This study was supported by the Natural Science Foundation of Guangdong Province (Grant No. 2020A0505100062), the Guangzhou City Science and Technology Key Topics Project (Grant No. 201904020025), the National Natural Science Foundation of China (Grant Nos. 31872800, 32070582, 82101937), and the Guangzhou City Postdoctoral Research Grant project (to Bangzhu Chen).

The protocol was conducted following the Declaration of Helsinki. Approval was granted by the Ethics Committee of The Third Affiliated Hospital of Guangzhou Medical University (Medical and ethical review [2021] No. 022). Before the experiment, each medium was prepared according to Juergen A. Knoblich&#39;s formula12 (Supplementary Tables 1-4), or a commercially available Cerebral Organoid Kit was used (see Table of Materials). The iPSCs used in this study were previously established by our laboratory and have obtained an informed exemption. The SCA3-iPSCs were generated from a 31-year-old female spinocerebellar ataxia type 3 (SCA3) patient genotyped as harboring 26/78 CAG repeats in the ATXN3 gene13 (Supplementary Figure 1A). The normal human iPSCs mentioned in a previous article were selected as NC-iPSCs14, and the ATXN3 gene was identified as having 14/14 CAG repeats (Supplementary Figure 1B).
1. Preparation of induced pluripotent stem cells (iPSCs)
<ol>
	<li>Collect 3 mL of peripheral blood by venipuncture with the informed consent of volunteers and patients.</li>
	<li>Isolate peripheral blood mononuclear cells according to the Ficoll-Paque method15.</li>
	<li>Establish iPSCs according to the protocol of the Sendai Reprogramming Kit (see Table of Materials).
	<ol>
		<li>Culture the iPSCs with mTeSR1 medium in 35 mm Petri dishes covered with Matrigel (a basement membrane matrix, see Table of Materials). Change the medium every day. The iPSC growth density must not exceed 75%.</li>
		<li>Digest the cells with PSC dissociation solution (see Table of Materials) and subculture them at a ratio of 1:5 every 3-5 days. 
		CAUTION: Sendai virus is used here. It must be operated in the biosafety cabinet, and self-protection measures must be taken. It should be clear whether it can be used legally in the local country. Local biosafety laws and regulations must be strictly followed when used.</li>
	</ol>
	</li>
</ol>
2. EB preparation (days 0-1)
<ol>
	<li>Remove the mTeSR1 medium from the iPSCs with a pipette and wash it 2x with 1 mL of 1x PBS.</li>
	<li>Remove the PBS with a pipette, and add 300 &#181;L of cell detachment solution (see Table of Materials) to digest the iPSCs into single cells for 3-4 min at 37 &#176;C.</li>
	<li>Resuspend the cells in 2 mL of EB-formation medium (Supplementary Table 1) and then centrifuge the sample for 5 min at 300 x g (room temperature).</li>
	<li>Pretreat the specialized 24-well plate with anti-adherence rinsing solution (500 &#181;L/well) for 5 min (see Table of Materials). 
	NOTE: Anti-adherence rinsing solution is essential for optimal EB and spheroid formation.</li>
	<li>Resuspend the cells in EB-formation medium containing Y-27632 (final concentration, 10 &#181;M, see Table of Materials), with a cell density of 1.5 x 106 cells/mL.</li>
	<li>Remove the anti-adherence rinsing solution, and rinse each well with 2 mL of EB-formation medium.</li>
	<li>Add the cells to the specialized 24-well plates at a density of 3 x 106 cells/well (Figure 1A, left). 
	NOTE: Normally, 300 EBs can be prepared in each well. This method can prepare large quantities of EBs of the same size.</li>
	<li>Centrifuge the plate at 100 x g for 2 min at room temperature. Uniformly distribute the cells in each chamber at the bottom of the plate (Figure 1A, right). 
	NOTE: If there is no suitable centrifuge, the plate can also be directly placed into the incubator for static culture, but the formation time of the EB ball will be several hours later than that under normal centrifugation.</li>
	<li>Incubate the samples at 37 &#176;C and 5% CO2 for 24 h. If centrifugation was not used in the previous step, incubate for 36 h. Keep the sample steady, and do not take it out of the incubator during this period.</li>
</ol>
3. Preparation of the soft light lamp (day 1)
<ol>
	<li>Use a transparent acrylic board with a thickness of 0.3-0.5 cm in the size of A5 paper. Paste white pads on the front and back of the acrylic plate.
	<ol>
		<li>Install a row of LED white lights on the edge of the plate so that the lights can enter from the side of the acrylic plate and then shoot out in parallel (Supplementary Figure 2A-F, Figure 1B). 
		NOTE: As the diameters of EBs in the early stage are approximately 200 &#181;m to 300 &#181;m, it is difficult to observe them clearly with the naked eye under the fluorescent lamp of clean benches. In contrast, due to the enhancement of diffuse reflection, we can detect the EBs clearly by using laterally illuminated soft light (Figure 1B, C). A 6-well plate is recommended for EB cultures in subsequent experiments. However, to better show the visual effect of soft light, dishes are sometimes used to take pictures and videos in this study instead of plates, so please do not misunderstand. The laterally illuminated soft light lamp can also be used for the 6-well plate.</li>
	</ol>
	</li>
</ol>
4. EB transfer and medium replacement (days 2-5)
<ol>
	<li>Prepare a new 6-well low adhesion plate, and add 2 mL of EB-formation medium to each well.</li>
	<li>Remove the EBs together with the medium with a 1000 &#181;L wide-bore pipette tip (see Table of Materials) and transfer them to the 6-well low adhesion plate (~100 EBs/well). 
	NOTE: The operation process adopts a soft light lamp (mentioned in step 3.) to make the EBs easier to observe. Turn off other indoor light sources to get the visual effect of the soft light better.</li>
	<li>Replace with the same volume of fresh EB-formation medium every day. Use the secondary flow to gather the EBs to the center and change the medium.
	<ol>
		<li>Aspirate the old medium by pipetting to the edge of the well slowly. Do not suck too hard; otherwise, the EBs will be removed together. Then, add fresh medium to resuspend the EBs. 
		NOTE: The principle secondary flow (Figure 1D). Induce a swirl flow by rotating the dish along a circular orbit. Due to the swirl flow, a secondary flow is induced directed toward the center. The EBs or organoids converge to the center of the well due to the secondary flow generated through rotation, after which medium change or embryoid transfer can be executed readily.</li>
	</ol>
	</li>
</ol>
5. Checking pluripotency by labeling with pluripotency marker OCT4 (day 4)
NOTE: When the diameter of the EBs is greater than 300 &#181;m, take several EBs for OCT4 marker immunofluorescence staining to detect their pluripotency.
<ol>
	<li>Fix the EBs in 4% paraformaldehyde at 4 &#176;C for 30 min, followed by washing in 1x PBS 3x for 10 min each time.</li>
	<li>Transfer the EBs to room temperature PBS containing 0.3% Triton X-100 and 3% BSA for 2 h, followed by washing in PBS 3x for 10 min each time. 
	NOTE: After being treated withTriton X-100, the EBs float on the liquid surface and can be easily sucked away with the liquid during cleaning. Operation under a stereomicroscope is recommended.</li>
	<li>Dilute the OCT4 primary antibody (see Table of Materials) with 1 mL of 1x PBS containing 1% BSA at a ratio of 1:200 and add to the EBs for incubation at 4 &#176;C overnight, then wash in PBS 3x for 10 min each time.</li>
	<li>Dilute the respective secondary antibody (see Table of Materials) with 1x PBS at 1:500 and add 1 mL to the EBs.</li>
	<li>After incubating at room temperature for 2 h, wash the cells in 1x PBS 3x for 10 min each time.</li>
	<li>Remove the PBS, add 2 mL of 1x PBS solution containing 1 &#181;g/mL DAPI, incubate at room temperature for 10 min, and then wash in PBS 3x for 10 min each time.</li>
	<li>Move the EB containing a small amount of liquid onto the slide, seal the slide with a cover glass coated with commercially available petroleum jelly (see Table of Materials) on the edge, and then observe and collect the image under the fluorescence confocal microscope. 
	NOTE: OCT4 expression represents EB pluripotency12. When the expression of OCT4 is less than 90%, the EBs should be discarded, and EBs should be prepared again.</li>
</ol>
6. Neural induction (days 5-7)
<ol>
	<li>Prepare a new 6-well plate with low adhesion, and add 3 mL of Neural induction medium (Supplementary Table 2) to each well.</li>
	<li>Turn on the lateral soft light (mentioned in step 3.) and turn off other indoor light sources.</li>
	<li>Transfer the EBs to the 6-well plate with added Neural induction medium (~100 EBs/well). Add as little as possible of the original medium to the new well. 
	NOTE: Introduce simple skills oforganoid transfer. Naturally, under gravity and with a relatively higher density than the medium, the resuspended EBs will gradually sink by applying the operation shown in Figure 1E. Hence, the EBs can be conveniently transferred. Since, compared to EBs, free cells and dead cell fragments sink more slowly, most of the free cells and dead cell fragments can thus be removed through this sedimentation method (Figure 1F).</li>
	<li>Incubate the samples at 37 &#176;C and 5% CO2 for 24 h. 
	NOTE: Under the microscope, the diameter of the EBs was approximately 500 &#181;m, and the edge was translucent, indicating that a neuroepithelial layer formed.</li>
	<li>Proceed to the next step.</li>
</ol>
7. Embedding in the basement membrane matrix (days 7&#8203;-10)
<ol>
	<li>Place the membrane matrix in a 4 &#176;C refrigerator for 60 min in advance to dissolve. Calculate the amount of the required matrix in advance. Approximately 100 EBs were embedded in 1.5 mL of the membrane matrix.</li>
	<li>Turn on the lateral soft light and turn off the light source on the top of the console.</li>
	<li>Keep the membrane matrix on ice to prevent solidification.</li>
	<li>Transfer a small amount of EBs to a 60 mm dish containing fresh Expansion medium (Supplementary Table 3) each time. Reduce the number of EBs to make it easier to remove a single EB.</li>
	<li>Then, use a new 6-well low adhesion plate. Suck a single EB (containing approximately 10 &#181;L medium) with a 200 &#181;L wide-bore pipette tip (see Table of Materials) each time, and then add it to the bottom of the 6-well plate to make droplets. Use five droplets per well. 
	NOTE: The key is to adjust the range of the pipette gun to 50 &#181;L and suck an EB, and then refer to the operation of Figure 1E. When the EB settles to the bore of the pipette tip, the tip quickly touches the well bottom of the plate and pushes out approximately 10 &#181;L of liquid to form a droplet.</li>
	<li>Add 15 &#181;L of the membrane matrix to each drop containing EB and mix it quickly. Embed the EB ball in the center of the droplet. 
	NOTE: EBs must not be aspirated with a standard pipette tip, which damages the EB. The 200 &#181;L wide-bore pipette tip needs to be used instead.</li>
	<li>Place the 6-well plate into a 37 &#176;C incubator for 30 min, and solidify the membrane matrix droplets containing EBs.</li>
	<li>Add 3 mL of the Expansion medium to each well and gently blow up the matrix-embedded EBs to suspend them.</li>
	<li>Incubate at 37 &#176;C and 5% CO2 for 3 days. 
	&#8203;NOTE: If budding on the surface of EB is observed, it means that an expanded neuroepithelium has been formed16.</li>
</ol>
8. Organoid maturation (days 10-40)
<ol>
	<li>Gently remove the original medium, and add 3 mL of Maturation medium (Supplementary Table 4) to each well.</li>
	<li>Place the organoid plate on a horizontal shaker in a 37 &#176;C incubator.</li>
	<li>Continue to rotate the culture horizontally. Set the shaker to the appropriate speed. 
	NOTE: When culturing cerebral organoids on a 6-well plate, a relative centrifugal force (RCF) of 0.11808 x g is more appropriate, according to the manufacturer of the horizontal shaker (see Table of Materials). According to the conversion between the relative centrifugal force and rotating speed17,18, RCF = 1.118 x 10&#8722;5 &#215; R &#215; rpm2, where RCF = relative centrifugal force (g), rpm = revolutions per minute (r/min), and R = rotation radius (cm), also known as shaking throw. The shaking throw parameters of different shakers may be different. Therefore, it can be estimated that the rotating speed is rpm = 299 x (RCF/R)1/2.</li>
	<li>Change the fresh Maturation medium every 2-3 days.</li>
	<li>After 20-30 days, gradually culture the cerebral organoids to maturity. 
	&#8203;NOTE: During this period, organoids can be used for experiments and detection, such as neural marker detection and transcriptome sequencing19,20,21.</li>
</ol>
9. Frozen sections and immunofluorescence of cerebral organoids
<ol>
	<li>Fix the organoids in 4% paraformaldehyde at 4 &#176;C for 16 h and then wash them 3x with 1x PBS for 10 min each time.</li>
	<li>Remove the PBS, and immerse the organoids in 30% sucrose at 4 &#176;C overnight.</li>
	<li>Embed the organoids in 10%/7.5% gelatine/sucrose at 37 &#176;C for 1 h and then quickly transfer them to the embedding mold.</li>
	<li>Add dry ice to 100% ethanol to prepare a dry ice/ethanol slurry, and place the organoid samples in it for quick freezing.</li>
	<li>Store the frozen samples in a &#8722;80 &#176;C freezer. When required, make frozen sections with a thickness of 20 &#181;m.</li>
	<li>Refer to Steps 5.3.-5.5. for immunofluorescence. Use the PAX6 antibody to label apical progenitor cells, the TUJ1 antibody (see Table of Materials) to label neuronal cells22,23,24, and DAPI for nuclear DNA staining.</li>
</ol>

<ol>
	<li>Jensen, C., Teng, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Is+it+time+to+start+transitioning+from+2D+to+3D+cell+culture.">Is it time to start transitioning from 2D to 3D cell culture.</a> Frontiers in Molecular Biosciences. 7 (33), (2020).</li><li>Quadrato, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cell+diversity+and+network+dynamics+in+photosensitive+human+brain+organoids.">Cell diversity and network dynamics in photosensitive human brain organoids.</a> Nature. 545 (7652), 48-53 (2017).</li><li>Lancaster, M. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cerebral+organoids+model+human+brain+development+and+microcephaly.">Cerebral organoids model human brain development and microcephaly.</a> Nature. 501 (7467), 373-379 (2013).</li><li>Qian, X., 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=et+al.Brain-region-specific+organoids+using+mini-bioreactors+for+modeling+ZIKV+exposure.">et al.Brain-region-specific organoids using mini-bioreactors for modeling ZIKV exposure.</a> Cell. 165 (5), 1238-1254 (2016).</li><li>Hu, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lung+cancer+organoids+analyzed+on+microwell+arrays+predict+drug+responses+of+patients+within+a+week.">Lung cancer organoids analyzed on microwell arrays predict drug responses of patients within a week.</a> Nature Communications. 12 (1), 2581 (2021).</li><li>Jung, D. 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+one-stop+microfluidic-based+lung+cancer+organoid+culture+platform+for+testing+drug+sensitivity.">A one-stop microfluidic-based lung cancer organoid culture platform for testing drug sensitivity.</a> Lab on a Chip. 19 (17), 2854-2865 (2019).</li><li>Jalili-Firoozinezhad, 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=A+complex+human+gut+microbiome+cultured+in+an+anaerobic+intestine-on-a-chip.">A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip.</a> Nature Biomedical Engineering. 3 (7), 520-531 (2019).</li><li>Gkatzis, K., Taghizadeh, S., Huh, D., Stainier, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Use+of+three-dimensional+organoids+and+lung-on-a-chip+methods+to+study+lung+development,+regeneration+and+disease.">Use of three-dimensional organoids and lung-on-a-chip methods to study lung development, regeneration and disease.</a> The European Respiratory Journal. 52 (5), 1800876 (2018).</li><li>Ye, Y., Pui, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Detection+of+nanoparticles+suspended+in+a+light+scattering+medium.">Detection of nanoparticles suspended in a light scattering medium.</a> Scientific Reports. 11 (1), 20268 (2021).</li><li>Staven, V., Waaseth, M., Wang, S., Gr&#248;nlie, I., Tho, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Utilization+of+the+tyndall+effect+for+enhanced+visual+detection+of+particles+in+compatibility+testing+of+intravenous+fluids:+Validity+and+reliability.">Utilization of the tyndall effect for enhanced visual detection of particles in compatibility testing of intravenous fluids: Validity and reliability.</a> PDA Journal of Pharmaceutical Science and Technology. 69 (2), 270-283 (2015).</li><li>Fukuma, Y., Inui, T., Imashiro, C., Kurashina, Y., Takemura, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Homogenization+of+initial+cell+distribution+by+secondary+flow+of+medium+improves+cell+culture+efficiency.">Homogenization of initial cell distribution by secondary flow of medium improves cell culture efficiency.</a> PloS One. 15 (7), 0235827 (2020).</li><li>Lancaster, M. A., Knoblich, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Generation+of+cerebral+organoids+from+human+pluripotent+stem+cells.">Generation of cerebral organoids from human pluripotent stem cells.</a> Nature Protocols. 9 (10), 2329-2340 (2014).</li><li>Ouyang, 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=CRISPR/Cas9-targeted+deletion+of+polyglutamine+in+spinocerebellar+ataxia+type+3-derived+induced+pluripotent+stem+cells.">CRISPR/Cas9-targeted deletion of polyglutamine in spinocerebellar ataxia type 3-derived induced pluripotent stem cells.</a> Stem Cells and Development. 27 (11), 756-770 (2018).</li><li>Xian, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+safety+and+effectiveness+of+genetically+corrected+iPSCs+derived+from+&#946;-thalassaemia+patients+in+nonmyeloablative+&#946;-thalassaemic+mice.">The safety and effectiveness of genetically corrected iPSCs derived from &#946;-thalassaemia patients in nonmyeloablative &#946;-thalassaemic mice.</a> Stem Cell Research and Therapy. 11 (1), 288 (2020).</li><li>Kanof, M. E., Smith, P. D., Zola, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+of+whole+mononuclear+cells+from+peripheral+blood+and+cord+blood.">Isolation of whole mononuclear cells from peripheral blood and cord blood.</a> Current Protocols in Immunology. , (2001).</li><li>Knight, G. 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=Engineering+induction+of+singular+neural+rosette+emergence+within+hPSC-derived+tissues.">Engineering induction of singular neural rosette emergence within hPSC-derived tissues.</a> eLife. 7, 37549 (2018).</li><li>Rieder, H. L., Smithwick, R. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RPM+or+RCF.">RPM or RCF.</a> The American Review of Respiratory Disease. 132 (6), 1371 (1985).</li><li>Dole, V. P., Cotzias, G. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+nomogram+for+the+calculation+of+relative+centrifugal+force.">A nomogram for the calculation of relative centrifugal force.</a> Science. 113 (2941), 552-553 (1951).</li><li>Velasco, 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=Individual+brain+organoids+reproducibly+form+cell+diversity+of+the+human+cerebral+cortex.">Individual brain organoids reproducibly form cell diversity of the human cerebral cortex.</a> Nature. 570 (7762), 523-527 (2019).</li><li>Jacob, F., 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+pluripotent+stem+cell-derived+neural+cells+and+brain+organoids+reveal+SARS-CoV-2+neurotropism+predominates+in+choroid+plexus+epithelium.">Human pluripotent stem cell-derived neural cells and brain organoids reveal SARS-CoV-2 neurotropism predominates in choroid plexus epithelium.</a> Cell Stem Cell. 27 (6), 937-950 (2020).</li><li>Kathuria, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transcriptomic+landscape+and+functional+characterization+of+induced+pluripotent+stem+cell-derived+cerebral+organoids+in+schizophrenia.">Transcriptomic landscape and functional characterization of induced pluripotent stem cell-derived cerebral organoids in schizophrenia.</a> JAMA Psychiatry. 77 (7), 745-754 (2020).</li><li>Pa&#351;ca, A. 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=Functional+cortical+neurons+and+astrocytes+from+human+pluripotent+stem+cells+in+3D+culture.">Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture.</a> Nature Methods. 12 (7), 671-678 (2015).</li><li>Hu, B. Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neural+differentiation+of+human+induced+pluripotent+stem+cells+follows+developmental+principles+but+with+variable+potency.">Neural differentiation of human induced pluripotent stem cells follows developmental principles but with variable potency.</a> Proceedings of the National Academy of Sciences of the United States of America. 107 (9), 4335-4340 (2010).</li><li>Tang, X. Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DSCAM/PAK1+pathway+suppression+reverses+neurogenesis+deficits+in+iPSC-derived+cerebral+organoids+from+patients+with+Down+syndrome.">DSCAM/PAK1 pathway suppression reverses neurogenesis deficits in iPSC-derived cerebral organoids from patients with Down syndrome.</a> The Journal of Clinical Investigation. 131 (12), 135763 (2021).</li><li>Costa, M., Paulson, H. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Toward+understanding+Machado-Joseph+disease.">Toward understanding Machado-Joseph disease.</a> Progress in Neurobiology. 97 (2), 239-257 (2012).</li><li>Trapnell, C., 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=Transcript+assembly+and+quantification+by+RNA-Seq+reveals+unannotated+transcripts+and+isoform+switching+during+cell+differentiation.">Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.</a> Nature Biotechnology. 28 (5), 511-515 (2010).</li><li>Love, M. I., Huber, W., Anders, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Moderated+estimation+of+fold+change+and+dispersion+for+RNA-seq+data+with+DESeq2.">Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.</a> Genome Biology. 15 (12), 550 (2014).</li><li>Clevers, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modeling+development+and+disease+with+organoids.">Modeling development and disease with organoids.</a> Cell. 165 (7), 1586-1597 (2016).</li><li>Klockgether, 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=Age+related+axonal+neuropathy+in+spinocerebellar+ataxia+type+3/Machado-Joseph+disease+(SCA3/MJD).">Age related axonal neuropathy in spinocerebellar ataxia type 3/Machado-Joseph disease (SCA3/MJD).</a> Journal of Neurology, Neurosurgery, and Psychiatry. 66 (2), 222-224 (1999).</li><li>Khan, L. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Expanded+polyglutamines+impair+synaptic+transmission+and+ubiquitin-proteasome+system+in+Caenorhabditis+elegans.">Expanded polyglutamines impair synaptic transmission and ubiquitin-proteasome system in Caenorhabditis elegans.</a> Journal of Neurochemistry. 98 (2), 576-587 (2006).</li><li>Teixeira-Castro, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Serotonergic+signalling+suppresses+ataxin+3+aggregation+and+neurotoxicity+in+animal+models+of+Machado-Joseph+disease.">Serotonergic signalling suppresses ataxin 3 aggregation and neurotoxicity in animal models of Machado-Joseph disease.</a> Brain: A Journal of Neurology. 138, 3221-3237 (2015).</li><li>Joers, J. 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=Neurochemical+abnormalities+in+premanifest+and+early+spinocerebellar+ataxias.">Neurochemical abnormalities in premanifest and early spinocerebellar ataxias.</a> Annals of Neurology. 83 (4), 816-829 (2018).</li><li>Sivitilli, A., Ghiasi, P., Attisano, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Production+of+phenotypically+uniform+human+cerebral+organoids+from+pluripotent+stem+cells.">Production of phenotypically uniform human cerebral organoids from pluripotent stem cells.</a> Bio-protocol. 11 (8), 3985 (2021).</li><li>Sivitilli, A. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Robust+production+of+uniform+human+cerebral+organoids+from+pluripotent+stem+cells.">Robust production of uniform human cerebral organoids from pluripotent stem cells.</a> Life Science Alliance. 3 (5), (2020).</li><li>Camp, J. G., Treutlein, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Human+development:+Advances+in+mini-brain+technology.">Human development: Advances in mini-brain technology.</a> Nature. 545 (7652), 39-40 (2017).</li><li>Giandomenico, S. L., Sutcliffe, M., Lancaster, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Generation+and+long-term+culture+of+advanced+cerebral+organoids+for+studying+later+stages+of+neural+development.">Generation and long-term culture of advanced cerebral organoids for studying later stages of neural development.</a> Nature Protocols. 16 (2), 579-602 (2021).</li><li>Yoon, S. 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=Reliability+of+human+cortical+organoid+generation.">Reliability of human cortical organoid generation.</a> Nature Methods. 16 (1), 75-78 (2019).</li><li>Lancaster, M. A., Knoblich, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Organogenesis+in+a+dish:+Modeling+development+and+disease+using+organoid+technologies.">Organogenesis in a dish: Modeling development and disease using organoid technologies.</a> Science. 345 (6194), 1247125 (2014).</li><li>Driehuis, E., Kretzschmar, K., Clevers, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Establishment+of+patient-derived+cancer+organoids+for+drug-screening+applications.">Establishment of patient-derived cancer organoids for drug-screening applications.</a> Nature Protocols. 15 (10), 3380-3409 (2020).</li></ol>

The authors have nothing to disclose.

Cerebral organoids open new avenues for medical research. Many useful applications of this technology are only beginning to be explored28. This research found that the transcriptome sequencing results of genetically diseased cerebral organoids and normal cerebral organoids can reflect the differences between disease and health. For example, the RNA-seq data analysis results (Figure 3B) are consistent with many reported studies on SCA3 diseases29</sup...

Compared to two-dimensional (2D) culture systems, three-dimensional (3D) culture systems have several advantages, including genuine replication and efficient reproduction of complex structures of certain organs1. Therefore, cerebral organoids are one of the important auxiliary methods for the research fields of human brain development and disease2, drug screening, and cell therapy.
Culturing cerebral organoids by the rotating suspension method is conducive to their development and maturation3. Although cerebral organoid culture systems have achieved great success, they still face critical challenges that limit their application. For example, manual cultivation involves complicated manipulation steps and introduces obstacles to achieving large-scale applications. Additionally, at each developmental stage in the culture of cerebral organoids, changes in different media and cytokines are needed4. However, in the early stage, the organoids or EBs have tiny sizes (approximately 200 &#181;m to 300 &#181;m) and are almost visually inaccessible without appropriate apparatus. Inevitably, a certain amount of precious organoid samples are flushed away when the medium is changed. Many techniques have been explored to overcome this in other kinds of organoid cultures, and some examples include immersing entire organoid chips in a culture medium for 3 days without intervention5; adding a fresh medium through the coverslip after the old medium is absorbed using absorbent paper5; or applying complex microfluidic pipelines for fluid exchange6,7,8. Another obstacle encountered in the early stage of organoid cultivation is the difficulty of achieving direct observations with the naked eye, which can cause poor operations that lead to organoid damage and loss during the organoid transfer steps. Therefore, it is necessary to establish a more feasible protocol that facilitates medium change and organoid transfer to generate organoids.
A corresponding optimized operation based on engineering principles is proposed to overcome these problems, which significantly and conveniently facilitates many organoid procedures. In nature, when the sun shines into a house through a window gap, the naked eye can see the dust dancing in the light beam. Due to the diffuse reflection of sunlight on dust, some light is refracted into the eyeball to produce a visual image. Inspired by the principle of this phenomenon9,10, this study made a soft light lamp and illuminated the EBs laterally. It was found that EBs could be visually clear without affecting the viewing scope. A secondary flow pointing to the center is generated in the liquid by rotating the culture plate due to eddy currents11. Originally dispersed EBs accumulate in the center of the plate. Based on this, and the phenomenon that the sedimentation velocity of organoids is faster than that of cells, an easy operation method of medium change and organoid transfer without centrifugation is proposed. The organoids in the culture medium can be effectively separated from free cells and dead cell fragments through this transfer operation.
Here, a protocol that is easy to operate is proposed to generate cerebral organoids from human pluripotent stem cells. The operation technology was optimized by applying the engineering principle, making operations in 3D culture as simple and feasible as those in 2D culture. The improved liquid exchange method and organoid transfer operation are also helpful for other types of organoid culture and the design of automatic culture machines.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>0.2 &#956;m Filter</td>
			<td>NEST Biotechnology, China</td>
			<td>331001</td>
			<td></td>
		</tr>
		<tr>
			<td>1000 &#956;L wide-bore pipette tip</td>
			<td>Thermo Fisher Scientific, USA</td>
			<td>9405163</td>
			<td></td>
		</tr>
		<tr>
			<td>200 &#956;L wide-bore pipette tip</td>
			<td>Thermo Fisher Scientific, USA</td>
			<td>9405020</td>
			<td></td>
		</tr>
		<tr>
			<td>2-Mercaptoethanol</td>
			<td>Merck, Germany</td>
			<td>8057400005</td>
			<td></td>
		</tr>
		<tr>
			<td>4% Paraformaldehyde</td>
			<td>Servicebio, China</td>
			<td>G1101</td>
			<td></td>
		</tr>
		<tr>
			<td>6-well low adhesion plate</td>
			<td>NEST Biotechnology, China</td>
			<td>703011</td>
			<td>It is used for EBs suspension cultures</td>
		</tr>
		<tr>
			<td>Aaccute cell detachment solution</td>
			<td>STEMCELL Technologies, Canada</td>
			<td>07920</td>
			<td>It is used to digest iPSC into single cells.</td>
		</tr>
		<tr>
			<td>AggreWell800 24-well</td>
			<td>STEMCELL Technologies, Canada</td>
			<td>34811</td>
			<td>Microporous culture plate for EBs preparation.</td>
		</tr>
		<tr>
			<td>Anti-Adherence Rinsing Solution</td>
			<td>STEMCELL Technologies, Canada</td>
			<td>07010</td>
			<td>Rinsing solution for cultureware to prevent cell adhesion</td>
		</tr>
		<tr>
			<td>B27-vit. A supplement</td>
			<td>Thermo Fisher Scientific, USA</td>
			<td>12587010</td>
			<td></td>
		</tr>
		<tr>
			<td>bFGF</td>
			<td>Peprotech, USA</td>
			<td>GMP100-18B</td>
			<td></td>
		</tr>
		<tr>
			<td>BSA</td>
			<td>Beyotime Biotechnology, China</td>
			<td>ST025</td>
			<td></td>
		</tr>
		<tr>
			<td>Centrifuge</td>
			<td>Eppendorf, Germany</td>
			<td>5810 R</td>
			<td>It can be used for centrifugation of various types of centrifuge tubes, reagent bottles and working plates.</td>
		</tr>
		<tr>
			<td>Cover glass</td>
			<td>Shitai Laboratory Equipment, China</td>
			<td>10212020C</td>
			<td></td>
		</tr>
		<tr>
			<td>DAPI</td>
			<td>Beyotime Biotechnology, China</td>
			<td>C1002</td>
			<td>Used for nuclear staining. After DAPI was combined with double stranded DNA, the maximum excitation wavelength was 364nm and the maximum emission wavelength was 454nm.</td>
		</tr>
		<tr>
			<td>DMEM-F12</td>
			<td>Thermo Fisher Scientific, USA</td>
			<td>11330032</td>
			<td></td>
		</tr>
		<tr>
			<td>ES-quality FBS</td>
			<td>Thermo Fisher Scientific, USA</td>
			<td>10270106</td>
			<td></td>
		</tr>
		<tr>
			<td>Ficoll Paque</td>
			<td>General Electric Company, USA</td>
			<td>17-5442-02</td>
			<td>Isolate the peripheral blood mononuclear cells according to Ficoll-Paque method.</td>
		</tr>
		<tr>
			<td>Gelatin</td>
			<td>Sangon Bioteach, China</td>
			<td>A609764</td>
			<td></td>
		</tr>
		<tr>
			<td>Glutamax supplement</td>
			<td>Thermo Fisher Scientific, USA</td>
			<td>35050061</td>
			<td></td>
		</tr>
		<tr>
			<td>Glutamax supplement</td>
			<td>Thermo Fisher Scientific, USA</td>
			<td>17504044</td>
			<td></td>
		</tr>
		<tr>
			<td>Goat anti-Chicken IgY&#160; secondary antibody</td>
			<td>Abcam, UK</td>
			<td>ab150171</td>
			<td>Goat anti-Chicken IgG. Conjugation: Alexa Fluor 647. Ex: 652 nm, Em: 668 nm. Use at 1:500 dilution.</td>
		</tr>
		<tr>
			<td>Goat anti-Mouse IgG secondary antibody</td>
			<td>Abcam, UK</td>
			<td>ab150120</td>
			<td>Goat anti-Mouse IgG. Conjugation: Alexa Fluor 594. Ex: 590 nm, Em: 617 nm. Use at 1:500 dilution.</td>
		</tr>
		<tr>
			<td>Goat anti-Rabbit IgG secondary antibody</td>
			<td>Abcam, UK</td>
			<td>ab150077</td>
			<td>Goat Anti-Rabbit IgG. Conjugation: Alexa Fluor 488. Ex: 495 nm, Em: 519 nm. Use at 1:500 dilution.</td>
		</tr>
		<tr>
			<td>Heparin</td>
			<td>Merck, Germany</td>
			<td>H3149</td>
			<td></td>
		</tr>
		<tr>
			<td>Horizontal shaker</td>
			<td>Servicebio, China</td>
			<td>DS-H200</td>
			<td>Relative centrifugal force (RCF) of 0.11808 x g is more appropriate, according to the manufacturer INFORS HT (Switzerland).</td>
		</tr>
		<tr>
			<td>Insulin</td>
			<td>Merck, Germany</td>
			<td>I9278-5ML</td>
			<td></td>
		</tr>
		<tr>
			<td>KOSR</td>
			<td>Thermo Fisher Scientific, USA</td>
			<td>10828028</td>
			<td></td>
		</tr>
		<tr>
			<td>Matrigel</td>
			<td>Corning, USA</td>
			<td>354277</td>
			<td>Matrigel will solidify in the environment higher than 4 &#176;C, so it should be sub packed at low temperature.</td>
		</tr>
		<tr>
			<td>MEM-NEAA</td>
			<td>Thermo Fisher Scientific, USA</td>
			<td>11140050</td>
			<td></td>
		</tr>
		<tr>
			<td>mTeSR1</td>
			<td>STEMCELL Technologies, Canada</td>
			<td>85850</td>
			<td>iPSC culture medium</td>
		</tr>
		<tr>
			<td>N2 supplement</td>
			<td>Thermo Fisher Scientific, USA</td>
			<td>17502048</td>
			<td></td>
		</tr>
		<tr>
			<td>Neurobasal</td>
			<td>Thermo Fisher Scientific, USA</td>
			<td>21103049</td>
			<td></td>
		</tr>
		<tr>
			<td>OCT4 primary antibody</td>
			<td>Abcam, UK</td>
			<td>ab19857</td>
			<td>Host: Rabbit. Dissolve with 500 &#956;L PBS. Use at 1:200 dilution.</td>
		</tr>
		<tr>
			<td>Pathological frozen slicer</td>
			<td>Leica, Germany</td>
			<td>Leica CM1860</td>
			<td></td>
		</tr>
		<tr>
			<td>PAX6 primary antibody</td>
			<td>Abcam, UK</td>
			<td>ab78545</td>
			<td>Host: Mouse. Use at 1:100 dilution.</td>
		</tr>
		<tr>
			<td>PBS</td>
			<td>STEMCELL Technologies, Canada</td>
			<td>37350</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin</td>
			<td>Thermo Fisher Scientific, USA</td>
			<td>15140122</td>
			<td></td>
		</tr>
		<tr>
			<td>PSC dissociation solution</td>
			<td>Beijing Saibei Biotechnology, China</td>
			<td>CA3001500</td>
			<td>Enzyme free dissociation solution can be used for iPSC digestion and passage.</td>
		</tr>
		<tr>
			<td>Sendai Reprogramming Kit</td>
			<td>Thermo Fisher Scientific, USA</td>
			<td>A16518</td>
			<td>Establish iPSC according to the protocol of Sendai Reprogramming Kit.</td>
		</tr>
		<tr>
			<td>Slide Glass</td>
			<td>Shitai Laboratory Equipment, China</td>
			<td>188105W</td>
			<td></td>
		</tr>
		<tr>
			<td>Soft light lamp</td>
			<td>NUT</td>
			<td>NUT</td>
			<td>A simple self made device, refer to supplementary figure 2 for preparation.</td>
		</tr>
		<tr>
			<td>STEMdiff Cerebral Organoid Kit</td>
			<td>STEMCELL Technologies, Canada</td>
			<td>8570</td>
			<td>Contain: 1. EB Formation Medium; 2. Induction Medium; 3. Expansion Medium; 4. Maturation Medium.</td>
		</tr>
		<tr>
			<td>STEMdiff Cerebral Organoid Maturation Kit</td>
			<td>STEMCELL Technologies, Canada</td>
			<td>8571</td>
			<td>Maturation Medium</td>
		</tr>
		<tr>
			<td>Sucrose</td>
			<td>Sangon Bioteach, China</td>
			<td>A502792</td>
			<td></td>
		</tr>
		<tr>
			<td>Triton X-100</td>
			<td>Merck, Germany</td>
			<td>X100</td>
			<td></td>
		</tr>
		<tr>
			<td>TUJ1 primary antibody</td>
			<td>Abcam, UK</td>
			<td>ab41489</td>
			<td>Host: Chicken. Use at 1:1000 dilution.</td>
		</tr>
		<tr>
			<td>Vaseline</td>
			<td>Sangon Bioteach, China</td>
			<td>A510146</td>
			<td></td>
		</tr>
		<tr>
			<td>Y-27632</td>
			<td>STEMCELL Technologies, Canada</td>
			<td>72302</td>
			<td>Prepare a 5 mM stock solution in PBS, resuspend 1 mg in 624 &#181;L of PBS.</td>
		</tr>
		<tr>
			<td>Weblink</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Raw sequencing data</td>
			<td>Genome Sequence Archive (Genomics, Proteomics &#38; Bioinformatics 2021) in National Genomics Data Center (Nucleic Acids Res 2022), China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences</td>
			<td>GSA-Human: HRA002430</td>
			<td>https://ngdc.cncb.ac.cn/gsa-human/</td>
		</tr>
	</tbody>
</table>

facilitating cerebral organoid culture via lateral soft light illumination

At present, cerebral organoid culture technology is still complicated to operate and difficult to apply on a large scale. It is necessary to find a simple and practical solution. Therefore, a more feasible cerebral organoid protocol is proposed in the present study. To solve the unavoidable inconvenience in medium change and organoid transfer in the early stage, the current research optimizes the operation technology by applying the engineering principle. A soft light lamp was adopted to laterally illuminate the embryoid body (EB) samples, allowing the EBs to be seen by the naked eye through the enhanced diffuse reflection effect. Using the principle of secondary flow generated by rotation, the organoids gather toward the center of the well, which facilitates the operation of medium change or organoid transfer. Compared to the dispersed cell, the embryoid body settles faster in the pipette. Using this phenomenon, most of the free cells and dead cell fragments can be effectively removed in a simple way, preventing EBs from incurring damage from centrifugation. This study facilitates the operation of cerebral organoid culture and helps to promote the application of brain organoids.

The present study induced iPSCs (Figure 2B) into cerebral organoids (Figure 2C). The EBs cultivated in the early stage expressed the OCT4 marker (Figure 2A), which indicated good pluripotency. In the later stage, the EBs developed into mature cerebral organoids (Figure 2D). The research cultivated iPSCs from normal healthy individuals and SCA3 patients into cerebral organoids (Figur...

Watch this Scientific Journal Video about Facilitating Cerebral Organoid Culture via Lateral Soft Light Illumination at JoVE.com

Facilitating Cerebral Organoid Culture via Lateral Soft Light Illumination

Cerebral organoids provide unprecedented opportunities for studying organ development and human disease pathology. Although great success has been achieved with cerebral organoid culture systems, there are still operational difficulties in applying this technology. The present protocol describes a cerebral organoid procedure that facilitates medium change and organoid transfer.

Facilitating Cerebral Organoid Culture via Lateral Soft Light Illumination

At present, cerebral organoid culture technology is still complicated to operate and difficult to apply on a large scale. It is necessary to find a simple ...

facilitating-cerebral-organoid-culture-via-lateral-soft-light

Research

JoVE Journal

Bioengineering

2.1K Views.  The Third Affiliated Hospital of Guangzhou Medical University. Cerebral organoids provide unprecedented opportunities for studying organ development and human disease pathology. Although great success has been achieved with cerebral organoid culture systems, there are still operational difficulties in applying this technology. The present protocol describes a cerebral organoid procedure that facilitates medium change and organoid transfer.

Video: Facilitating Cerebral Organoid Culture via Lateral Soft Light Illumination

Light-mediated Formation and Patterning of Hydrogels for Cell Culture Applications

Click chemistries have been investigated for use in numerous biomaterials applications, including drug delivery, tissue engineering, and cell culture. In particular, light-mediated click reactions, such as photoinitiated thiol&#8722;ene and thiol&#8722;yne reactions, afford spatiotemporal control over material properties and allow the design of systems with a high degree of user-directed property control. Fabrication and modification of hydrogel-based biomaterials using the precision afforded by light and the versatility offered by these thiol&#8722;X photoclick chemistries are of growing interest, particularly for the culture of cells within well-defined, biomimetic microenvironments. Here, we describe methods for the photoencapsulation of cells and subsequent photopatterning of biochemical cues within hydrogel matrices using versatile and modular building blocks polymerized by a thiol&#8722;ene photoclick reaction. Specifically, an approach is presented for constructing hydrogels from allyloxycarbonyl (Alloc)-functionalized peptide crosslinks and pendant peptide moieties and thiol-functionalized poly(ethylene glycol) (PEG) that rapidly polymerize in the presence of lithium acylphosphinate photoinitiator and cytocompatible doses of long wavelength ultraviolet (UV) light. Facile techniques to visualize photopatterning and quantify the concentration of peptides added are described. Additionally, methods are established for encapsulating cells, specifically human mesenchymal stem cells, and determining their viability and activity. While the formation and initial patterning of thiol-alloc hydrogels are shown here, these techniques broadly may be applied to a number of other light and radical-initiated material systems (e.g., thiol-norbornene, thiol-acrylate) to generate patterned substrates.

We describe a sequential process for light-mediated formation and subsequent biochemical patterning of synthetic hydrogel matrices for three-dimensional cell culture applications. The construction and modification of hydrogels with cytocompatible photoclick chemistry is demonstrated. Additionally, facile techniques to quantify and observe patterns and determine cell viability within these hydrogels are presented.

Click chemistries have been investigated for use in numerous biomaterials applications, including drug delivery, tissue engineering, and cell culture. In ...

Soft Lithographic Procedure for Producing Plastic Microfluidic Devices with View-ports Transparent to Visible and Infrared Light

Infrared (IR) spectro-microscopy of living biological samples is hampered by the absorption of water in the mid-IR range and by the lack of suitable microfluidic devices. Here, a protocol for the fabrication of plastic microfluidic devices is demonstrated, where soft lithographic techniques are used to embed transparent Calcium Fluoride (CaF2) view-ports in connection with observation chamber(s). The method is based on a replica casting approach, where a polydimethylsiloxane (PDMS) mold is produced through standard lithographic procedures and then used as the template to produce a plastic device. The plastic device features ultraviolet/visible/infrared (UV/Vis/IR) -transparent windows made of CaF2 to allow for direct observation with visible and IR light. The advantages of the proposed method include: a reduced need for accessing a clean room micro-fabrication facility, multiple view-ports, an easy and versatile connection to an external pumping system through the plastic body, flexibility of the design, e.g., open/closed channels configuration, and the possibility to add sophisticated features such as nanoporous membranes.

A protocol for the fabrication of plastic microfluidic devices with transparent view-ports for visible and infrared light imaging is described.

Infrared (IR) spectro-microscopy of living biological samples is hampered by the absorption of water in the mid-IR range and by the lack of suitable ...

Production of Extracellular Matrix Fibers via Sacrificial Hollow Fiber Membrane Cell Culture

Engineered scaffolds derived from extracellular matrix (ECM) have driven significant interest in medicine for their potential in expediting wound closure and healing. Extraction of extracellular matrix from fibrogenic cell cultures in vitro has potential for generation of ECM from human- and potentially patient-specific cell lines, minimizing the presence of xenogeneic epitopes which has hindered the clinical success of some existing ECM products. A significant challenge in in vitro production of ECM suitable for implantation is that ECM production by cell culture is typically of relatively low yield. In this work, protocols are described for the production of ECM by cells cultured within sacrificial hollow fiber membrane scaffolds. Hollow fiber membranes are cultured with fibroblast cell lines in a conventional cell medium and dissolved after cell culture to yield continuous threads of ECM. The resulting ECM fibers produced by this method can be decellularized and lyophilized, rendering it suitable for storage and implantation.

The goal of this protocol is production of whole extracellular matrix fibers targeted for wound repair which are suitable for preclinical evaluation as part of a regenerative scaffold implant. These fibers are produced by the culture of fibroblasts on hollow fiber membranes and extracted by dissolution of the membranes.

Engineered scaffolds derived from extracellular matrix (ECM) have driven significant interest in medicine for their potential in expediting wound closure ...

Handling and Assessment of Human Primary Prostate Organoid Culture

This paper describes a detailed protocol for three-dimensional (3D) culturing, handling, and evaluation of human primary prostate organoids. The process involves seeding of epithelial cells sparsely in a 3D matrix gel on a 96-well microplate with media changes to cultivate expansion into organoids. Morphology is then assessed by whole-well capturing of z-stack images. Compression of z-stacks creates a single in-focus image from which organoids are measured to quantify a variety of outputs, including circularity, roundness, and area.DNA, RNA, and protein can be collected from organoids recovered from the matrix gel. Cell populations of interest can be assessed by organoid dissociation and flow cytometry. Formalin-fixation-paraffin-embedding (FFPE) followed by sectioning is used for the histological assessment and antibody staining. Whole-mount immunofluorescent staining preserves organoid morphology and facilitates observation of protein localization in organoids in situ. Commercial assays that are traditionally used for 2D monolayer cells can be modified for 3D organoids. Used together, the techniques in this protocol provide a robust toolbox to quantify prostate organoid growth, morphologic characteristics, and expression of differentiation markers.

Here, we present a protocol to guide human primary prostate organoid handling then suggest endpoints to assess phenotype. Seeding, culture maintenance, recovery from matrix gel, morphologic quantification, embedding and sectioning, FFPE sectioning, whole-mount staining, and application of commercial assays are described.

This paper describes a detailed protocol for three-dimensional (3D) culturing, handling, and evaluation of human primary prostate organoids. The process ...

Applications for Open Source Microplate-Compatible Illumination Panels

Microplates are commonly used in the modern laboratory environment for a wide variety of tasks both in small-scale laboratory benchtop operations as well as large-scale high-throughput screening (HTS) campaigns. Though laboratory automation has greatly increased the utility of microplates there remain instances where automation-based instrumentation is not feasible, cost-effective or compatible with microplate formatting needs. In these cases, microplates must be manually prepared. Problematic to manual microplate manipulations is that a number of difficulties can arise pertaining to the accurate tracking of sample operations, data record keeping and quality control (QC) inspection for well artifacts or formatting errors. As microplate well densities increase (i.e., 96-well, 384-well, 1536-well) the potential for introducing errors also drastically increases.&#160; Moreover, for small bench-top laboratory operations there exists a need to improve the ease and accuracy of sample handling in a cost-effective fashion. Herein, we describe a system that acts as a semi-automated pipetting guide referred to as the Microplate Assistive Pipetting Light Emitter (M.A.P.L.E.). &#160;M.A.P.L.E. has multiple uses for supporting compound hit-picking and microplate preparation for assay development in high-throughput screening or laboratory benchtop operations, as well as QC/quality assurance (QA) diagnostic evaluation of microplate quality or visualizing well formatting errors.

Microplate Assistive Pipetting Light Emitter (M.A.P.L.E.) is a computer-driven device that systematically illuminates microtiter wells to provide guidance for the manual preparation of microplates.&#160; M.A.P.L.E. improves the accuracy of microplate preparation while automating data recordkeeping. &#160;In addition, it can assist with examining microplate quality or aid in the detection of errors.&#160; &#160;

Microplates are commonly used in the modern laboratory environment for a wide variety of tasks both in small-scale laboratory benchtop operations as well ...

Bioinspired Soft Robot with Incorporated Microelectrodes

Bioinspired soft robotic systems that mimic living organisms using engineered muscle tissue and biomaterials are revolutionizing the current biorobotics paradigm, especially in biomedical research. Recreating artificial life-like actuation dynamics is crucial for a soft-robotic system. However, the precise control and tuning of actuation behavior still represents one of the main challenges of modern soft robotic systems. This method describes a low-cost, highly scalable, and easy-to-use procedure to fabricate an electrically controllable soft robot with life-like movements that is activated and controlled by the contraction of cardiac muscle tissue on a micropatterned sting ray-like hydrogel scaffold. The use of soft photolithography methods makes it possible to successfully integrate multiple components in the soft robotic system, including micropatterned hydrogel-based scaffolds with carbon nanotubes (CNTs) embedded gelatin methacryloyl (CNT-GelMA), poly(ethylene glycol) diacrylate (PEGDA), flexible gold (Au) microelectrodes, and cardiac muscle tissue. In particular, the hydrogels alignment and micropattern are designed to mimic the muscle and cartilage structure of the sting ray. The electrically conductive CNT-GelMA hydrogel acts as a cell scaffold that improves the maturation and contraction behavior of cardiomyocytes, while the mechanically robust PEGDA hydrogel provides structural cartilage-like support to the whole soft robot. To overcome the hard and brittle nature of metal-based microelectrodes, we designed a serpentine pattern that has high flexibility and can avoid hampering the beating dynamics of cardiomyocytes. The incorporated flexible Au microelectrodes provide electrical stimulation across the soft robot, making it easier to control the contraction behavior of cardiac tissue.

A bioinspired scaffold is fabricated by a soft photolithography technique using mechanically robust and electrically conductive hydrogels. The micropatterned hydrogels provide directional cardiomyocyte cell alignment, resulting in a tailored direction of actuation. Flexible microelectrodes are also integrated into the scaffold to bring electrical controllability for a self-actuating cardiac tissue.

Bioinspired soft robotic systems that mimic living organisms using engineered muscle tissue and biomaterials are revolutionizing the current biorobotics ...

Building a Simple and Versatile Illumination System for Optogenetic Experiments

Controlling biological processes using light has increased the accuracy and speed with which researchers can manipulate many biological processes. Optical control allows for an unprecedented ability to dissect function and holds the potential for enabling novel genetic therapies. However, optogenetic experiments require adequate light sources with spatial, temporal, or intensity control, often a bottleneck for researchers. Here we detail how to build a low-cost and versatile LED illumination system that is easily customizable for different available optogenetic tools. This system is configurable for manual or computer control with adjustable LED intensity. We provide an illustrated step-by-step guide for building the circuit, making it computer-controlled, and constructing the LEDs. To facilitate the assembly of this device, we also discuss some basic soldering techniques and explain the circuitry used to control the LEDs. Using our open-source user interface, users can automate precise timing and pulsing of light on a personal computer (PC) or an inexpensive tablet. This automation makes the system useful for experiments that use LEDs to control genes, signaling pathways, and other cellular activities that span large time scales. For this protocol, no prior expertise in electronics is required to build all the parts needed or to use the illumination system to perform optogenetic experiments.

This protocol describes how to perform optogenetic experiments for controlling gene expression with red and far-red light using PhyB and PIF3. Included are step-by-step instructions for building a simple and flexible illumination system, which enables the control of gene expression or other optogenetics with a computer.

Controlling biological processes using light has increased the accuracy and speed with which researchers can manipulate many biological processes. Optical ...

Experimental and Data Analysis Workflow for Soft Matter Nanoindentation

Nanoindentation refers to a class of experimental techniques where a micrometric force probe is used to quantify the local mechanical properties of soft biomaterials and cells. This approach has gained a central role in the fields of mechanobiology, biomaterials design&#160;and tissue engineering, to obtain a proper mechanical characterization of soft materials with a resolution comparable to the size of single cells (&#956;m). The most popular strategy to acquire such experimental data is to employ an atomic force microscope (AFM); while this instrument offers an unprecedented resolution in force (down to pN) and space (sub-nm), its usability is often limited by its complexity that prevents routine measurements of integral indicators of mechanical properties, such as Young&#39;s Modulus (E). A new generation of nanoindenters, such as those based on optical fiber sensing technology, has recently gained popularity for its ease of integration while allowing to apply sub-nN forces with &#181;m spatial resolution, therefore being suitable to probe local mechanical properties of hydrogels and cells.
In this protocol, a step-by-step guide detailing the experimental procedure to acquire nanoindentation data on hydrogels and cells using a commercially available ferrule-top optical fiber sensing nanoindenter is presented. Whereas some steps are specific to the instrument used herein, the proposed protocol can be taken as a guide for other nanoindentation devices, granted some steps are adapted according to the manufacturer&#39;s guidelines. Further, a new open-source Python software equipped with a user-friendly graphical user interface for the analysis of nanoindentation data is presented, which allows for screening of incorrectly acquired curves, data filtering, computation of the contact point through different numerical procedures, the conventional computation of E, as well as a more advanced analysis particularly suited for single-cell nanoindentation data.

The protocol presents a complete workflow for soft material nanoindentation experiments, including hydrogels and cells. First, the experimental steps to acquire force spectroscopy data are detailed; then, the analysis of such data is detailed through a newly developed open-source Python software, which is free to download from GitHub.

Nanoindentation refers to a class of experimental techniques where a micrometric force probe is used to quantify the local mechanical properties of soft ...

Inactivation of Pathogens via Visible-Light Photolysis of Riboflavin-5&#8242;-Phosphate

Riboflavin-5&#39;-phosphate (or flavin mononucleotide; FMN) is sensitive to visible light. Various compounds, including reactive oxygen species (ROS), can be generated from FMN photolysis upon irradiation with visible light. The ROS generated from FMN photolysis are harmful to microorganisms, including pathogenic bacteria such as Staphylococcus aureus (S. aureus). This article presents a protocol for deactivating S. aureus, as an example, via photochemical reactions involving FMN under visible light irradiation. The superoxide radical anion (<img alt="Equation 1" src="/files/ftp_upload/63531/63531eq01v3.png" style="margin: auto;" />) generated during the FMN photolysis is evaluated via nitro blue tetrazolium (NBT) reduction. The microbial viability of S. aureus that is attributed to reactive <img alt="Equation 1" src="/files/ftp_upload/63531/63531eq01v3.png" style="margin: auto;" /> species was used to determine the effectiveness of the process. The bacterial inactivation rate is proportional to FMN concentration. Violet light is more efficient in inactivating S. aureus than blue light irradiation, while the red or green light does not drive FMN photolysis. The present article demonstrates FMN photolysis as a simple and safe method for sanitary processes.

Inactivation of Pathogens via Visible-Light Photolysis of Riboflavin-5&#8242;-Phosphate

Here, we present a protocol to inactivate pathogenic bacteria with reactive oxygen species produced during photolysis of flavin mononucleotide (FMN) under blue and violet light irradiation of low intensity. FMN photolysis is demonstrated to be a simple and safe method for sanitary processes.

Riboflavin-5&#39;-phosphate (or flavin mononucleotide; FMN) is sensitive to visible light. Various compounds, including reactive oxygen species (ROS), can ...

Reconstituting Cytoarchitecture and Function of Human Epithelial Tissues on an Open-Top Organ-Chip

Nearly all human organs are lined with epithelial tissues, comprising one or multiple layers of tightly connected cells organized into three-dimensional (3D) structures. One of the main functions of epithelia is the formation of barriers that protect the underlining tissues against physical and chemical insults and infectious agents. In addition, epithelia mediate the transport of nutrients, hormones, and other signaling molecules, often creating biochemical gradients that guide cell positioning and compartmentalization within the organ. Owing to their central role in determining organ-structure and function, epithelia are important therapeutic targets for many human diseases that are not always captured by animal models. Besides the obvious species-to-species differences, conducting research studies on barrier function and transport properties of epithelia in animals is further compounded by the difficulty of accessing these tissues in a living system. While two-dimensional (2D) human cell cultures are useful for answering basic scientific questions, they often yield poor in vivo predictions. To overcome these limitations, in the last decade, a plethora of micro-engineered biomimetic platforms, known as organs-on-a-chip, have emerged as a promising alternative to traditional in vitro and animal testing. Here, we describe an Open-Top Organ-Chip (or Open-Top Chip), a platform designed for modeling organ-specific epithelial tissues, including skin, lungs, and the intestines. This chip offers new opportunities for reconstituting the multicellular architecture and function of epithelial tissues, including the capability to recreate a 3D stromal component by incorporating tissue-specific fibroblasts and endothelial cells within a mechanically active system. This Open-Top Chip provides an unprecedented tool for studying epithelial/mesenchymal and vascular interactions at multiple scales of resolution, from single cells to multi-layer tissue constructs, thus allowing molecular dissection of the intercellular crosstalk of epithelialized organs in health and disease.

The present protocol describes the capabilities and the essential culture modalities of the Open-Top Organ-Chip for the successful establishment and maturation of full-thickness organ-on-chip cultures of primary tissues (skin, alveolus, airway, and intestine), providing the opportunity to investigate different functional aspects of the human epithelial/mesenchymal and vascular niche interface in vitro.

Nearly all human organs are lined with epithelial tissues, comprising one or multiple layers of tightly connected cells organized into three-dimensional ...