NH is funded by the MRC (MR/S009930/1) and the Wellcome Trust (204267/Z/16/Z), PD is funded by the MRC PhD DTP, KLF is funded by the BBSRC iCASE.

NOTE: All tissue culture work detailed below should be done in a Class II laminar flow hood.
1. Human induced pluripotent stem cell (hiPSCs) differentiation to the hindgut endoderm
<ol li="">
	<li>To coat a cell culture flask with extracellular matrix, first calculate the amount of the matrix needed. Here is an example of a 12-well plate being coated with Matrigel. Calculate the required amount of extracellular matrix to coat a 12 well plate. Use the following formula: 
	<img alt="Equation 1" src="/files/ftp_upload/61199/61199equ01.jpg" /> 
	NOTE: Coat cell culture dishes with extracellular matrix of choice. If using Matrigel, use a concentration of 0.035 mg/cm2 24 h prior to seeding for differentiation. Check batch concentration of extracellular matrix on product sheet and prepare smaller aliquots ahead of experiments according to manufacturer&#8217;s instructions.</li>
	<li>Dilute the required amount of extracellular matrix in cold DMEM media using a p1000 pipette.</li>
	<li>Mix well using a 5 mL stripette.</li>
	<li>Add 500&#956;L of diluted matrix to each well plate. Shake the plate gently to evenly distribute the diluted extracellular matrix and incubate for a minimum of 12 h at 37 &#176;C.</li>
	<li>Before seeding cells to the plate, wash each well with 500 &#181;L of PBS to remove excess extracellular matrix. This will prevent cell detachment during the differentiation.</li>
	<li>Leave the last wash in the wells until ready to seed to prevent the drying of extracellular matrix.</li>
	<li>To seed for hiPSCs differentiation towards definitive endoderm (DE) or hindgut (HG), take a flask of hiPSCs cultured in a maintenence media of choice (e.g.: essential 8 media) and aspirate the media. (Here, we seed cells at 25,000 cells/cm2). 
	NOTE: Seeding density is crucial for successful differentiation and needs to be optimized for each individual hiPSC cell line.</li>
	<li>Wash the cells in the flask with 5 mL of PBS. Aspirate the PBS.</li>
	<li>Add 2.5 mL of cell dissociation solution (e.g., TrypLE) and leave at RT for 4 min. Aspirate the cell dissociation solution and tap the flask gently to detach the cells.</li>
	<li>Wash the flask with 5 mL of DMEM media warmed to 37 &#176;C and collect all the cells into a 15 mL tube.</li>
	<li>Take 10 &#181;L of resuspended cell solution and measure the cell density with a hemocytometer.</li>
	<li>Take enough of the cell suspension to collect 1.05 x 106 cells and place in a 15 mL tube.</li>
	<li>Spin at 160 x g for 3 min. While the cells are being centrifuged, aspirate PBS from the extracellular matrix coated 12 well plate.</li>
	<li>Following centrifugation, aspirate the supernatant and resuspend the cell pellet in 12 mL of maintenance media with ROCK inhibitor (10 &#181;M).</li>
	<li>Using a p1000 pipette, add 1 mL of cell suspension to each well of the 12 well plate. Resuspend the cells well to ensure equal distribution between the wells.</li>
	<li>Shake the plate gently to distribute the cells within the wells of the plate but avoid swirling of the media as it will concentrate the cells in the middle of the wells.</li>
	<li>Place in a 37 &#176;C, 5% CO2 incubator.</li>
	<li>Change media to maintenance media (e.g., essential 8 media) only (no ROCK inhibitor) 24 h post seeding.</li>
	<li>To begin differentiation to DE, prepare endoderm basal media according to Table 1. 
	NOTE: At the start of the differentiation cells should be at between 60-80% confluence.</li>
	<li>Prepare 12 mL of DE media by adding Activin A (100 ng/mL) and Wnt3 (50 ng/mL) to the endoderm basal media.</li>
	<li>Warm up the media to 37 &#176;C.</li>
	<li>Aspirate media from each well of the tissue culture plate or flask.</li>
	<li>Start the DE differentiation by adding 1 mL of DE media to each well of the 12 well plate.</li>
	<li>At 24 h after starting DE differentiation (D1 DE), prepare fresh DE media and perform media change.</li>
	<li>Repeat step 1.24 at 48 h (D2 DE). If a lot of cell death is present at this stage, wash all wells with 500 &#181;L of PBS before media change. 
	NOTE: To confirm successful endoderm differentiation, perform flow cytometry to assess expression of SOX17. We normally expect &#62;80% of cells to be SOX17 positive by D3 DE. If expression of SOX17 is suboptimal cell seeding density should be optimized as well as concentrations of Act-A.</li>
	<li>Start HG differentiation at this point, i.e. 72 h post start of DE differentiation. Prepare 12 mL of HG media by adding CHIR99021 (3 &#181;M)&#160; and RA (1 &#956;M) to endoderm basal media (Table 1). 
	NOTE: At D3 DE the cell should have formed a uniform monolayer. Optimal DE differentiation is crucial for further stages of differentiation.</li>
	<li>Aspirate DE media.</li>
	<li>Start HG differentiation by adding 1 mL of HG media to each well of the 12 well plate.</li>
	<li>Continue the differentiation for 4 days with daily media changes. 
	NOTE: To determine success of DE posteriorization, perform flow cytometry to assess expression of CDX2. By D4 of HG differentiation we normally expect &#62;80% of cells to be CDX2 positive. If posteriorization is suboptimal, concentration of CHIR99021 should be optimized.</li>
	<li>To collect a sample for RNA extraction, aspirate differentiation media and wash the well with 500 ul of PBS.</li>
	<li>Aspirate PBS and add a suitable volume of cell lysis buffer from an RNA extraction kit.</li>
	<li>Using a p1000 pipette, scrape the bottom of the well to ensure lysis of all the cells.</li>
	<li>Aspirate the cell lysate and place in a clean tube.</li>
	<li>Proceed to RNA extraction or freeze the lysate at -20 &#176;C until ready for RNA extraction.</li>
	<li>For immunostaining, aspirate differentiation media and wash wells with 500 &#181;L of PBS.</li>
	<li>Aspirate the PBS and add 500 &#181;L of 4% PFA. 
	NOTE: PFA is toxic. Use appropriate PPE and follow local laboratory procedures for PFA disposal.</li>
	<li>Incubate at 4 &#176;C for 20 min.</li>
	<li>Remove PFA and wash the wells with 500 &#181;L of PBS three times.</li>
	<li>Leave the last PBS wash on the cells until ready to perform immunostaining.</li>
</ol>
2. Passaging of intestinal organoids
<ol>
	<li>Prepare intestinal basal media according to Table 2.</li>
	<li>To transfer from 2D to 3D cell culture, use a 6 well plate to generate DE cells form hiPSCS. Detach the monolayer of cells form the 6 cell plate using a 5 mL stripette.</li>
	<li>Collect cells into a 15 mL centrifuge tube, before centrifuging at 400 x g for 1 min to produce a cell pellet.</li>
	<li>Resuspend the cell pellet in intestinal growth media containing growth factors: SB202190 (10 &#181;M), A83-01 (500 nM), Gastrin (10 nM), Noggin (100 ng/&#181;L), EGF (500 ng/&#181;L), R-Spondin1 (100 ng/mL), CHIR99021 (6 &#181;M), ROCK inhibitor (10 &#181;M).</li>
	<li>Add appropriate volume of extracellular matrix dependent on the number of wells being plated into. This can be calculated using the equations below. 
	[1] Total volume of extracellular matrix/media (&#181;L) = 30 &#181;L * number of wells of 48-well plate 
	[2] Required volume of extracellular matrix (&#181;L) = Answer from [1] * 2/3 
	[3] Required volume of media (&#181;L) = Answer from [1] * 1/3</li>
	<li>Add 30 &#181;L of cell suspension to the center of each well of a 48-well plate.</li>
	<li>Incubate the plate in a 37&#160;&#176;C incubator for a minimum of 5 min to allow the extracellular matrix to set.</li>
	<li>Once the extracellular matrix domes have set, add 300 &#181;L of intestinal growth media containing all growth factors to each well.</li>
	<li>Return the plate to a 37&#160;&#176;C incubator with 5% CO2. 
	NOTE: If after 48 h no organoids can be observed and/or there is significant cell death ROCKi and NOGGIN concentrations may need to be optimized.</li>
	<li>To passage the organoids, observe the cells under a light microscope to assess density and size of organoids and determine whether they need passaging.</li>
	<li>Replace cell culture media with ice cold PBS. 
	NOTE: Organoid cultures will need splitting approximately every 5-7 days. Passaging of intestinal organoid cultures is required once there is an accumulation of cell debris evident within the organoid lumen and a yellowing of the surrounding intestinal growth medium.</li>
	<li>Mechanically detach organoids and extracellular matrix sphere from the plate using a scraping motion with a 5 mL stripette.</li>
	<li>Collect the organoids from each well into a 15 mL centrifuge tube.</li>
	<li>Centrifuge organoid suspension at 400 x g for 1 min to pellet the organoids. Aspirate the supernatant until reaching the top of the cell pellet, being careful when having reached the visible extracellular matrix layer.</li>
	<li>Resuspend the pellet in 15 mL of ice cold PBS. 
	NOTE: This step serves to wash any remaining extracellular matrix that was not removed in the initial spin.</li>
	<li>Centrifuge at 400 x g for 1 min. Aspirate the media until the pellet, containing the organoids.</li>
	<li>Resuspend in 1 mL of ice cold PBS. Using a p200 pipette, manually disrupt the intact organoids by pipetting up and down several times. 
	NOTE: Observe the size of the organoids using light microscope to determine whether they need to be further dissociated.</li>
	<li>Add 9 mL of media without growth factors.</li>
	<li>Centrifuge at 400 x g for 1 min. Aspirate the supernatant until the organoids pellet.</li>
	<li>Calculate the required amount of extracellular matrix and media using the equations below: 
	[1] Total volume of extracellular matrix/media (&#181;L) = 30 &#181;L * number of wells of 48-well plate 
	[2] Required volume of extracellular matrix (&#181;L) = Answer from [1] * 2/3 
	[3] Required volume of media (&#181;L) = Answer from [1] * 1/3</li>
	<li>Resuspend the organoid pellet in the calculated volume of intestinal media with growth factors (including Noggin &#38; ROCK inhibitor).</li>
	<li>Add the required volume of extracellular matrix into this cell suspension and resuspend to ensure even distribution of organoids.</li>
	<li>Pipette 30 &#181;L of this suspension into the center of each well of a 48 well plate (preferably pre-heated in a 37 &#176;C incubator).</li>
	<li>Return the plate to a 37 &#176;C incubator for 5 min until the extracellular matrix has set.</li>
	<li>Prepare intestinal media with growth factors (+ ROCK inhibitor) (approximately 17 mL per 48 well plate).</li>
	<li>Add 300 &#181;L to each well.</li>
	<li>Incubate at 37 &#176;C at 5% CO2.</li>
	<li>Following passaging, aspirate the media for the intestinal organoids and replace with fresh intestinal media with growth factors (without Noggin &#38; ROCK inhibitor) every 2-4 days. 
	NOTE:&#160;If after 48 hours no organoids can be observed and/or there is significant cell death ROCKi and NOGGIN concentrations may need to be optimized. 
	NOTE: Intestinal organoids respond to a range of inflammatory mediators in vivo. TNF&#945; is a cell signaling protein involved in several inflammatory processes.</li>
	<li>To trigger an inflammatory response in intestinal organoids, prepare TNF&#945; at a concentration of 40 ng/mL in basal media only.</li>
	<li>Aspirate media from 48 well plate.</li>
	<li>Add 300 &#181;L of prepared basal media containing 40 ng/mL TNF&#945;.</li>
	<li>Incubate plate at 37&#160;&#176;C for 48 hours to replicate a pro-inflammatory environment. 
	NOTE: Intestinal organoids respond to a range of inflammatory mediators in vivo. TNF&#945; is a cell signaling protein involved in several inflammatory processes.</li>
	<li>Dispose of any remaining cells by aspiration into a vacuum trap containing 5% Trigene.</li>
</ol>

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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=Directed+differentiation+of+human+pluripotent+stem+cells+into+intestinal+tissue+in+vitro.">Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro.</a> Nature. 470, 105-109 (2011).</li><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, 1762-1772 (2011).</li><li>Giacalone, J. 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The authors have nothing to disclose.

Here, we describe a protocol for the differentiation of human pluripotent cells into human intestinal organoids. We demonstrate their use to study inflammation; however, this can be applied to various contexts, and coupled with CRISPR/Cas9 gene editing approaches14, on any genetic background. Once differentiated, following the natural developmental differentiation sequence of definitive endoderm, hindgut endoderm and then intestinal epithelium, the resulting organoids can be continually cultured and passaged for more than 12 months.
A critical aspect of this protocol is the initial plating density of undifferentiated stem cells prior to endoderm differentiation. If this is not optimized sufficiently cells will likely die during the initial DE differentiation step (if cells are too sparse) or reduce the efficiency of the DE differentiation (if the cells are too dense). The correct starting density needs to be optimized for the cell line being used, and the correct density should generate a monolayer by the end of DE D3. Flow cytometry should be used to determine efficiency of DE specification and we typically see &#62;80% of cells positive for SOX17 and/or CXCR4. When the number of SOX17 positive cells is less than 60%, the efficiency of HG patterning is impacted, which results in fewer organoids forming when transferred to the extracellular matrix. This will ultimately cause the resulting organoid cultures to fail. To determine if patterning DE to HG has been successful, we assess the number of CDX2 positive cells by flow cytometry and typically expect to see &#62;80% positive cells. Again, if the number of CDX2 positive cells falls below 50% this will have an adverse effect on the number of intestinal organoids that are generated when transferred to 3D extracellular matrix culture.
Following transfer of 2D monolayers into 3D culture, small compact spheres should appear 24-48 h following transfer. Large sheets of dead cells can appear depending on the differentiation efficiency for the cell line used. Instead of immediately passaging cultures to remove these debris, we allow the organoids to fully form and develop their more complex, folded structure. Waiting 7-10 days before attempting the first passing ensures that sufficient dividing cells are present to generate many new intestinal organoids. Any debris that are still present in the culture can be easily removed during the passaging process by slowly spinning the dissociated organoid/debris mixtures in a tube with sufficient speed to pellet the organoids but leave sheet of cells floating in the media. Media and cellular debris can then be aspirated so that only the pellet of organoids remains.
The limitation of this approach is that hiPSC-derived cell types are not often fully mature in terms of gene expression and functional profiles. To determine if hiPSC-derived intestinal tissue is suitable for specific applications the organoids should be characterized for different cell types including enterocytes (VIL), enteroendocrine cells (neurog3), goblet cells (MUC2), transient amplifying cells (CD133), paneth cells (FZD5) and LGR5+ stem cells (LGR5) to determine the organoid cellular composition.
Overall, the major advantage of this protocol over many other organoid differentiation protocols is that this culture platform is very cost-effective due to replacement of several recombinant proteins and conditioned media preparations with small molecules15,16. The differentiation into HG is very simple and fast and can be applied to both human embryonic and induced pluripotent stem cells with identical outcomes. When followed rigorously, and optimized for the cell lines being used it provides a relatively simple model platform free of contaminating mesenchymal cells that can then be applied to study intestinal epithelium in a variety of context including inflammation, host pathogen interactions7. Intestinal fibrosis modeling could be investigated by providing pro-fibrotic stimuli and then assessing expression of extracellular matrix proteins such as collagen, laminin and fibronectin by QPCR, western blot and ELISA. Using CRISPR/Cas9 gene editing techniques on undifferentiated stem cell lines prior to differentiation allows for the creation of gene knockout or protein overexpression organoids that could be used to create disease specific organoids and more complex disease models14,17,18.

The properties of pluripotent stem cells (PSCs), such as self-renewal and the ability to differentiate to any cell type of the human body, make them valuable tools in the study of development, disease pathology and drug testing1. Human induced pluripotent stem cells (hiPSC) are particularly useful for disease modelling studies as they can be derived from patients, directly capturing the genome responsible for the disease phenotype2,3. Such hiPSCs can be differentiated to the cell type affected by the genetic defect allowing careful examination of molecular mechanism of the disease4.
Differentiation protocols for human PSCs aim to direct differentiation of cells via the main developmental stages by activation or inhibition of specific signaling pathways governing lineage commitment and specification. Maintenance of hiPSC in a pluripotent state requires moderate levels of Activin A (Act-A) signaling, while a high dosage of Act-A for 3 days commits hiPSC to a definitive endoderm (DE) fate5,6. Act-A and Wnt pathways direct anterior-posterior identity of the DE. Signaling by Act-A induces foregut (FG) markers such as HHEX, HNF4&#945; and GATA4, while blocking expression of hindgut (HG) genes such as CDX2. Wnt signaling induces posteriorization of the DE, which then adopts a HG gene expression profile7,8. Once HG cell identity is established, differentiation can be moved from 2D to 3D and directed towards the formation of intestinal organoids.
Intestinal organoids are typically cultured in a 3D extracellular matrix (e.g., Matrigel or other compatible ECMs) based culture system9, comprised of laminin, collagen IV and entactin and enriched with growth factors such as EGF, FGF, PDGF and IGF-1 to contribute to the support survival and proliferation. The organoids are cultured in a defined medium containing Gastrin, Noggin and CHIR to stimulate and support intestinal stem cell growth and proliferation during long-term culture.
After intestinal epithelial cells are embedded into the extracellular matrix, intestinal crypts begin to form and expand eventually forming spheroids. These mature into organoid structures that mimic physiological functioning of intestinal epithelium. Organoids can typically be cultured for more than 1 year without significant loss of functional and gene expression profiles. Passaging is required on a weekly basis using enzymatic digestion of the organoids into smaller fragments which then self-reassemble into complete organoids.
Established organoid lines can be used as a reliable model of numerous disorders linked to the intestine, including Crohn&#8217;s Disease, Ulcerative Colitis and colorectal cancers10,11,12,13. This is a preferred model to animal cells as they express human genes linked to these disorders and respond to external stimuli more closely resembling that which occurs in human tissue in vivo.

<table>
	<tbody>
		<tr>
			<td>A83-01</td>
			<td>Tocris</td>
			<td>2939</td>
			<td></td>
		</tr>
		<tr>
			<td>Activin A</td>
			<td>R&#38;D</td>
			<td>338-AC</td>
			<td></td>
		</tr>
		<tr>
			<td>Advanced DMEM/F12 (1X)</td>
			<td>Life Technologies</td>
			<td>12654-010</td>
			<td></td>
		</tr>
		<tr>
			<td>B27 supplement</td>
			<td>Gibco</td>
			<td>17504044</td>
			<td></td>
		</tr>
		<tr>
			<td>CHIR99021</td>
			<td>Sigma</td>
			<td>SML1046-5MG</td>
			<td></td>
		</tr>
		<tr>
			<td>Epidermal Growth Factor</td>
			<td>R&#38;D Systems</td>
			<td>236-EG-01M</td>
			<td></td>
		</tr>
		<tr>
			<td>Gastrin</td>
			<td>Sigma Aldrich</td>
			<td>G9145</td>
			<td></td>
		</tr>
		<tr>
			<td>GlutaMAX (100X)</td>
			<td>Life Technologies</td>
			<td>15630-056</td>
			<td></td>
		</tr>
		<tr>
			<td>Growth Factor reduced Matrigel</td>
			<td>BD</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES Buffer solution (1M)</td>
			<td>Life Technologies</td>
			<td>15630-080</td>
			<td></td>
		</tr>
		<tr>
			<td>N2 Supplement (100X)</td>
			<td>Gibco</td>
			<td>17502-048</td>
			<td></td>
		</tr>
		<tr>
			<td>N-acetyl-cysteine</td>
			<td>Sigma Aldrich</td>
			<td>A7250</td>
			<td></td>
		</tr>
		<tr>
			<td>Nicotinamide</td>
			<td>Sigma Aldrich</td>
			<td>N0636</td>
			<td></td>
		</tr>
		<tr>
			<td>Noggin</td>
			<td>R&#38;D Systems</td>
			<td>6057-NG</td>
			<td></td>
		</tr>
		<tr>
			<td>Non-essential amino acids</td>
			<td>Gibco</td>
			<td>11140-050</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraformaldehyde</td>
			<td>VWR</td>
			<td>9713.5</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin/Streptomycin</td>
			<td>Gibco</td>
			<td>15140122</td>
			<td></td>
		</tr>
		<tr>
			<td>Phosphate Buffered Saline</td>
			<td>Gibco</td>
			<td>14190-094</td>
			<td></td>
		</tr>
		<tr>
			<td>Retinoic Acid</td>
			<td>Sigma</td>
			<td>302-79-4</td>
			<td></td>
		</tr>
		<tr>
			<td>ROCK inhibitor</td>
			<td>Tocris</td>
			<td>1254/1</td>
			<td></td>
		</tr>
		<tr>
			<td>ROCK inhibitor Y-27632</td>
			<td>Tocris</td>
			<td>1254</td>
			<td></td>
		</tr>
		<tr>
			<td>RPMI</td>
			<td>Sigma</td>
			<td>R8758-500ml</td>
			<td></td>
		</tr>
		<tr>
			<td>R-Spondin-1</td>
			<td>Peprotech</td>
			<td>120-38</td>
			<td></td>
		</tr>
		<tr>
			<td>SB202190</td>
			<td>Tocris</td>
			<td>1264</td>
			<td></td>
		</tr>
		<tr>
			<td>TrypLe Express</td>
			<td>Gibco</td>
			<td>12604-021</td>
			<td></td>
		</tr>
		<tr>
			<td>Wnt 3a</td>
			<td>R&#38;D</td>
			<td>5036-WN</td>
			<td></td>
		</tr>
	</tbody>
</table>

generation of hipsc-derived intestinal organoids for developmental and disease modelling applications

hiPSC-derived intestinal organoids are epithelial structures that self-assemble from differentiated cells into complex 3D structures, representative of the human intestinal epithelium, in which they exhibit crypt/villus-like structures. Here, we describe the generation of hiPSC-derived intestinal organoids by the stepwise differentiation of hiPSCs into definitive endoderm, which is then posteriorized to form hindgut epithelium before being transferred into 3D culture conditions. The 3D culture environment consists of extracellular matrix (ECM) (e.g., Matrigel or other compatible ECM) supplemented with SB202190, A83-01, Gastrin, Noggin, EGF, R-spondin-1 and CHIR99021. Organoids undergo passaging every 7 days, where they are mechanically disrupted before transfer to fresh extracellular matrix and allowed to expand. QPCR and immunocytochemistry confirm that hiPSC-derived intestinal organoids contain mature intestinal epithelial cell types including goblet cells, Paneth cells and enterocytes. Additionally, organoids show evidence of polarization by expression of villin localized on the apical surface of epithelial cells.
The resulting organoids can be used to model human intestinal development as well as numerous human intestinal diseases including inflammatory bowel disease. To model intestinal inflammation, organoids can be exposed to inflammatory mediators such as TNF-&#945;, TGF-&#946;, and bacterial LPS. Organoids exposed to proinflammatory cytokines display an inflammatory and fibrotic phenotype in response. Pairing of healthy versus hiPSCs derived from patients with IBD may be useful in understanding mechanisms driving IBD. This may reveal novel therapeutic targets and novel biomarkers to assist in early disease diagnosis.

A schematic of the differentiation protocol is shown in Figure 1A. On day 1 of the protocol, hiPSCs should be compact and forming small colonies with total confluence approximately 50-60%. 24 hours following induction of differentiation towards DE cells begin to migrate away from the stem cell colonies to form a monolayer of cells. This continues over the following 3 days and should form a complete monolayer on D3 of DE differentiation (Figure 1). Gene expression should be monitored over the course of differentiation with pluripotency markers (OCT4, NANOG, SOX2) highly expressed on D0 and rapidly downregulated during DE differentiation. During DE differentiation T expression should peak on D1, followed by EOMES and MIXL on D2. On D2 DE genes (SOX17, FOXA2, GATA4, CXCR4) should begin to be expressed and peak at D3 (Figure 2 and Figure 3). Cells should be a monolayer by DE D3 and can then be posteriorized into hindgut endoderm. During the posteriorization event 3D structures will start to form as early as D2. However, sometimes they will only start to appear at D4 or not at all; this is not always indicative of whether or not the cells will proceed and form intestinal organoids (Figure 1). During HG specification CDX2 and HNF4a expression should be induced and increase over time (Figure 3).
Following transfer of 2D sheets of cells into extracellular matrix, clumps of 2D cells will be observed for the first 24 h. After 48 h sheets of cells should begin to auto organize into more compacted 3D spheroid structures that are initially small (Figure 4A) then gradually increase in size and complexity over 7-10 days of culture (Figure 4B &#38; Figure 4C). Organoids should not be passaged until they have achieved a clear organoid/spheroid morphology with obvious epithelium with the lumen facing towards the center of the organoid/spheroid (Figure 4D). At this stage immunocytochemistry can be used to confirm expression of intestinal markers such as villin and CDX2 (Figure 5). Not all clumps of 2D cells will develop into organoids and there will be some contaminating dead cells within the extracellular matrix. These dead sheets of cells should be ignored until the surviving cells have formed large organoids and are ready for passaging.
To model inflammation, TNF&#945; can be added to the tissue culture medium for 24-48 h. Following incubation with proinflammatory molecules, organoids are harvested using the same technique used for their isolation and passaging and then lysed using a cell buffer compatible application such as QPCR or western blotting. If shorter exposures are required, organoids should first be removed from the extracellular matrix and exposed to TNF&#945; in suspension using a 1.5 mL tube. Treatment of intestinal organoids with TNF&#945; for 48 h typically induces expression of pro-inflammatory markers (TNF&#945;, IL1B, IL8, IL23) while negatively affecting expression of intestinal epithelial markers (LGR5, VIL) (Figure 6).
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td colspan="2">Endoderm basal media</td>
			<td>50 mL</td>
		</tr>
		<tr>
			<td colspan="2">RPMI 1640</td>
			<td>48.5 mL</td>
		</tr>
		<tr>
			<td colspan="2">B27 Supplement</td>
			<td>1 mL</td>
		</tr>
		<tr>
			<td colspan="2">1% NEAA</td>
			<td>0.5 mL</td>
		</tr>
	</tbody>
</table>
Table 1: Composition of endodermal basal media for endoderm differentiation.
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td colspan="2">Intestinal Basal Media</td>
			<td>50 mL</td>
		</tr>
		<tr>
			<td colspan="2">Advanced DMEM/F12</td>
			<td>46.5 mL</td>
		</tr>
		<tr>
			<td colspan="2">HEPES Buffer</td>
			<td>0.5 mL</td>
		</tr>
		<tr>
			<td colspan="2">GlutaMAX</td>
			<td>0.5 mL</td>
		</tr>
		<tr>
			<td colspan="2">Nicotinamide</td>
			<td>0.5 mL</td>
		</tr>
		<tr>
			<td colspan="2">N2 Supplement</td>
			<td>0.5 mL</td>
		</tr>
		<tr>
			<td colspan="2">B27 Supplement</td>
			<td>1.0 mL</td>
		</tr>
		<tr>
			<td colspan="2">Pen/Strep</td>
			<td>0.5 mL</td>
		</tr>
	</tbody>
</table>
Table 2: Composition of intestinal basal media for culture of intestinal organoids
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/61199/61199fig01.jpg" /> 
Figure 1: Morphological changes during differentiation of hiPSC via definitive endoderm to the hindgut lineage. 
(A)&#160;Schematic overview of intestinal differentiation protocol. This cell line of hiPSC forms loose colonies of small cells with a high nucleus to cytoplasm ratio. As the differentiation proceeds, the cells undergo changes consistent with transition from the epithelial to the mesenchymal phenotype and by DE D3 form a uniform monolayer. Once appropriate signals are delivered, DE cells elongate and form a more densely packed monolayer with 3D spheroids appearing as soon as HD D3 but this is dependent upon cell line used and is not a requirement for transition to 3D culture (B). Scale bar: 100 &#181;m. <a href="https://www.jove.com/files/ftp_upload/61199/61199fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/61199/61199fig02.jpg" /> 
Figure 2: Differentiation of hiPSCs to HG endoderm induces expression of endodermal genes. 
Immunostaining of hiPSC differentiating to definitive endoderm shows changes in expression of TFs at protein level. Pluripotency markers (NANOG and OCT4) are downregulated by DE D3 (A). Expression of mesendoderm marker BRA(T) is present at D1 of the protocol (B) and DE specific TFs SOX17 and FOXA2 appear on D2 (B &#38; C). Scale bar: 200 mm. <a href="https://www.jove.com/files/ftp_upload/61199/61199fig02large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/61199/61199fig03v2.jpg" /> 
Figure 3: Gene expression changes by qPCR during hiPSC differentiation to hindgut endoderm (HG). 
Genes associated with pluripotency are downregulated (OCT4, NANOG, SOX2) followed by transient expression of mesendoderm genes (T, EOMES, MIXL1), and finally expression of DE genes (SOX17, FOXA2, CXCR4) and hindgut genes (CDX2, GATA4, HNF4a). Data presented as mean &#177;SD.&#160;<a href="https://www.jove.com/files/ftp_upload/61199/61199fig03largev2.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/61199/61199fig04.jpg" /> 
Figure 4: HG endoderm self-assembles to form 3D intestinal organoids in 3D extracellular matrix culture. 
HG endoderm is transferred into a suitable 3D extracellular matrix culture and initially forms small solid clumps of cells (A). Clumps of HG endoderm expand over 7-10 days of culture (B) and then become asymmetrical and begin to form a more complex epithelium (C) eventually giving rise to organoids with clear epithelial morphology and a luminal surface facing towards the centre of the organoid (D). Scale bars = 50 &#181;m <a href="https://www.jove.com/files/ftp_upload/61199/61199fig04large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 5" class="xfigimg" src="/files/ftp_upload/61199/61199fig05.jpg" /> 
Figure 5: Established hiPSC-derived intestinal organoids express intestinal markers. 
Immunocytochemistry showing expression of CDX2 and Villin. Scale bars = 100 &#181;m <a href="https://www.jove.com/files/ftp_upload/61199/61199fig05large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 6" class="xfigimg" src="/files/ftp_upload/61199/61199fig06v2.jpg" /> 
Figure 6: Effect of TNF&#945; on the inflammatory profile &#38; intestinal cell expression of healthy intestinal organoids. 
Inflammatory profile of healthy colonic organoids following 48 hour treatment with TNF&#945; (40 ng/mL). Expression of pro-inflammatory markers (TNF&#945;, IL-8 &#38; IL-23) increases following exposure to TNF&#945;, while at the same time expression of intestinal epithelial markers (LGR5, VIL) are downregulated. Statistical analyses were performed by two-sided student&#8217;s t-test. Data are expressed as mean &#177; SD of each group. *P &#60; .01; **P &#60; .001; ***P &#60; .0001. (n=3). <a href="https://www.jove.com/files/ftp_upload/61199/61199fig06largev2.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about Generation of hiPSC-Derived Intestinal Organoids for Developmental and Disease Modelling Applications at JoVE.com

Generation of hiPSC-Derived Intestinal Organoids for Developmental and Disease Modelling Applications

This protocol allows for the differentiation of human pluripotent cells into intestinal organoids. The protocol mimics normal human development by differentiating cells into a population of definitive endoderm, hindgut endoderm and then intestinal epithelium. This makes the protocol suitable for studying both intestinal development as well as disease modelling applications.

hiPSC-derived intestinal organoids are epithelial structures that self-assemble from differentiated cells into complex 3D structures, representative of ...

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2.3K Views.  University of Nottingham. This protocol allows for the differentiation of human pluripotent cells into intestinal organoids. The protocol mimics normal human development by differentiating cells into a population of definitive endoderm, hindgut endoderm and then intestinal epithelium. This makes the protocol suitable for studying both intestinal development as well as disease modelling applications.

Video: Generation of hiPSC-Derived Intestinal Organoids for Developmental and Disease Modelling Applications

Windowing Chicken Eggs for Developmental Studies

The study of development has been greatly aided by the use of the chick embryo as an experimental model.  The ease of accessibility of the embryo has allowed for experiments to map cell fates using several approaches, including chick quail chimeras and focal dye labeling.  In addition, it allows for molecular perturbations of several types, including placement of protein-coated beads and introduction of plasmid DNA using in ovo electroporation.  These experiments have yielded important data on the development of the central and peripheral nervous systems.  For many of these studies, it is necessary to open the eggshell and reclose it without perturbing the embryo's growth.  The embryo can be examined at successive developmental stages by re-opening the eggshell.  While there are several excellent methods for opening chicken eggs, in this article we demonstrate one method that has been optimized for long survival times.  In this method, the egg rests on its side and a small window is cut in the shell.  After the experimental procedure, the shell is used to cover the egg for the duration of its development.  Clear plastic tape overlying the eggshell protects the embryo and helps retain hydration during the remainder of the incubation period.  This method has been used beginning at two days of incubation and has allowed survival through mature embryonic ages.

The ease of accessibility of the embryo has allowed for experiments to map cell fates using several approaches, including chick quail chimeras and focal dye labeling. In this article we demonstrate one egg preparation method that has been optimized for long survival times.

The study of development has been greatly aided by the use of the chick embryo as an experimental model.  The ease of accessibility of the embryo has ...

Absolute Quantum Yield Measurement of Powder Samples

Measurement of fluorescence quantum yield has become an important tool in the search for new solutions in the development, evaluation, quality control and research of illumination, AV equipment, organic EL material, films, filters and fluorescent probes for bio-industry.
Quantum yield is calculated as the ratio of the number of photons absorbed, to the number of photons emitted by a material. The higher the quantum yield, the better the efficiency of the fluorescent material.
For the measurements featured in this video, we will use the Hitachi F-7000 fluorescence spectrophotometer equipped with the Quantum Yield measuring accessory and Report Generator program. All the information provided applies to this system. 
Measurement of quantum yield in powder samples is performed following these steps:
<ol>
 <li>Generation of instrument correction factors for the excitation and emission monochromators. This is an important requirement for the correct measurement of quantum yield. It has been performed in advance for the full measurement range of the instrument and will not be shown in this video due to time limitations.</li>
 <li>Measurement of integrating sphere correction factors. The purpose of this step is to take into consideration reflectivity characteristics of the integrating sphere used for the measurements.</li>
 <li>Reference and Sample measurement using direct excitation and indirect excitation.</li>
 <li>Quantum Yield calculation using Direct and Indirect excitation. Direct excitation is when the sample is facing directly the excitation beam, which would be the normal measurement setup. However, because we use an integrating sphere, a portion of the emitted photons resulting from the sample fluorescence are reflected by the integrating sphere and will re-excite the sample, so we need to take into consideration indirect excitation. This is accomplished by measuring the sample placed in the port facing the emission monochromator, calculating indirect quantum yield and correcting the direct quantum yield calculation.</li>
 <li>Corrected quantum yield calculation.</li>
 <li>Chromaticity coordinates calculation using Report Generator program.</li>
</ol>
The Hitachi F-7000 Quantum Yield Measurement System offer advantages for this
application, as follows:
<ul>
 <li>High sensitivity (S/N ratio 800 or better RMS). Signal is the Raman band of water measured under the following conditions: Ex wavelength 350 nm, band pass Ex and Em 5 nm, response 2 sec), noise is measured at the maximum of the Raman peak. High sensitivity allows measurement of samples even with low quantum yield. Using this system we have measured quantum yields as low as 0.1 for a sample of salicylic acid and as high as 0.8 for a sample of magnesium tungstate.</li>
 <li>Highly accurate measurement with a dynamic range of 6 orders of magnitude allows for measurements of both sharp scattering peaks with high intensity, as well as broad fluorescence peaks of low intensity under the same conditions. </li>
 <li>High measuring throughput and reduced light exposure to the sample, due to a high scanning speed of up to 60,000 nm/minute and automatic shutter function. </li>
 <li>Measurement of quantum yield over a wide wavelength range from 240 to 800 nm.</li>
 <li>Accurate quantum yield measurements are the result of collecting instrument spectral response and integrating sphere correction factors before measuring the sample.</li>
 <li>Large selection of calculated parameters provided by dedicated and easy to use software.
</li>
</ul> 
During this video we will measure sodium salicylate in powder form which is known to have a quantum yield value of 0.4 to 0.5.

In this video we will demonstrate measuring and calculating absolute quantum yield and chromaticity coordinates directly in powder samples using the Hitachi F-7000 Quantum Yield Measuring System.

Measurement of fluorescence quantum yield has become an important tool in the search for new solutions in the development, evaluation, quality control and ...

A Protocol for Lentiviral Transduction and Downstream Analysis of Intestinal Organoids

Intestinal crypt-villus structures termed organoids, can be kept in sustained culture three dimensionally when supplemented with the appropriate growth factors. Since organoids are highly similar to the original tissue in terms of homeostatic stem cell differentiation, cell polarity and presence of all terminally differentiated cell types known to the adult intestinal epithelium, they serve as an essential resource in experimental research on the epithelium. The possibility to express transgenes or interfering RNA using lentiviral or retroviral vectors in organoids has increased opportunities for functional analysis of the intestinal epithelium and intestinal stem cells, surpassing traditional mouse transgenics in speed and cost. In the current video protocol we show how to utilize transduction of small intestinal organoids with lentiviral vectors illustrated by use of doxycylin inducible transgenes, or IPTG inducible short hairpin RNA for overexpression or gene knockdown. Furthermore, considering organoid culture yields minute cell counts that may even be reduced by experimental treatment, we explain how to process organoids for downstream analysis aimed at quantitative RT-PCR, RNA-microarray and immunohistochemistry. Techniques that enable transgene expression and gene knock down in intestinal organoids contribute to the research potential that these intestinal epithelial structures hold, establishing organoid culture as a new standard in cell culture.

In this video protocol we give a step by step explanation of lentiviral transduction in organoids of primary intestinal epithelium and of processing and downstream analysis of these cultures by quantitative RT-PCR, RNA-microarray and immunohistochemistry.

Intestinal crypt-villus structures termed organoids, can be kept in sustained culture three dimensionally when supplemented with the appropriate growth ...

A Mouse Model of Intestinal Partial Obstruction

Intestinal obstructions, that impede or block peristaltic movement, can be caused by abdominal adhesions and most gastrointestinal (GI) diseases including tumorous growths. However, the cellular remodeling mechanisms involved in, and caused by, intestinal obstructions are poorly understood. Several animal models of intestinal obstructions have been developed, but the mouse model is the most cost/time effective. The mouse model uses the surgical implantation of an intestinal partial obstruction (PO) that has a high mortality rate if it is not performed correctly. In addition, mice receiving PO surgery fail to develop hypertrophy if an appropriate blockade is not used or not properly placed. Here, we describe a detailed protocol for PO surgery which produces reliable and reproducible intestinal obstructions with a very low mortality rate. This protocol utilizes a surgically placed silicone ring that surrounds the ileum which partially blocks digestive movement in the small intestine. The partial blockage makes the intestine become dilated due to the halt of digestive movement. The dilation of the intestine induces smooth muscle hypertrophy on the oral side of the ring that progressively develops over 2 weeks until it causes death. The surgical PO mouse model offers an in vivo model of hypertrophic intestinal tissue useful for studying pathological changes of intestinal cells including smooth muscle cells (SMC), interstitial cells of Cajal (ICC), PDGFR&#945;+, and neuronal cells during the development of intestinal obstruction.

Intestinal obstructions are a partial or complete blockage of the intestine that can cause severe abdominal pain, nausea, vomiting, and preventing the passage of stool. This procedure for creating intestinal partial obsructions in mice is reliable in studying the mechanisms underlying pathological cell growth and death in the intestine.

Intestinal obstructions, that impede or block peristaltic movement, can be caused by abdominal adhesions and most gastrointestinal (GI) diseases including ...

Fabrication of Amyloid-&#946;-Secreting Alginate Microbeads for Use in Modelling Alzheimer's Disease

According to the amyloid cascade hypothesis, the earliest trigger in the development of Alzheimer&#8217;s disease (AD) is the accumulation of toxic amyloid-&#946; (A&#946;) fragments, eventually leading to the classical features of the disease: amyloid plaques, neurofibrillary tangles and synaptic and neuronal loss. The lack of relevant non-transgenic preclinical models reflective of disease progression is one of the main factors hindering the discovery of effective drug treatments. To this end, we have developed a protocol for the fabrication of alginate microbeads containing amyloid-secreting cells useful for the study of the effects of chronic A&#946; production.
Chinese hamster ovary cells previously transfected with a human APP gene, secreting A&#946; (i.e., 7PA2 cells), were used in this study. A three-dimensional (3D) in vitro model for the sustained release of A&#946; was fabricated by encapsulation of 7PA2 cells in alginate. The process was optimized to target a bead diameter of 500-600 &#956;m for further in vivo studies. Optimization of 7PA2 cell encapsulation in alginate was performed altering fabrication parameters, e.g., alginate concentration, gel flow rate, electrostatic potential, head vibration frequency, gelling solution. Levels of secreted A&#946; were analyzed over time and compared between alginate beads and standard cell culture methods (up to 96 h).
A concentration of 1.5 x 106 7PA2 cells/mL and an alginate concentration of 2% (w/v) buffered with HEPES and subsequent gelation in 0.5 M calcium chloride for 5 min were found to fabricate the most stable microbeads. Fabricated microbeads were 1) of uniform size, 2) with an average diameter of 550 &#956;m, 3) containing about 100-150 cells per microbead and 4) able to secrete A&#946;.
In conclusion, our optimized method for the production of stable alginate microbeads containing amyloid-producing 7PA2 cells might enable the modeling of important aspects of AD both in vitro and in vivo.

This protocol illustrates a cell encapsulation method by rapid physical gelation of alginate to immobilize cells. Obtained microbeads allow controlled and sustained secretion of amyloid-&#946; over time and can be used to study the effects of secreted amyloid-&#946; in in vitro and in vivo models.

According to the amyloid cascade hypothesis, the earliest trigger in the development of Alzheimer&#8217;s disease (AD) is the accumulation of toxic ...

Mucociliary Epithelial Organoids from Xenopus Embryonic Cells: Generation, Culture and High-Resolution Live Imaging

Mucociliary epithelium provides the first line of defense by removing foreign particles through the action of mucus production and cilia-mediated clearance. Many clinically relevant defects in the mucociliary epithelium are inferred as they occur deep within the body. Here, we introduce a tractable 3D model for mucociliary epithelium generated from multipotent progenitors that were microsurgically isolated from Xenopus laevis embryos. The mucociliary epithelial organoids are covered with newly generated epithelium from deep ectoderm cells and later decorated with distinct patterned multiciliated cells, secretory cells, and mucus-producing goblet cells that are indistinguishable from the native epidermis within 24 h. The full sequences of dynamic cell transitions from mesenchymal to epithelial that emerge on the apical surface of organoids can be tracked by high-resolution live imaging. These in vitro cultured, self-organizing mucociliary epithelial organoids offer distinct advantages in studying the biology of mucociliary epithelium with high-efficiency in generation, defined culture conditions, control over number and size, and direct access for live imaging during the regeneration of the differentiated epithelium.

We describe a simple protocol to develop mucociliary epithelial organoids from deep ectoderm cells isolated from Xenopus laevis embryos. The multipotent progenitors regenerate epithelial goblet cell precursors and allow live tracking of the initiation and progression of the cell transitions on the surface of organoids.

Mucociliary epithelium provides the first line of defense by removing foreign particles through the action of mucus production and cilia-mediated ...

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 ...

Quantitative Analysis of Aspergillus nidulans Growth Rate using Live Microscopy and Open-Source Software

It is well established that colony growth of filamentous fungi, mostly dependent on changes in hyphae/mycelia apical growth rate, is macroscopically estimated on solidified media by comparing colony size. However, to quantitatively measure the growth rate of genetically different fungal strains or strains under different environmental/growth conditions (pH, temperature, carbon and nitrogen sources, antibiotics, etc.) is challenging. Thus, the pursuit of complementary approaches to quantify growth kinetics becomes mandatory in order to better understand fungal cell growth. Furthermore, it is well-known that filamentous fungi, including Aspergillus spp., have distinct modes of growth and differentiation under sub-aerial conditions on solid media or submerged cultures. Here, we detail a quantitative microscopic method for analyzing growth kinetics of&#160;the model fungus Aspergillus nidulans, using live imaging in both submerged cultures and solid media. We capture images, analyze, and quantify growth rates of different fungal strains in a reproducible and reliable manner using an open source, free software for bio-images (e.g., Fiji), in a way that does not require any prior image analysis expertise from the user.

Quantitative Analysis of Aspergillus nidulans Growth Rate using Live Microscopy and Open-Source Software

We present a label-free live imaging protocol using transmitted light microscopy techniques to capture images, analyze and quantify growth kinetics of the filamentous fungus A. nidulans in both submerged cultures and solid media. This protocol can be used in conjunction with fluorescence microscopy.

It is well established that colony growth of filamentous fungi, mostly dependent on changes in hyphae/mycelia apical growth rate, is macroscopically ...

Analyzing Oxidative Stress in Murine Intestinal Organoids using Reactive Oxygen Species-Sensitive Fluorogenic Probe

Reactive oxygen species (ROS) play essential roles in intestinal homeostasis. ROS are natural by-products of cell metabolism. They are produced in response to infection or injury at the mucosal level as they are involved in antimicrobial responses and wound healing. They are also critical secondary messengers, regulating several pathways, including cell growth and differentiation. On the other hand, excessive ROS levels lead to oxidative stress, which can be deleterious for cells and favor intestinal diseases like chronic inflammation or cancer. This work provides a straightforward method to detect ROS in the intestinal murine organoids by live imaging and flow cytometry, using a commercially available fluorogenic probe. Here the protocol describes assaying the effect of compounds that modulate the redox balance in intestinal organoids and detect ROS levels in specific intestinal cell types, exemplified here by the analysis of the intestinal stem cells genetically labeled with GFP. This protocol may be used with other fluorescent probes.

The present protocol describes a method to detect reactive oxygen species (ROS) in the intestinal murine organoids using qualitative imaging and quantitative cytometry assays. This work can be potentially extended to other fluorescent probes to test the effect of selected compounds on ROS.

Reactive oxygen species (ROS) play essential roles in intestinal homeostasis. ROS are natural by-products of cell metabolism. They are produced in ...

Laser Microdissection for Species-Agnostic Single-Tissue Applications

Single-cell methodologies have revolutionized the analysis of the transcriptomes of specific cell types. However, they often require species-specific genetic &#34;toolkits,&#34; such as promoters driving tissue-specific expression of fluorescent proteins. Further, protocols that disrupt tissues to isolate individual cells remove cells from their native environment (e.g., signaling from neighbors) and may result in stress responses or other differences from native gene expression states. In the present protocol, laser microdissection (LMD) is optimized to isolate individual nematode tail tips for the study of gene expression during male tail tip morphogenesis.
LMD allows the isolation of a portion of the animal without the need for cellular disruption or species-specific toolkits and is thus applicable to any species. Subsequently, single-cell RNA-seq library preparation protocols such as CEL-Seq2 can be applied to LMD-isolated single tissues and analyzed using standard pipelines, given that a well-annotated genome or transcriptome is available for the species. Such data can be used to establish how conserved or different the transcriptomes are that underlie the development of that tissue in different species.
Limitations include the ability to cut out the tissue of interest and the sample size. A power analysis shows that as few as 70 tail tips per condition are required for 80% power. Tight synchronization of development is needed to obtain this number of animals at the same developmental stage. Thus, a method to synchronize animals at 1 h intervals is also described.

A protocol is described that uses laser microdissection to isolate individual nematode tissues for RNA-sequencing. The protocol does not require species-specific genetic toolkits, allowing gene expression profiles to be compared between different species at the level of single-tissue samples.

Single-cell methodologies have revolutionized the analysis of the transcriptomes of specific cell types. However, they often require species-specific ...