This work was supported by the Intramural Research Program of the National Institutes of Health (NIH) at the National Institute of Neurological Disorders and Stroke. We would like to thank Dr. Ronald D. McKay for his discussion and comments on this project.

Single-cell based non-colony type monolayer (NCM) culture of hPSCs.
1. Preparations
<ol>
	<li>Make 500 ml&#160;of medium for culture of mouse embryonic fibroblasts (MEFs): DMEM medium supplemented with 10% FBS, 2 mM L-glutamine, and 0.1 mM non-essential amino acids (NEAA).</li>
	<li>Isolate mouse embryonic fibroblasts (MEFs) cells derived from the CF1 strain following a routine protocol16 and culture MEFs on 0.1% gelatin-coated 6-well cell culture plate in DMEM medium. Alternatively, purchase MEF stocks at passage 3 from commercial resources.</li>
	<li>Prepare Matrigel plates.
	<ol>
		<li>Dilute 5 ml&#160;of hESC-qualified Matrigel stock with 5 ml&#160;of DMEM/F12 medium (chilled at ~4 &#176;C) and store as 50% aliquots in a -20 &#176;C freezer. Thaw the frozen Matrigel stock in a refrigerator (~4 &#176;C) O/N and further dilute the Matrigel in cold DMEM/F12 medium (to give rise to a 2.5% working concentration).</li>
		<li>Coat 6-well cell culture plates with 1.5 ml&#160;of 2.5% Matrigel per well, store the coated plates in refrigerator O/N (Note: use the Matrigel-coated plate within 2 weeks).</li>
		<li>Remove the Matrigel plate from the refrigerator, allow the plate to warm at RT in the cell culture hood for 10 to 30 min (Note: do not warm the plate in a cell culture incubator), and aspirate DMEM medium prior to plating hPSCs.</li>
	</ol>
	</li>
	<li>Make 500 ml&#160;hESC medium: 80% DMEM/F12 medium, 20% KSR, 2 mM L-glutamine, 0.1 mM non-essential amino acids, 0.1 mM &#946;-mercaptoethanol, and 4 ng/ml&#160;of FGF-2.</li>
	<li>Prepare 10 ml&#160;of 2X&#160;hPSC freezing medium: 60% FBS, 20% DMSO, and 20 &#181;M Y-27632 in mTeSR1 medium, sterilize by filtration, and use the medium within 1 week.</li>
</ol>
2. Protocol 1 (Basic): Grow hPSC Colonies on Feeders
<ol>
	<li>Use MEF passage numbers at 5 or 6 (designated as p5 and p6) for hPSC culture in order to get consistent results. Mitotically inactivate MEFs by treating the cells with 10 &#956;g/ml&#160;mitomycin C for 3 hr at 37 &#176;C, wash the cells 3x with 1X Dulbecco&#8217;s Phosphate-Buffered Saline (D-PBS), and then dissociate MEFs with 0.05% Trypsin in 0.53 mM EDTA. Alternatively, irradiate MEFs at a dose of 8,000 rads with an X-ray irradiator.</li>
	<li>Count cell numbers using the Trypan Blue stain exclusion method under microscope. Alternatively, use an automatic cell counter.</li>
	<li>Plate irradiated MEFs on 6-well polystyrene plates coated with 0.1% gelatin at a density of 1.88 x 105 cells per well (i.e., 1.96 x 104 cells/cm2). Incubate the cells at 37 &#176;C and 5% CO2 for 24 hr.</li>
	<li>Remove the MEF culture medium by aspiration with a Pasteur pipette (Note: no wash steps needed at this time).</li>
	<li>Triturate hPSC colonies from previous culture into small clumps, examine the clumps under microscope to ensure their sizes ranging from 50 to 100 &#956;m in diameters, and plate hPSC clumps on the top of MEF feeder layers in one well containing 2 ml&#160;of hPSC medium.</li>
	<li>Change hESC medium daily for 3 to 5 days, record colony growth by photograph, mark any morphologically altered or differentiated colonies (~5%), and manually remove the marked colonies by gently aspiration with a Pasteur pipette.</li>
	<li>Rinse the remaining colonies on MEFs twice (2 min each with D-PBS), and incubate the colonies with 2 ml&#160;of 1 mg/ml&#160;collagenase IV in hPSC medium for 10 to 30 min), and examine the detachment of hPSC colonies from the MEF-coated surface (Note: use a scraper to help the detachment process only if the colonies are tightly attached to the plate).</li>
	<li>Add 5 ml&#160;of hPSC medium to each well to minimize&#160;enzymatic reactions, transfer colonies to a 15 ml&#160;tube, allow hPSC colonies to sediment for 3 to 5 min at RT, and ensure the sedimentation of colonies by direct visualization of the cells at the bottom of the tube (Note: do not centrifuge the tube at this step).</li>
	<li>Remove the supernatants containing residual MEFs and dissociated single cells, resuspend the colonies with 5 ml&#160;of hESC medium, and repeat the sedimentation step twice.</li>
	<li>Remove the medium, triturate hPSC colonies into small clumps, store in 1X hPSC freezing medium (or CryoStore CS10 freezing medium) for cryopreservation (1 confluent well per frozen vial) or plate on a 6-well plate for cell passaging.</li>
</ol>
3. Protocol 2: Convert hPSC Colonies from Feeders to NCM
<ol>
	<li>Rinse hPSC pellets in D-PBS once, incubate the pellets with 1 ml&#160;of 1X Accutase for 10 min, and examine the enzymatic reaction under a microscope to ensure single-cell dissociation.</li>
	<li>Terminate the enzymatic reactions by gently resuspending the cells in 5 ml&#160;of mTeSR1 medium containing 10 &#956;M Y-27632 followed by centrifugation at 200 x&#160;g&#160;at RT for 5 min (Note, do not use excessive centrifugation forces which cause cell damage).</li>
	<li>Add 5 ml&#160;of mTeSR1 medium to the pellet, resuspend the pellet as single cells, and filter dissociated cells through a 40&#160;&#181;m cell strainer (to remove any residual cell aggregates).</li>
	<li>Seed 1.3-2 x 106&#160;hPSCs into one well (1.4-2.1 x 105&#160;cells/cm2) of a 6-well plate coated with 2.5% hESC-qualified Matrigel, add mTeSR1 medium up to 2.5 ml, and include 10 &#181;M Y-27632 in the medium (to facilitate the initial 24&#160;hr single-cell plating). Alternatively, utilize the following small molecules to replace 10 &#956;M Y-27632 for enhancing single-cell plating: 1 &#181;M Y-39983 (ROCK I inhibitor), 1 &#181;M phenylbenzodioxane (ROCK II inhibitor), 1 &#181;M thiazovivin (a novel ROCK inhibitor), and 2 &#956;M JAK inhibitor 1.</li>
	<li>Replace the medium with drug-free mTeSR1 medium on the next day (within 24 hr), dissociate cells from one extra well, and count cell number to determine single-cell plating efficiency (Note: approximately, 50 to 90% of single-cell plating efficiency that can be achieved at this stage).</li>
	<li>Allow the cells to grow as a single-cell-formed monolayer for a few days with 3 ml&#160;of mTeSR1 medium. Change medium daily.</li>
	<li>Empirically determine the schedule for passaging adapted NCM depending on the cell density. Passage when cell growth reaches confluence at day 3 or day 4, or at the 4&#160;hr&#160;time point after the disappearance of cell-to-cell borders. Dissociate the cells in 1 ml&#160;of Accutase, use a 1 to&#160;3 splitting ratio (i.e., 1 confluent well of cells plated in 3 wells of 6-well plate) for cell passaging, and stabilize adapted NCM by 5 passages.</li>
	<li>Cell freezing
	<ol>
		<li>Utilize one confluent well (~ 5-6 x106&#160;cells) for one frozen vial: dissociate cells from one confluent well with 1 ml&#160;of Accutase for 10 min.</li>
		<li>Dilute with 5 ml&#160;of mTeSR1 medium and centrifuge cells as described above.</li>
		<li>Resuspend the pellet in 500 &#956;l&#160;of mTeSR1 medium and then slowly add 500 &#956;l&#160;of 2X hPSC freezing medium (containing 20 &#956;M Y-27632) in a cryopreservation vial. Alternatively, resuspend the cells in 1X hPSC freezing medium containing 2 &#956;M JAK inhibitor 1 or 1X CryoStor CS10 medium in the presence of either 10 &#181;M Y-27632 or 2 &#956;M JAK inhibitor 1.</li>
		<li>Place frozen vials into an ice-chilled cryocontainer (bottom-filled with isopranol) and transfer the cryocontainer to a -80 &#176;C freezer immediately.</li>
		<li>Transfer cells from the -80 &#176;C freezer to a liquid nitrogen tank (on the next day) for long-term cryopreservation.</li>
	</ol>
	</li>
	<li>Cell thawing
	<ol>
		<li>Utilize one cryopreservation vial for plating 1 well of a 6-well plate.</li>
		<li>Pre-warm mTeSR1 medium in a 37 &#176;C water bath for 10 min, thaw cells in the same water bath for 2 min, drop-wise add cells to 5 ml&#160;of pre-warmed mTeSR1 medium containing 10 &#181;M Y-27632, and centrifuge as described above.</li>
		<li>Gently resuspend the cell pellets with 2 ml&#160;of mTeSR1 medium containing 10 &#181;M Y-27632 and slowly transfer cells to a well pre-coated with Matrigel (Note: avoid producing air bubbles).</li>
		<li>Change medium daily and expect hPSC growth to reach confluence at day 3 or 4.</li>
	</ol>
	</li>
</ol>
4. Protocol 3: Convert hPSC Colonies on Matrigel to NCM Culture
<ol>
	<li>Remove a Matrigel-coated plate from refrigerator, place the plate in the tissue culture hood for 10 to 30 min, remove the medium from each well of the plate, and add 2 ml&#160;of pre-warmed mTeSR1 medium to each well.</li>
	<li>Transfer triturated hPSC clumps from the feeder culture (Step 2.10 of the basic protocol) to the above Matrigel plate. Add mTeSR1 medium up to 2.5 ml&#160;final volume in each well.</li>
	<li>Change medium daily for 3 to 4 days until colonies reach 80 to 90% confluence.</li>
	<li>For cell passaging: rinse the colonies with D-PBS twice, treat the cells with 1 ml&#160;of 2 mg/ml&#160;dispase at 37 &#176;C for 15 to 20 min, and sediment and passage cells as clumps.</li>
	<li>For NCM culture: repeat Steps 3.1 to 3.9 described in Protocol&#160;2.</li>
</ol>
5. Protocol 4: NCM Culture of hPSCs on LN-521
<ol>
	<li>Thaw the recombinant LN-521 solution at 4 &#176;C before the day of use and make the laminin coating solution (LCS) by diluting the thawed laminin with 1X D-PBS (containing Ca2+/Mg2+) to a final concentration of 10 &#956;g/ml.</li>
	<li>Add 1 ml&#160;of the LCS to one well in 6-well plate (note: avoid dry-out during the coating process).</li>
	<li>Seal the coated plate with Parafilm to prevent evaporation and store the plate in refrigerator (4 &#176;C) O/N (note: use the plate within 1 week).</li>
	<li>Gently remove the LCS with a Pasteur pipette without touching the coated surface and add 2 ml&#160;of mTeSR1 medium to one well.</li>
	<li>Warm all culture solutions (including D-PBS) in a 37 &#176;C water bath for 25 min.</li>
	<li>Convert hPSC colonies to NCM
	<ol>
		<li>Dissociate cell aggregates to single cells with Accutase as described in Protocol 2.</li>
		<li>Seed 1.3-2 x 106&#160;hPSCs into one LN-521-coated well (1.4-2.1 x 105&#160;cells/cm2) without the presence of ROCK inhibitors.</li>
		<li>Change medium daily for 3 to 4 days.</li>
		<li>Dissociate the cells in 1 ml&#160;of Accutase at day 3 or 4 for the next cell passaging using a 1 to 3 splitting ratio.</li>
	</ol>
	</li>
</ol>
6. Protocol 5: NCM Culture for Plasmid DNA Transfection
<ol>
	<li>Adapt hPSC colonies to NCM culture as described in Protocols 2 to 4.</li>
	<li>Plate dissociated hPSCs in 12-well plate with a cell density of 7.5 x 105 cells/well in mTeSR1 medium in the presence of 10 &#956;M Y-27632.</li>
	<li>Replace mTeSR1 medium with drug-free mTeSR1 medium between 4-8 hr after plating the cells.</li>
	<li>For each transfection, dilute 2.5 &#956;g of expression plasmids (e.g., pmaxGFP) and 5 &#956;l of Lipofectamine 2000 in separate Eppendorf tubes in 125 &#956;l&#160;each of Opti-MEM Reduced Serum Medium.</li>
	<li>After 5 min, mix the diluted reagents and incubate for 20 min at RT (to form transfection complexes).</li>
	<li>Add the 250&#160;&#956;l&#160;transfection complexes to each well containing hPSCs in 1 ml mTeSR1 medium and incubate the cells at 37 &#176;C in a CO2 incubator for 24 hr.</li>
	<li>Examine the transfection efficiency under a fluorescence microscope and photograph randomly for calculation of the actual transfection efficiency.</li>
</ol>
7. Protocol 6: NCM Culture for Transfection of MicroRNAs
<ol>
	<li>Dissociate semi-confluent hPSCs at day 2 under NCM conditions by adding 1 ml&#160;of Accutase per well in 6-well plate.</li>
	<li>Add 10 ml&#160;of mTeSR1 medium to dilute enzymatic reactions and centrifuge at 200 x g for 5 min.</li>
	<li>Resuspend the cell pellet with mTeSR1 medium, seed the cells at a density of 7.5 x 105 cells per well in a 12-well plate in mTeSR1 medium containing 10 &#956;M Y-27632, and let the cells attach for 4 hr.</li>
	<li>Replace the medium with Y27632-free mTeSR1 medium.</li>
	<li>Use commercially available microRNAs (e.g., a non-targeting miRIDIAN miRNA Transfection Control labeled with Dy547). Titrate concentrations ranging from 0-160 nM using the provided reagents and follow the manufacturers&#8217; instructions.</li>
	<li>Optimize transfection efficiency for each concentration in hPSC lines by imaging the Dy547 fluorescence of the live cells under a microscope at 24 hr after the transfection.</li>
	<li>Calculate the transfection efficiencies based on the percentage of Dy547 positive cells over all imaged cells.</li>
</ol>
8. Protocol 7: NCM Culture for Transduction of Lentiviral Vector
<ol>
	<li>Repeat steps 7.1 to 7.4 of Protocol 6.</li>
	<li>Calculate the amounts of viral particles to be used for transduction: Use the following formula: TU = (MOI x CN) / VT, whereas TU denotes the total numbers of transforming units, MOI equals the desired multiplicity of infection in the well (MOI or TU/cell), CN specifies the number of cells in each well, and VT indicates stock viral titers (TU/ml). For example, given that stock viral titers for SMART-shRNA vector equals 1 x 109 TU/ml&#160;(transforming units per ml), 7.5 x 105 cells per well at the time of transduction, and an expected MOI of 20: use 15 &#956;l&#160;of the stock viral particles for each well (note: this condition is recommended for transient lentiviral induction).</li>
	<li>Pre-warm 300 &#956;l&#160;of mTeSR1 medium with 10 mg/ml&#160;of polybrene for 30 min.</li>
	<li>Add 15 &#956;l&#160;of stock viral particles into the pre-warmed mTeSR1 medium containing polybrene and gently mix the solution.</li>
	<li>Replace the cell culture medium with 300&#160;&#956;l&#160;of prewarmed medium containing the viral particles.</li>
	<li>After 4 hr incubation, examine turboGFP fluorescence (a maker for shRNA expression) to determine the transduction efficiency.</li>
	<li>Add 300 &#956;l&#160;of additional mTeSR1 medium to the transducing well when the cells begin to express turboGFP.</li>
	<li>After 12-16 hr incubation, reexamine turbo-GFP expression.</li>
	<li>Perform desired follow-up experiments with these transduced cells within 72 hr.</li>
</ol>

<ol>
	<li>Cherry, A. B., Daley, G. Q. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reprogrammed+cells+for+disease+modeling+and+regenerative+medicine.">Reprogrammed cells for disease modeling and regenerative medicine.</a> Annu Rev Med. 64, 277-290 (2013).</li><li>Takahashi, K., Yamanaka, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Induction+of+pluripotent+stem+cells+from+mouse+embryonic+and+adult+fibroblast+cultures+by+defined+factors.">Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors.</a> Cell. 126, 663-676 (2006).</li><li>Thomson, J. 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=Embryonic+stem+cell+lines+derived+from+human+blastocysts.">Embryonic stem cell lines derived from human blastocysts.</a> Science. 282, 1145-1147 (1998).</li><li>Burridge, P. W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Production+of+de+novo+cardiomyocytes:+human+pluripotent+stem+cell+differentiation+and+direct+reprogramming.">Production of de novo cardiomyocytes: human pluripotent stem cell differentiation and direct reprogramming.</a> Cell Stem Cell. 10, 16-28 (2012).</li><li>Mallon, B. 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=StemCellDB:+The+Human+Pluripotent+Stem+Cell+Database+at+the+National+Institutes+of+Health.">StemCellDB: The Human Pluripotent Stem Cell Database at the National Institutes of Health.</a> Stem Cell Res. 10, 57-66 (2012).</li><li>Chen, K. 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=Human+pluripotent+stem+cell+culture:+considerations+for+maintenance,+expansion,+and+therapeutics.">Human pluripotent stem cell culture: considerations for maintenance, expansion, and therapeutics.</a> Cell Stem Cell. 14, 13-26 (2014).</li><li>Bendall, S. 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=IGF+and+FGF+cooperatively+establish+the+regulatory+stem+cell+niche+of+pluripotent+human+cells+in+vitro.">IGF and FGF cooperatively establish the regulatory stem cell niche of pluripotent human cells in vitro.</a> Nature. 448, 1015-1021 (2007).</li><li>Moogk, D., 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+ESC+colony+formation+is+dependent+on+interplay+between+self-renewing+hESCs+and+unique+precursors+responsible+for+niche+generation.">Human ESC colony formation is dependent on interplay between self-renewing hESCs and unique precursors responsible for niche generation.</a> Cytometry A. 77, 321-327 (2010).</li><li>Chen, K. 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=Non-colony+type+monolayer+culture+of+human+embryonic+stem+cells.">Non-colony type monolayer culture of human embryonic stem cells.</a> Stem Cell Res. 9, 237-248 (2012).</li><li>Amit, 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=Suspension+culture+of+undifferentiated+human+embryonic+and+induced+pluripotent+stem+cells.">Suspension culture of undifferentiated human embryonic and induced pluripotent stem cells.</a> Stem Cell Rev. 6, 248-259 (2010).</li><li>Dang, S. 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=scalable+embryonic+stem+cell+differentiation+culture.">scalable embryonic stem cell differentiation culture.</a> Stem Cells. 22, 275-282 (2004).</li><li>Serra, 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=Process+engineering+of+human+pluripotent+stem+cells+for+clinical+application.">Process engineering of human pluripotent stem cells for clinical application.</a> Trends Biotechnol. 30, 350-359 (2012).</li><li>Steiner, D., 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=propagation+and+controlled+differentiation+of+human+embryonic+stem+cells+in+suspension.">propagation and controlled differentiation of human embryonic stem cells in suspension.</a> Nat Biotechnol. 28, 361-364 (2010).</li><li>Watanabe, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+ROCK+inhibitor+permits+survival+of+dissociated+human+embryonic+stem+cells.">A ROCK inhibitor permits survival of dissociated human embryonic stem cells.</a> Nat Biotechnol. 25, 681-686 (2007).</li><li>Androutsellis-Theotokis, 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=Notch+signalling+regulates+stem+cell+numbers+in+vitro+and+in+vivo.">Notch signalling regulates stem cell numbers in vitro and in vivo.</a> Nature. 442, 823-826 (2006).</li><li>Jozefczuk, 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=Preparation+of+mouse+embryonic+fibroblast+cells+suitable+for+culturing+human+embryonic+and+induced+pluripotent+stem+cells.">Preparation of mouse embryonic fibroblast cells suitable for culturing human embryonic and induced pluripotent stem cells.</a> J Vis Exp. , (2012).</li><li>Kozhich, O. 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=Standardized+Generation+and+Differentiation+of+Neural+Precursor+Cells+from+Human+Pluripotent+Stem+Cells.">Standardized Generation and Differentiation of Neural Precursor Cells from Human Pluripotent Stem Cells.</a> Stem Cell Rev. , (2012).</li><li>Kunova, 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=Adaptation+to+robust+monolayer+expansion+produces+human+pluripotent+stem+cells+with+improved+viability.">Adaptation to robust monolayer expansion produces human pluripotent stem cells with improved viability.</a> Stem Cells Transl Med. 2, 246-254 (2013).</li><li>Tsutsui, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+optimized+small+molecule+inhibitor+cocktail+supports+long-term+maintenance+of+human+embryonic+stem+cells.">An optimized small molecule inhibitor cocktail supports long-term maintenance of human embryonic stem cells.</a> Nat Commun. 2, 167 (2011).</li><li>Amps, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Screening+ethnically+diverse+human+embryonic+stem+cells+identifies+a+chromosome+20+minimal+amplicon+conferring+growth+advantage.">Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage.</a> Nat Biotechnol. 29, 1132-1144 (2011).</li><li>Baker, D. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Adaptation+to+culture+of+human+embryonic+stem+cells+and+oncogenesis+in+vivo.">Adaptation to culture of human embryonic stem cells and oncogenesis in vivo.</a> Nat Biotechnol. 25, 207-215 (2007).</li><li>Lee, A. 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=Tumorigenicity+as+a+clinical+hurdle+for+pluripotent+stem+cell+therapies.">Tumorigenicity as a clinical hurdle for pluripotent stem cell therapies.</a> Nat Med. 19, 998-1004 (2013).</li><li>Domogatskaya, 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=Laminin-511+but+not+-332,+-111,+or+-411+enables+mouse+embryonic+stem+cell+self-renewal+in+vitro.">Laminin-511 but not -332, -111, or -411 enables mouse embryonic stem cell self-renewal in vitro.</a> Stem Cells. 26, 2800-2809 (2008).</li><li>Domogatskaya, 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=Functional+diversity+of+laminins.">Functional diversity of laminins.</a> Annu Rev Cell Dev Biol. 28, 523-553 (2012).</li><li>Rodin, 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=Long-term+self-renewal+of+human+pluripotent+stem+cells+on+human+recombinant+laminin-511.">Long-term self-renewal of human pluripotent stem cells on human recombinant laminin-511.</a> Nat Biotechnol. 28, 611-615 (2010).</li><li>Liew, C. 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=Transient+and+stable+transgene+expression+in+human+embryonic+stem+cells.">Transient and stable transgene expression in human embryonic stem cells.</a> Stem Cells. 25, 1521-1528 (2007).</li><li>Braam, S. 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=Genetic+manipulation+of+human+embryonic+stem+cells+in+serum+and+feeder-free+media.">Genetic manipulation of human embryonic stem cells in serum and feeder-free media.</a> Methods Mol Biol. 584, 413-423 (2010).</li><li>Braam, S. 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=Improved+genetic+manipulation+of+human+embryonic+stem+cells.">Improved genetic manipulation of human embryonic stem cells.</a> Nat Methods. 5, 389-392 (2008).</li></ol>

The authors declare that they have no competing financial interests.

There are two major ways to culture hPSCs in vitro: conventional colony-type culture (of cells on feeders or extracellular matrices) and suspension culture of hPSCs as aggregates without feeders6. The limitations of both colony-type and suspension culture methods include accumulated heterogeneity and inheritable epigenetic changes. NCM culture, based on both single-cell passaging and high-density cell plating, represents a new culture method for hPSC growth6,18. Although various single-cell...

The capacity of hPSCs to differentiate toward multilineage adult tissues has opened new avenues to treating patients who suffer from severe diseases that involve cardiovascular, hepatic, pancreatic, and neurological systems1-4. Various cell types derived from hPSCs would also provide robust cellular platforms for disease modeling, genetic engineering, drug screening, and toxicological testing1,4. The key issue that ensures their future clinical and pharmacological applications is the generation of large numbers of clinical-grade hPSCs through in vitro cell culture. However, current culture systems are either insufficient or inherently variable, involving various feeder and feeder-free cultures of hPSCs as colonies5,6.
Colony-type growth of hPSCs shares many structural features of the inner cell mass (ICM) of early mammalian embryos. The ICM is prone to differentiate into the three germ-layers in a multicellular environment because of the existence of heterogeneous signaling gradients. Thus, the acquisition of heterogeneity in early embryonic development is considered as a required process for differentiation, but an unwanted feature of hPSC culture. The heterogeneity in hPSC culture is often induced by excessive apoptotic signals and spontaneous differentiation due to suboptimal growth conditions. Thus, in colony-type culture, the heterogeneous cells are often observed in the periphery of the colonies7,8. It has been also shown that the cells in human embryonic stem cell (hESC) colonies exhibit differential responses to signaling molecules such as BMP-4&#160;9. Moreover, colony culture methods produce low cell yields as well as very low cell recovery rates from cryopreservation due to uncontrollable growth rates and apoptotic signaling pathways6,9. In recent years, various suspension cultures have been developed for culturing hPSCs, particularly for expansion of large amounts of hPSCs in feeder- and matrix-free conditions6,10-13. Obviously, different culture systems have their own advantages and disadvantages. In general, the heterogeneous nature of hPSCs represents one of the major drawbacks in colony-type and aggregated culture methods, which are suboptimal for delivering DNA and RNA materials into hPSCs for genetic engineering6.
Clearly, there is an imperative need to develop new systems that circumvent some shortcomings of current culture methods. The discoveries of small molecule inhibitors (such as the ROCK inhibitor Y-27632 and JAK inhibitor 1) that improve single-cell survival pave the way for dissociated-hPSC culture14,15. With the use of these small molecules, we have recently developed a culture method based on non-colony type (NCM) growth of dissociated-hPSCs9. This novel culture method combines both single-cell passaging and high-density plating methods, allowing us to produce large amounts of homogeneous hPSCs under consistent growth cycles without major chromosomal abnormalities9. Alternatively, NCM culture might be implemented with different small molecules and defined matrices (such as laminins) in order to optimize the culture method for wide applications. Here, we present several detailed protocols based on NCM culture and delineate detailed procedures for genetic engineering. To demonstrate the versatility of NCM protocols, we also tested NCM culture with diverse ROCK inhibitors and with the single laminin isoform 521 (i.e., LN-521).

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">Countess automated cell counter&#160;&#160;</td>
			<td style="width:220px;">Invitrogen Inc.&#160;</td>
			<td style="width:187px;">C10227</td>
			<td style="width:187px;">Automatic cell counting</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">Faxitron Cabinet X-ray System</td>
			<td style="width:220px;">Faxitron X-ray Corporation, Wheeling, IL&#160;</td>
			<td style="width:187px;">Model RX-650</td>
			<td style="width:187px;">X-ray irradiation of MEFs</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">MULTIWELL six-well plates&#160;</td>
			<td style="width:220px;">Becton Dickinson Labware</td>
			<td style="width:187px;">353046</td>
			<td style="width:187px;">Polystyrene plates&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">DMEM</td>
			<td style="width:220px;">Invitrogen Inc.</td>
			<td style="width:187px;">11965&#8211;092</td>
			<td style="width:187px;">For MEF medium</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">mitomycin C</td>
			<td style="width:220px;">Roche&#160;</td>
			<td style="width:187px;">107 409</td>
			<td style="width:187px;">Mitotic inhibitor</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">Trypsin</td>
			<td style="width:220px;">Invitrogen Inc.</td>
			<td style="width:187px;">25300-054</td>
			<td style="width:187px;">For MEF dissociation</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">DMEM/F12&#160;</td>
			<td style="width:220px;">Invitrogen Inc.</td>
			<td style="width:187px;">11330&#8211;032</td>
			<td style="width:187px;">For hPSC medium</td>
		</tr>
		<tr height="45">
			<td height="45" style="height:45px;width:203px;">Opti-MEM I Reduced Serum Medium&#160;</td>
			<td style="width:220px;">Invitrogen Inc.</td>
			<td style="width:187px;">31985-062</td>
			<td style="width:187px;">For hPSC transfection</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">Heat-inactivated FBS</td>
			<td style="width:220px;">Invitrogen Inc.</td>
			<td style="width:187px;">16000&#8211;044</td>
			<td style="width:187px;">Component of MEF medium</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">Knockout Serum Replacer&#160;</td>
			<td style="width:220px;">Invitrogen Inc.</td>
			<td style="width:187px;">10828&#8211;028</td>
			<td style="width:187px;">KSR, Component of hPSC medium</td>
		</tr>
		<tr height="45">
			<td height="45" style="height:45px;width:203px;">Dulbecco&#8217;s Phosphate-Buffered Saline</td>
			<td style="width:220px;">Invitrogen Inc.</td>
			<td style="width:187px;">14190-144</td>
			<td style="width:187px;">D-PBS, free of Ca2+/Mg2+</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">Non-essential amino acids&#160;</td>
			<td style="width:220px;">Invitrogen&#160;</td>
			<td style="width:187px;">11140&#8211;050</td>
			<td style="width:187px;">NEAA, component of hPSC medium</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">L-Glutamine&#160;</td>
			<td style="width:220px;">Invitrogen&#160;</td>
			<td style="width:187px;">25030&#8211;081</td>
			<td style="width:187px;">Component of hPSC medium</td>
		</tr>
		<tr height="20">
			<td height="41" rowspan="2" style="height:41px;width:203px;">mTeSR1 &#38; Supplements</td>
			<td rowspan="2" style="width:220px;">StemCell Technologies</td>
			<td rowspan="2" style="width:187px;">5850</td>
			<td style="width:187px;">Animal protein-free</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:187px;">medium</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">TeSR2 &#38; Supplements</td>
			<td style="width:220px;">StemCell Technologies</td>
			<td style="width:187px;">5860</td>
			<td style="width:187px;">Xeno-free medium</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">&#946;-mercaptoethanol&#160;</td>
			<td style="width:220px;">Sigma&#160;</td>
			<td style="width:187px;">7522</td>
			<td style="width:187px;">Component of hPSC medium</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:203px;"> 
			MEF (CF-1) ATCC</td>
			<td style="width:220px;">American Type Culture Collection (ATCC)&#160;</td>
			<td style="width:187px;">SCRC-1040</td>
			<td style="width:187px;">For feeder culture of hPSCs</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">hESC-qualified Matrigel</td>
			<td style="width:220px;">BD Bioscience</td>
			<td style="width:187px;">354277</td>
			<td style="width:187px;">For feeder-free culture of hPSCs</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">Laminin-521</td>
			<td style="width:220px;">BioLamina</td>
			<td style="width:187px;">LN521-02</td>
			<td style="width:187px;">Human recombinant protein</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">FGF-2 (recombinant FGF, basic)</td>
			<td style="width:220px;">R&#38;D Systems, MN</td>
			<td style="width:187px;">223-FB</td>
			<td style="width:187px;">Growth factor in hPSC medium</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">CryoStor CA10&#160;</td>
			<td style="width:220px;">StemCell Technologies</td>
			<td style="width:187px;">7930</td>
			<td style="width:187px;"></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">Accutase</td>
			<td style="width:220px;">Innovative Cell Technologies</td>
			<td style="width:187px;">AT-104</td>
			<td style="width:187px;">1X mixed enzymatic solution</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">JAK inhibitor I</td>
			<td style="width:220px;">EMD4 Biosciences</td>
			<td style="width:187px;">420099</td>
			<td style="width:187px;">An inhibitor of Janus kinase</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">Y-27632</td>
			<td style="width:220px;">EMD4 Biosciences</td>
			<td style="width:187px;">688000</td>
			<td style="width:187px;">ROCK inhibitor</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">Y-27632</td>
			<td style="width:220px;">Stemgent</td>
			<td style="width:187px;">04-0012</td>
			<td style="width:187px;">ROCK inhibitor</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">Y-39983</td>
			<td style="width:220px;">Stemgent</td>
			<td style="width:187px;">04-0029</td>
			<td style="width:187px;">ROCK I inhibitor</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">Phenylbenzodioxane&#160;</td>
			<td style="width:220px;">Stemgent</td>
			<td style="width:187px;">04-0030</td>
			<td style="width:187px;">ROCK II inhibitor</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">Thiazovivin</td>
			<td style="width:220px;">Stemgent</td>
			<td style="width:187px;">04-0017</td>
			<td style="width:187px;">A novel ROCK inhibitor</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">BD Falcon Cell Strainer&#160;</td>
			<td style="width:220px;">BD Bioscience</td>
			<td style="width:187px;">352340</td>
			<td style="width:187px;">40-&#181;m cell strainer</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">Nalgene 5100-0001 Cryo 1&#176;C</td>
			<td style="width:220px;">Thermo Scientific&#160;</td>
			<td style="width:187px;">C6516F-1</td>
			<td style="width:187px;">&#8220;Mr. Frosty&#8221; Freezing Container</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">Lipofectamine 2000&#160;</td>
			<td style="width:220px;">Invitrogen Inc.</td>
			<td style="width:187px;">11668-027</td>
			<td style="width:187px;">Transfection reagents</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">DharmaFECT Duo&#160;</td>
			<td style="width:220px;">Thermo Scientific</td>
			<td style="width:187px;">T-2010-02</td>
			<td style="width:187px;">Transfection reagent</td>
		</tr>
		<tr height="61">
			<td height="61" style="height:61px;width:203px;">Non-targeting miRIDIAN miRNA Transfection Control</td>
			<td style="width:220px;">Thermo Scientific</td>
			<td style="width:187px;">IP-004500-01-05</td>
			<td style="width:187px;">Labeled with Dy547, to monitor the delivery of microRNAs&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">SMART-shRNA</td>
			<td style="width:220px;">Thermo Scientific&#160;</td>
			<td style="width:187px;">To be determined</td>
			<td style="width:187px;">Lentiviral vector</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">pmaxGFP</td>
			<td>amaxa Inc (Lonza)</td>
			<td>Included in every transfection kit</td>
			<td style="width:187px;">Expression plasmid for transfection control</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">4-Oct</td>
			<td style="width:220px;">Santa Cruz Biotechnology</td>
			<td style="width:187px;">sc-5279</td>
			<td style="width:187px;">Mouse IgG2b, pluripotent marker</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">SSEA-1</td>
			<td>Santa Cruz Biotechnology</td>
			<td style="width:187px;">sc-21702</td>
			<td style="width:187px;">Mouse IgM, differentiation marker</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">SSEA-4</td>
			<td style="width:220px;">Santa Cruz Biotechnology</td>
			<td style="width:187px;">sc-21704</td>
			<td style="width:187px;">Mouse IgG3, pluripotent marker</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">Tra-1-60</td>
			<td style="width:220px;">Santa Cruz Biotechnology</td>
			<td style="width:187px;">sc-21705&#160;</td>
			<td style="width:187px;">Mouse IgM, pluripotent marker</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">Tra-1-81</td>
			<td style="width:220px;">Santa Cruz Biotechnology</td>
			<td style="width:187px;">sc-21706</td>
			<td style="width:187px;">Mouse IgM, pluripotent marker</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">CK8 (C51)</td>
			<td style="width:220px;">Santa Cruz Biotechnology</td>
			<td style="width:187px;">sc-8020</td>
			<td style="width:187px;">Mouse IgG1, against cytokeratin 8</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">&#945;-fetoprotein</td>
			<td style="width:220px;">Santa Cruz Biotechnology</td>
			<td style="width:187px;">sc-8399</td>
			<td style="width:187px;">AFP, mouse IgG2a</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">HNF-3&#946; (P-19)</td>
			<td style="width:220px;">Santa Cruz Biotechnology</td>
			<td style="width:187px;">sc-9187</td>
			<td style="width:187px;">FOXA2, goat polyclonal antibody</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">Troponin T (Av-1)</td>
			<td style="width:220px;">Thermo Scientific</td>
			<td style="width:187px;">MS-295-P0</td>
			<td style="width:187px;">Mouse IgG1</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">Desmin&#160;</td>
			<td style="width:220px;">Thermo Scientific</td>
			<td style="width:187px;">RB-9014-P1</td>
			<td style="width:187px;">Rabbit IgG</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">Anti-NANOG</td>
			<td style="width:220px;">ReproCELL Inc, Japan</td>
			<td style="width:187px;">RCAB0004P-F</td>
			<td style="width:187px;">Polyclonal antibody&#160;</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">Rat anti-GFAP</td>
			<td style="width:220px;">Zymed</td>
			<td style="width:187px;">13-0300</td>
			<td style="width:187px;">Glial fibrillary acidic protein</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">Albumin (clone HSA1/25.1.3)</td>
			<td style="width:220px;">Cedarlane Laboratories Ltd. (</td>
			<td style="width:187px;">CL2513A</td>
			<td style="width:187px;">Mouse IgG1,</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">Smooth muscle actin (clone 1A4)</td>
			<td style="width:220px;">DakoCytomation Inc</td>
			<td style="width:187px;">IR611/IS611</td>
			<td style="width:187px;">Mouse IgG2a</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">Nestin</td>
			<td style="width:220px;">Chemicon International</td>
			<td style="width:187px;">MAB5326</td>
			<td style="width:187px;">Rabbit polyclonal antibody</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:203px;">TUBB3</td>
			<td style="width:220px;">Convance Inc</td>
			<td style="width:187px;">MMS-435P</td>
			<td style="width:187px;">Tuj1, mouse IgG2a</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">HNF4&#945; (C11F12)</td>
			<td style="width:220px;">Cell Signaling Technologies</td>
			<td style="width:187px;">3113</td>
			<td style="width:187px;">Rabbit monoclonal antibody</td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:203px;">Paraformaldehyde (solution)</td>
			<td style="width:220px;">Electron Microscopy Sciences</td>
			<td style="width:187px;">15710</td>
			<td style="width:187px;">PFA, fixative, diluted in D-PBS</td>
		</tr>
	</tbody>
</table>

alternative cultures for human pluripotent stem cell production, maintenance, and genetic analysis

Human pluripotent stem cells (hPSCs) hold great promise for regenerative medicine and biopharmaceutical applications. Currently, optimal culture and efficient expansion of large amounts of clinical-grade hPSCs are critical issues in hPSC-based therapies. Conventionally, hPSCs are propagated as colonies on both feeder and feeder-free culture systems. However, these methods have several major limitations, including low cell yields and generation of heterogeneously differentiated cells. To improve current hPSC culture methods, we have recently developed a new method, which is based on non-colony type monolayer (NCM) culture of dissociated single cells. Here, we present detailed NCM protocols based on the Rho-associated kinase (ROCK) inhibitor Y-27632. We also provide new information regarding NCM culture with different small molecules such as Y-39983 (ROCK I inhibitor), phenylbenzodioxane (ROCK II inhibitor), and thiazovivin (a novel ROCK inhibitor). We further extend our basic protocol to cultivate hPSCs on defined extracellular proteins such as the laminin isoform 521 (LN-521) without the use of ROCK inhibitors. Moreover, based on NCM, we have demonstrated efficient transfection or transduction of plasmid DNAs, lentiviral particles, and oligonucleotide-based microRNAs into hPSCs in order to genetically modify these cells for molecular analyses and drug discovery. The NCM-based methods overcome the major shortcomings of colony-type culture, and thus may be suitable for producing large amounts of homogeneous hPSCs for future clinical therapies, stem cell research, and drug discovery.

A general schema of NCM culture
Figure 1 represents a typical NCM culture schema showing the dynamic changes of hPSCs after high-density single-cell plating in the presence of the ROCK inhibitor Y-27632. These morphological changes include intercellular connections after plating, cellular clusters formation, and exponential cell growth followed by cell condensation (Figure 1A). A representative experiment indicates WA01 (H1) hESCs, plated as s...

Watch this Scientific Journal Video about Alternative Cultures for Human Pluripotent Stem Cell Production, Maintenance, and Genetic Analysis at JoVE.com

Alternative Cultures for Human Pluripotent Stem Cell Production, Maintenance, and Genetic Analysis

Here, we present human pluripotent stem cell (hPSC) culture protocols, based on non-colony type monolayer (NCM) growth of dissociated single cells. This new method, utilizing Rho-associated kinase inhibitors or the laminin isoform 521 (LN-521), is suitable for producing large amounts of homogeneous hPSCs, genetic manipulation, and drug discovery.

Human pluripotent stem cells (hPSCs) hold great promise for regenerative medicine and biopharmaceutical applications. Currently, optimal culture and ...

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12.3K Views.  National Institutes of Health. Here, we present human pluripotent stem cell (hPSC) culture protocols, based on non-colony type monolayer (NCM) growth of dissociated single cells. This new method, utilizing Rho-associated kinase inhibitors or the laminin isoform 521 (LN-521), is suitable for producing large amounts of homogeneous hPSCs, genetic manipulation, and drug discovery.

Video: Alternative Cultures for Human Pluripotent Stem Cell Production, Maintenance, and Genetic Analysis

Mouse Epidermal Neural Crest Stem Cell (EPI-NCSC) Cultures

EPI-NCSC are remnants of the embryonic neural crest in an adult location, the bulge of hair follicles. They are multipotent stem cells that have the physiological property to generate a wide array of differentiated cell types, including neurons, nerve supporting cells, smooth muscle cells, bone/cartilage cells and melanocytes. EPI-NCSC are easily accessible in the hairy skin and can be isolated as a highly pure population of stem cells. This video provides a detailed protocol for preparing mouse EPI-NCSC cultures from whisker follicles. The whisker pad of an adult mouse is removed, and whisker follicles dissected. The follicles are then cut longitudinally and subsequently transversely above and below the bulge region. The bulge is removed from the collagen capsule and placed in a culture plate. EPI-NCSC start to emigrate from the bulge explants 3 to 4 days later.

Mouse Epidermal Neural Crest Stem Cell EPI-NCSC Cultures

Here we show our method to isolate mouse epidermal neural crest stem cells (EPI-NCSC). Technique involves micro-dissecting whisker follicles, isolating the bulge and placeing it into tissue culture. EPI-NCSC start to emigrate from bulge explants onto the substratum within 3 - 4 days.

EPI-NCSC are remnants of the embryonic neural crest in an adult location, the bulge of hair follicles. They are multipotent stem cells that have the ...

Culture and Maintenance of Human Embryonic Stem Cells  

Human embryonic stem (hES) cells must be monitored and cared for in order to maintain healthy, undifferentiated cultures. At minimum, the cultures must be  fed  every day by performing a complete medium change to replenish lost nutrients and to keep the cultures free of unwanted differentiation factors. Although a small amount of differentiation is normal and expected in stem cell cultures, the culture should be routinely cleaned up by manually removing, or "picking" differentiated areas. Identifying and removing excess differentiation from hES cell cultures are essential techniques in the maintenance of a healthy population of cells.

Culture and Maintenance of Human Embryonic Stem Cells

This protocol demonstrates how to maintain healthy, undifferentiated human embryonic stem (ES) cells.

Human embryonic stem (hES) cells must be monitored and cared for in order to maintain healthy, undifferentiated cultures. At minimum, the cultures must be ...

Preparation of Pooled Human Platelet Lysate (pHPL) as an Efficient Supplement for Animal Serum-Free Human Stem Cell Cultures

Platelet derived growth factors have been shown to stimulate cell proliferation efficiently in vivo1,2 and in vitro. This effect has been reported for mesenchymal stromal cells (MSCs), fibroblasts and endothelial colony-forming cells with platelets activated by thrombin3-5 or lysed by freeze/thaw cycles6-14 before the platelet releasate is added to the cell culture medium. The trophic effect of platelet derived growth factors has already been tested in several trials for tissue engineering and regenerative therapy.1,15-17 Varying efficiency is considered to be at least in part due to individually divergent concentrations of growth factors18,19 and a current lack of standardized protocols for platelet preparation.15,16 This protocol presents a practicable procedure to generate a pool of human platelet lysate (pHPL) derived from routinely produced platelet rich plasma (PRP) of forty to fifty single blood donations. By several freeze/thaw cycles the platelet membranes are damaged and growth factors are efficiently released into the plasma. Finally, the platelet fragments are removed by centrifugation to avoid extensive aggregate formation and deplete potential antigens. The implementation of pHPL into standard culture protocols represents a promising tool for further development of cell therapeutics propagated in an animal protein-free system.

Preparation of Pooled Human Platelet Lysate pHPL as an Efficient Supplement for Animal Serum-Free Human Stem Cell Cultures

Human platelet lysate is a rich source of growth factors and a potent supplement in cell culture. This protocol presents the process of preparing a large pool of human platelet lysate by starting from platelet rich plasma, performing several freeze-thaw cycles and depleting the platelet fragments.

Platelet derived growth factors have been shown to stimulate cell proliferation efficiently in vivo1,2 and in vitro. This effect has been reported for ...

Video Bioinformatics Analysis of Human Embryonic Stem Cell Colony Growth

Because video data are complex and are comprised of many images, mining information from video material is difficult to do without the aid of computer software.  Video bioinformatics is a powerful quantitative approach for extracting spatio-temporal data from video images using computer software to perform dating mining and analysis. In this article, we introduce a video bioinformatics method for quantifying the growth of human embryonic stem cells (hESC) by analyzing time-lapse videos collected in a Nikon BioStation CT incubator equipped with a camera for video imaging. In our experiments, hESC colonies that were attached to Matrigel were filmed for 48 hours in the BioStation CT.  To determine the rate of growth of these colonies, recipes were developed using CL-Quant software which enables users to extract various types of data from video images.  To accurately evaluate colony growth, three recipes were created. The first segmented the image into the colony and background, the second enhanced the image to define colonies throughout the video sequence accurately, and the third measured the number of pixels in the colony over time.  The three recipes were run in sequence on video data collected in a BioStation CT to analyze the rate of growth of individual hESC colonies over 48 hours. To verify the truthfulness of the CL-Quant recipes, the same data were analyzed manually using Adobe Photoshop software. When the data obtained using the CL-Quant recipes and Photoshop were compared, results were virtually identical, indicating the CL-Quant recipes were truthful. The method described here could be applied to any video data to measure growth rates of hESC or other cells that grow in colonies. In addition, other video bioinformatics recipes can be developed in the future for other cell processes such as migration, apoptosis, and cell adhesion.  

Video bioinformatics is the automated processing, analysis, understanding, and data mining of biological spatio-temporal data extracted from microscopic videos. The purpose of this article is to demonstrate a method for measuring human embryonic stem cell colony growth using a video bioinformatics method.

Because video data are complex and are comprised of many images, mining information from video material is difficult to do without the aid of computer ...

Transfecting and Nucleofecting Human Induced Pluripotent Stem Cells

Genetic modification is continuing to be an essential tool in studying stem cell biology and in setting forth potential clinical applications of human embryonic stem cells (HESCs)1. While improvements in several gene delivery methods have been described2-9, transfection remains a capricious process for HESCs, and has not yet been reported in human induced pluripotent stem cells (iPSCs). In this video, we demonstrate how our lab routinely transfects and nucleofects human iPSCs using plasmid with an enhanced green fluorescence protein (eGFP) reporter. Human iPSCs are adapted and maintained as feeder-free cultures to eliminate the possibility of feeder cell transfection and to allow efficient selection of stable transgenic iPSC clones following transfection. For nucleofection, human iPSCs are pre-treated with ROCK inhibitor11, trypsinized into small clumps of cells, nucleofected and replated on feeders in feeder cell-conditioned medium to enhance cell recovery. Transgene-expressing human iPSCs can be obtained after 6 hours. Antibiotic selection is applied after 24 hours and stable transgenic lines appear within 1 week. Our protocol is robust and reproducible for human iPSC lines without altering pluripotency of these cells.

Despite recent advancements in genetic modification, transfection of human embryonic stem cells (HESCs) remains a capricious process. To our knowledge, systematic and efficient methods to transfect human induced pluripotent stem cells (iPSCs) have not been reported. Here, we describe robust protocols to efficiently transfect and nucleofect human iPSCs.

Genetic modification is continuing to be an essential tool in studying stem cell biology and in setting forth potential clinical applications of human ...

Selecting and Isolating Colonies of Human Induced Pluripotent Stem Cells Reprogrammed from Adult Fibroblasts

Herein we present a protocol of reprogramming human adult fibroblasts into human induced pluripotent stem cells (hiPSC) using retroviral vectors encoding Oct3/4, Sox2, Klf4 and c-myc (OSKM) in the presence of sodium butyrate 1-3. We used this method to reprogram late passage (&gt;p10) human adult fibroblasts derived from Friedreich's ataxia patient (GM03665, Coriell Repository). The reprogramming approach includes highly efficient transduction protocol using repetitive centrifugation of fibroblasts in the presence of virus-containing media. The reprogrammed hiPSC colonies were identified using live immunostaining for Tra-1-81, a surface marker of pluripotent cells, separated from non-reprogrammed fibroblasts and manually passaged 4,5. These hiPSC were then transferred to Matrigel plates and grown in feeder-free conditions, directly from the reprogramming plate. Starting from the first passage, hiPSC colonies demonstrate characteristic hES-like morphology. Using this protocol more than 70% of selected colonies can be successfully expanded and established into cell lines. The established hiPSC lines displayed characteristic pluripotency markers including surface markers TRA-1-60 and SSEA-4, as well as nuclear markers Oct3/4, Sox2 and Nanog. 
The protocol presented here has been established and tested using adult fibroblasts obtained from Friedreich's ataxia patients and control individuals 6, human newborn fibroblasts, as well as human keratinocytes.

We present a protocol for efficient reprogramming of human somatic cells into human induced pluripotent stem cells (hiPSC) using retroviral vectors encoding Oct3/4, Sox2, Klf4 and c-myc (OSKM) and identification of correctly reprogrammed hiPSC by live staining with Tra-1-81 antibody.

Herein we present a protocol of reprogramming human adult fibroblasts into human induced pluripotent stem cells (hiPSC) using retroviral vectors encoding ...

Generation of Human Cardiomyocytes: A Differentiation Protocol from Feeder-free Human Induced Pluripotent Stem Cells

In order to investigate the events driving heart development and to determine the molecular mechanisms leading to myocardial diseases in humans, it is essential first to generate functional human cardiomyocytes (CMs). The use of these cells in drug discovery and toxicology studies would also be highly beneficial, allowing new pharmacological molecules for the treatment of cardiac disorders to be validated pre-clinically on cells of human origin. Of the possible sources of CMs, induced pluripotent stem (iPS) cells are among the most promising, as they can be derived directly from readily accessible patient tissue and possess an intrinsic capacity to give rise to all cell types of the body 1. Several methods have been proposed for differentiating iPS cells into CMs, ranging from the classical embryoid bodies (EBs) aggregation approach to chemically defined protocols 2,3. In this article we propose an EBs-based protocol and show how this method can be employed to efficiently generate functional CM-like cells from feeder-free iPS cells.

Pluripotent stem cells, either embryonic or induced pluripotent stem (iPS) cells, constitute a valuable source of human differentiated cells, including cardiomyocytes. Here, we will focus on cardiac induction of iPS cells, showing how to use them to obtain functional human cardiomyocytes through an embryoid bodies-based protocol.

In order to investigate the events driving heart development and to determine the molecular mechanisms leading to myocardial diseases in humans, it is ...

Efficient Generation Human Induced Pluripotent Stem Cells from Human Somatic Cells with Sendai-virus

A few years ago, the establishment of human induced pluripotent stem cells (iPSCs) ushered in a new era in biomedicine. Potential uses of human iPSCs include modeling pathogenesis of human genetic diseases, autologous cell therapy after gene correction, and personalized drug screening by providing a source of patient-specific and symptom relevant cells. However, there are several hurdles to overcome, such as eliminating the remaining reprogramming factor transgene expression after human iPSCs production. More importantly, residual transgene expression in undifferentiated human iPSCs could hamper proper differentiations and misguide the interpretation of disease-relevant in vitro phenotypes. With this reason, integration-free and/or transgene-free human iPSCs have been developed using several methods, such as adenovirus, the piggyBac system, minicircle vector, episomal vectors, direct protein delivery and synthesized mRNA. However, efficiency of reprogramming using integration-free methods is quite low in most cases.
Here, we present a method to isolate human iPSCs by using Sendai-virus (RNA virus) based reprogramming system. This reprogramming method shows consistent results and high efficiency in cost-effective manner.

Here, we present our established method to reprogram human somatic cells into transgene-free human iPSCs with Sendai virus, which shows consistent outcome and enhanced efficiency.

A few years ago, the establishment of human induced pluripotent stem cells (iPSCs) ushered in a new era in biomedicine. Potential uses of human iPSCs ...

Automated Production of Human Induced Pluripotent Stem Cell-Derived Cortical and Dopaminergic Neurons with Integrated Live-Cell Monitoring

Manual culture and differentiation protocols for human induced pluripotent stem cells (hiPSC) are difficult to standardize, show high variability and are prone to spontaneous differentiation into unwanted cell types. The methods are labor-intensive and are not easily amenable to large-scale experiments. To overcome these limitations, we developed an automated cell culture system coupled to a high-throughput imaging system and implemented protocols for maintaining multiple hiPSC lines in parallel and neuronal differentiation. We describe the automation of a short-term differentiation protocol using Neurogenin-2 (NGN2) over-expression to produce hiPSC-derived cortical neurons within 6&#8210;8 days, and the implementation of a long-term differentiation protocol to generate hiPSC-derived midbrain dopaminergic (mDA) neurons within 65 days. Also, we applied the NGN2 approach to a small molecule-derived neural precursor cells (smNPC)&#160;transduced with GFP lentivirus and established a live-cell automated neurite outgrowth assay. We present an automated system with protocols suitable for routine hiPSC culture and differentiation into cortical and dopaminergic neurons. Our platform is suitable for long term hands-free culture and high-content/high-throughput hiPSC-based compound, RNAi and CRISPR/Cas9 screenings to identify novel disease mechanisms and drug targets.

We show the automation of human induced pluripotent stem cell (hiPSC) cultures and neuronal differentiations compatible with automated imaging and analysis.

Manual culture and differentiation protocols for human induced pluripotent stem cells (hiPSC) are difficult to standardize, show high variability and are ...

A Two-Step Strategy that Combines Epigenetic Modification and Biomechanical Cues to Generate Mammalian Pluripotent Cells

Cell phenotype can be reversed or modified with different methods, with advantages and limitations that are specific for each technique. Here we describe a new strategy that combines the use of chemical epigenetic erasing with mechanosensing-related cues, to generate mammalian pluripotent cells. Two main steps are required. In the first step, adult mature (terminally differentiated) cells are exposed to the epigenetic eraser 5-aza-cytidine to drive them into a pluripotent state. This part of the protocol was developed, based on the increasing understanding of the epigenetic mechanisms controlling cell fate and differentiation, and involves the use of the epigenetic modifier to erase cell differentiated state and then drive into a transient high plasticity window.
In the second step, erased cells are encapsulated in polytetrafluoroethylene (PTFE) micro-bioreactors, also known as Liquid Marbles, to promote 3D cell rearrangement to extend and stably maintain the acquired high plasticity. PTFE is a non-reactive hydrophobic synthetic compound and its use permits the creation of a cellular microenvironment, which cannot be achieved in traditional 2D culture systems. This system encourages and boosts the maintenance of pluripotency though bio-mechanosensing-related cues.
The technical procedures described here are simple strategies to allow for the induction and maintenance of a high plasticity state in adult somatic cells. The protocol allowed the derivation of high plasticity cells in all mammalian species tested. Since it does not involve the use of gene transfection and is free of viral vectors, it may represent a notable technological advance for translational medicine applications. Furthermore, the micro-bioreactor system provides a notable advancement in stem cell organoid technology by in vitro re-creating a specific micro-environment that allows for the long-term culture of high plasticity cells, namely as ESCs, iPSCs, epigenetically erased cells and MSCs.

We here present a method that combines the use of chemical epigenetic erasing with mechanosensing-related cues to efficiently generate mammalian pluripotent cells, without the need of gene transfection or retroviral vectors. This strategy is, therefore, promising for translational medicine and represents a notable advancement in stem cell organoid technology.

Cell phenotype can be reversed or modified with different methods, with advantages and limitations that are specific for each technique. Here we describe ...