under physiological conditions and what genetic and environmental factors might cause their dysfunction could lead to better treatment options for diabetic patients. The ability to measure calcium levels in beta-cells serves as an important indicator of beta-cell function, as the influx of calcium ions triggers insulin release. Here we describe a protocol for monitoring the glucose-stimulated calcium influx in zebrafish beta-cells by using GCaMP6s, a genetically encoded sensor of calcium. The method allows monitoring the intracellular calcium dynamics with single-cell resolution in ex vivo mounted islets. The glucose-responsiveness of beta-cells within the same islet can be captured simultaneously under different glucose concentrations, which suggests the presence of functional heterogeneity among zebrafish beta-cells. Furthermore, the technique provides high temporal and spatial resolution, which reveals the oscillatory nature of the calcium influx upon glucose stimulation. Our approach opens the doors to use the zebrafish as a model to investigate the contribution of genetic and environmental factors to beta-cell function and dysfunction.

Beta-cell functionality is important for blood-glucose homeostasis, which is evaluated at single-cell resolution using a genetically encoded reporter for calcium influx.

Pancreatic beta-cells respond to increasing blood glucose concentrations by secreting the hormone insulin. The dysfunction of beta-cells leads to ...

Visualizing the Interaction Between the Qdot-labeled Protein and Site-specifically Modified &#955; DNA at the Single Molecule Level

The fluorescence microscopy&#160;has made great contributions in dissecting the mechanisms of complex biological processes at the single molecule level. In single molecule assays for studying DNA-protein interactions, there are two important factors for consideration: the DNA substrate with enough length for easy observation and labeling a protein with a suitable fluorescent probe. 48.5 kb &#955; DNA is a good candidate for the DNA substrate. Quantum dots (Qdots), as a class of fluorescent probes, allow long-time observation (minutes to hours) and high-quality image acquisition. In this paper, we present a protocol to study DNA-protein interactions at the single-molecule level, which includes preparing a site-specifically modified &#955; DNA and labeling a target protein with streptavidin-coated Qdots. For a proof of concept, we choose ORC (origin recognition complex) in budding yeast as a protein of interest and visualize its interaction with an ARS (autonomously replicating sequence) using TIRFM. Compared with other fluorescent probes, Qdots have obvious advantages in single molecule studies due to its high stability against photobleaching, but it should be noted that this property limits its application in quantitative assays.

Here, we present a protocol to study DNA-protein interactions by total internal reflection fluorescence microscopy (TIRFM) using a site-specifically modified &#955; DNA substrate and a Quantum-dot labeled protein.

The fluorescence microscopy&#160;has made great contributions in dissecting the mechanisms of complex biological processes at the single molecule level. ...

3D Culturing of Organoids from the Intestinal Villi Epithelium Undergoing Dedifferentiation

Clonogenicity of organoids from the intestinal epithelium is attributed to the presence of stem cells therein. The mouse small intestinal epithelium is compartmentalized into crypts and villi: the stem and proliferating cells are confined to the crypts, whereas the villi epithelium contains only differentiated cells. Hence, the normal intestinal crypts, but not the villi, can give rise to organoids in 3D cultures. The procedure described here is applicable only to villus epithelium undergoing dedifferentiation leading to stemness. The method described uses the Smad4-loss-of-function:&#946;-catenin gain-of-function (Smad4KO:&#946;-cateninGOF) conditional mutant mouse. The mutation causes the intestinal villi to dedifferentiate and generate stem cells in the villi. Intestinal villi undergoing dedifferentiation are scraped off the intestine using glass slides, placed in a 70 &#181;m strainer and washed several times to filter out any loose cells or crypts prior to plating in BME-R1 matrix to determine their organoid-forming potential. Two main criteria were used to ensure that the resulting organoids were developed from the dedifferentiating villus compartment and not from the crypts: 1) microscopically evaluating&#160;the isolated villi to ensure absence of any tethered crypts, both before and after plating in the 3D matrix, and 2) monitoring the time course of organoid development from the villi. Organoid initiation from the villi occurs only two to five days after plating and appears irregularly shaped, whereas the crypt-derived organoids from the same intestinal epithelium are apparent within sixteen hours of plating and appear spherical. The limitation of the method, however, is that the number of organoids formed, and the time required for organoid initiation from the villi vary depending on the degree of dedifferentiation. Hence, depending upon the specificity of the mutation or the insult causing the dedifferentiation, the optimal stage at which villi can be harvested to assay their organoid forming potential, must be determined empirically.

The procedure describes isolation of the villi from the mouse intestinal epithelium undergoing dedifferentiation to determine their organoid forming potential.

Clonogenicity of organoids from the intestinal epithelium is attributed to the presence of stem cells therein. The mouse small intestinal epithelium is ...