We thank Elizabeth Benevides for proofreading the article. We thank Drs. John Hussman and Gene Blatt for their helpful discussions and comments.

1. Generation of Neural Progenitor Cells
<ol>
	<li>Maintain hiPSCs derived from fibroblasts and PBMCs in 6-well plates on a &#947;-irradiated mouse embryonic feeder (MEF) cell layer in human iPSC medium supplemented with small-molecules (see the Materials Table). 
	NOTE: Daily maintenance is a modified version of previously reported procedures1,16.
	<ol>
		<li>Plate 6 x 105 MEFs onto each well of a 6-well tissue culture grade plate in 300 &#956;L/well recommended medium (following manufacturer&#39;s protocol).</li>
		<li>After 48 h, replace MEFs medium with 300 &#956;L/well hiPSC medium for 1 h before adding hiPSCs.</li>
		<li>Quickly thaw hiPSCs in a 37 &#176;C water bath and slowly add 1 mL hiPSC medium dropwise. Transfer the hiPSCs and medium to a 15 mL conical tube. Add medium to bring the total volume to 5 mL. Centrifuge for 4 min at 129 x g, aspirate the supernatant, gently re-suspend the pellet in 1 mL hiPSC medium with ROCK inhibitor at 1:1,000 concentration.</li>
		<li>Plate the cell suspension (typically seeded at 300,000 cells/well) onto the MEF cell layer and incubate at 37 &#176;C, 5% CO2, 95% humidity.</li>
		<li>Monitor iPSC culture closely using a light microscope. After 48 h, remove cultures that have uneven edges, have grown to become cystic-like or appear yellowish-brown under the light microscope to minimize spontaneous differentiation. 
		NOTE: After 7 - 10 days, hiPSC colonies should form. Colonies should be round, with clearly defined borders and uniform cell densities, and devoid of loosely packed non-uniform cells.</li>
		<li>Manually select round hiPSC colonies to clear the culture of spontaneously differentiated cells. Expand the colonies by placing them on fresh MEF layers. Expand 1:3 every 7 days when cultures near confluency and freeze1,16.</li>
	</ol>
	</li>
	<li>After expansion and freezing cells (for backup), grow hiPSC colonies on plates until they reach 50 - 75% confluence.</li>
	<li>Seven-days post plating, use mild enzymatic treatment (5-10 min with 300 &#956;L of enzyme solution) and gentle trituration (2-4 times with a 1,000 &#181;L pipet) to harvest and prepare hiPSCs for neural precursor cell differentiation.</li>
	<li>Centrifuge the cell suspension at 129 x g for 4 min, aspirate the supernatant, and resuspend the pellet in 5 mL human iPSC medium. Transfer the cell suspension to a 0.1% gelatin coated 5 cm cell culture dish for 1 h at 37 &#176;C to eliminate MEFs and to maximize the hiPSC yield. Transfer the medium (with non-adherent cells) to another 5 cm gelatin coated dish.</li>
	<li>Transfer the non-adherent cells to a 15 mL centrifuge tube using a transfer pipet. Gently rinse the plates with 3 mL medium and add it to the 15 mL tube.</li>
	<li>Centrifuge the cell suspension at 129 x g for 4 min, aspirate the supernatant, and gently resuspend the pellet in medium. Determine the cell count using an automated cell counter. Plate 9,000 cells/well in a 96-well low-adhesion V-bottom plate.</li>
	<li>Centrifuge the plate at 163 x g for 3 min. Incubate the plate at 37 &#176;C, 95% humidity and 5% CO2. Using a pipette, change 50% medium every other day by removing half of the medium and replacing it with fresh chemically-defined differentiating medium 1 (DM1; Figure 1; Table of Materials) for 14 days.</li>
</ol>
2. Serum-Free Embryoid Body (SFEB) Induction (Figure 2)
<ol>
	<li>Place 40 &#181;m cell culture inserts into 6-well plates and add 1 mL DM1 medium at least 1 h prior to the addition of aggregates.</li>
	<li>On day 14, transfer the aggregates with 20 &#181;L medium using a 200 &#181;L wide mouth tip onto 40 &#181;m cell culture inserts and change the medium to DM2. 
	NOTE: Cell culture inserts are specialized inserts that sit slightly off the bottom of the well and consist of a polytetrafluoroethylene membrane suspended across a plastic frame. This membrane is biocompatible and can efficiently sustain nutrient and oxygen transport to the SFEBs, which are placed on top. They are commonly used with organotypic hippocampal slice cultures taken from mouse or rat7,17,18.
	<ol>
		<li>Transfer 4-6 aggregates to one cell culture insert and allow adequate space between the aggregates. Remove as much excess solution as possible using a fine pipette tip (e.g. 200 &#956;L tip). 
		NOTE: It is acceptable to briefly disturb the SFEB as they will move on the cell culture insert as the solution in removed from around the SFEBs.</li>
		<li>Maintain the cultures in 1 mL of DM2 at 37 &#176;C, 95% humidity and 5% CO2. Using a pipette, change 75% medium every other day by removing three quarters of the medium and replacing with three quarters fresh medium. For example, remove 750 &#956;L of medium and add 750 &#956;L of fresh medium.</li>
	</ol>
	</li>
	<li>After 14 days of culture, switch to DM3 medium with 75% medium change every other day and for another 16 days.</li>
	<li>To maintain the SFEBs on cell culture inserts beyond 30 days, change the medium every other day for 60, 90 and 120 days. 
	NOTE: The SFEBs will grow to about 1,000 &#956;m in diameter and are typically 100-150 &#956;m thick1.</li>
</ol>
3. Determining SFEB Composition
<ol>
	<li>Detach the SFEBs from the insert by gently pipetting medium using a 200 &#181;L wide mouth pipette tip. To transfer the SFEBs, use a wide mouth pipette tip to gently suction the bodies into the pipet tip. After loading SFEB into the pipet tip, gently transfer to 12-well plates and wash with 300 &#956;L phosphate buffered saline (PBS) per well. 
	NOTE: SFEBs will be suspended in solution in the 12-well plates. This is important to allow full penetration of the fixative, the blocking solution, and antibodies. If using multiple SFEBs for staining, up to 10 SFEBs can be added per well of a 12 well plate. This will conserve solutions and antibodies.</li>
	<li>Fix SFEBs with 300 &#956;L per well 4% paraformaldehyde at room temperature for 30-45 min. Wash fixed SFEBs twice with 300 &#956;L PBS, 3-5 min each wash. 
	Caution: Wear appropriate personal protective equipment when handling paraformaldehyde. 
	NOTE: Probe for immunoreactivity to markers to determine maturity, cell type etc. For marking neurons in this study chicken-Tuj1 was used at 1:500, for additional markers please see Table 2 and references1,16.</li>
	<li>Permeabilize and block with 0.1% Triton-X100 in PBS and 10% normal donkey serum (blocking solution; 300 &#956;L per well) for 1 h at room temperature.</li>
	<li>Remove the blocking solution and treat SFEBs with 300 &#956;L primary antibodies in blocking solution. Incubate at 4 &#176;C overnight. Wash SFEBs thrice (3-5 min per wash) in 300 &#956;L PBS containing 0.1% Triton-X.</li>
	<li>Prepare secondary antibodies 1:1000 in blocking solution. Incubate SFEBs for 1 h at room temperature with secondary antibodies. Wash SFEBs with 300 &#956;L PBS, 3 times for 3-5 min each. 
	NOTE: At this stage SFEBs can be prepared for imaging.</li>
	<li>To image, pipette SFEBs onto a glass slide using a wide-bore pipette. Remove excess solution around the SFEB using gentle suction. 
	NOTE: For similar staining conditions, multiple SFEBs can be placed on the same glass slide.</li>
	<li>Add a drop of mounting medium on the SFEBs, place a glass coverslip, and gently press to ensure that there are no air bubbles. Allow the mounting medium to harden and proceed to imaging and quantification (step 3.8). 
	NOTE: After the mounting medium hardens, the SFEBs are ready for imaging.</li>
	<li>Perform cell quantification by taking multiple regions of interest (ROI) across the SFEB and using a z-stack combined with a maximal projection image through each ROI on a standard confocal microscope as described in references1,16. 
	NOTE: Whole SFEBs can be quantified using image-based tiling (see references1,16 for details). Since the SFEBs thin to approximately 100 &#956;m, there is minimal scattering of light in the tissue and thus there is no need for 2-photon microscopy. Earlier uses of this protocol with fibroblast-derived iPSCs produced a SFEB fate map that revealed complex and diverse structure with subpopulations of interneurons with transcriptional identities that resembled CGE and anterior forebrain fates1,16.</li>
</ol>
4. Recording Neuronal activity in SFEBs Using MEAs
<ol>
	<li>Prepare 12-well MEA plates as per manufacturer&#39;s instructions.</li>
	<li>Wash the MEA plates 3 times for 5 min with sterile H2O under aseptic conditions to clean. Wash for 5 min with 75% ethanol and then with 100% ethanol to sterilize the plate.</li>
	<li>Bake the plate inverted in an oven for 4-5 h at 50 &#176;C to complete the sterilization process.</li>
	<li>Add 500 &#181;L 0.2% polyethyleneimine solution (PEI) to each well and incubate 1 h at room temperature. Aspirate PEI and wash the wells 4x with sterile distilled H2O. Air dry in the hood overnight.</li>
	<li>Prepare a 20 &#181;L/mL solution of laminin in L15 medium and add 10 &#181;L laminin to the center of each well. 
	NOTE: Do not coat the surrounding reference and grounding electrodes.</li>
	<li>Add sterile dH2O to the surrounding reservoirs to prevent medium or laminin evaporation. Incubate the plate for 1 h at 37 &#176;C.</li>
	<li>Add SFEBs (see sections 1 and 2) to the laminin coated MEA plates by gently suctioning them into a wide mouth pipette tip and transfer them. Add 200 &#181;L DM2 medium to each well and incubate overnight at 37 &#176;C, 95% humidity and 5% CO2.</li>
	<li>Add an additional 200 &#181;L medium after 24 h and allow it to recover for 30 min at 37 &#176;C, 95% humidity, 5% CO2 before reading the plate.</li>
	<li>Place the MEA plate in the plate reader (preheated to 37 &#176;C) to record neuronal activity. Record activity for 10 min with the associated MEA recording software. See reference19 for details.</li>
	<li>Generate raw data-continuous streams and raster plots of neuronal activity using statistical analysis software19. 
	NOTE: MEA recordings are taken 7 days post SFEB plating. For this study, recordings were taken for 10 min to detect network burst activity, continuous trace, and raster plots. SFEBs can be maintained long-term on MEA plates and can be recorded over longer periods of time using environmentally controlled conditions (Figure 6).</li>
</ol>

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The authors have no competing financial interests.

The protocol described here provides the conditions for differentiating a hiPSC source into a 3-D structure that recapitulates an early developmental stage of the frontal cortex. This procedure yields structures that can be interrogated for electrophysiology while also being amenable to microscopy. The final morphology of the SFEB resembles that of organotypic brain slice cultures and allows high quality detailed confocal imaging. This protocol can successfully generate SFEBs from both fibroblast and peripheral-blood mon...

We have previously reported a 3-D model system, generated from patient-derived human induced pluripotent stem cells (hiPSCs) that recapitulates some aspects of early cortical network development1. This 3-D model, a serum-free embryoid body (SFEB), improves on previous simple aggregation hiPSC models2,3. A growing body of work is revealing that 3-D structures like our SFEBs, approximate aspects of neural development commonly observed in vivo and at an earlier time point than observed in 2-dimensional (2-D)/monolayer hiPSC models4,5. Initial studies have been focused on the self-organizing complexity of 3-D bodies without demonstrating their physiological complexity2.
The protocol described here has been used on undifferentiated hiPSCs derived from fibroblasts and peripheral blood mononuclear cells (PBMCs). These cells are maintained on &#947;-irradiated mouse embryonic feeders (MEFs). These hiPSC colonies are manually cleaned of spontaneously differentiated cells, enzymatically harvested, and resuspended in medium containing Rho-Kinase inhibitor Y-27632 (ROCKi). Undifferentiated hiPSCs are subjected to dissociation and centrifugation before being transferred to 96-well low adhesion V-bottom plates. After plating, neural induction is initiated using dual SMAD inhibition (SB431542 and LDN193189 along with dickkopf 1 (DKK-1)) to drive an anterior-frontal forebrain neuronal-fate lineage6. After 14 days, the SFEBs are transferred to cell culture inserts in a 6-well plate. Once transferred, the round SFEBs begin to spread and thin, while maintaining local network connections as is often observed in hippocampal organotypic slice culture preparations using similar cell culture inserts1,7.
The use of an SFEB based 3-D platform in this format is amenable to the efficient production of cortical networks that may be interrogated using cell based physiological assays such as calcium imaging or electrophysiological assays such as single cell recordings or multi-electrode array (MEA)1. Although 3-D systems bear the markers of early cortical development, other studies have shown that these 3-D bodies may require longer incubation times to allow for the inherently slower pace of human tissue development8. This SFEB protocol successfully generates 3-D SFEBs from undifferentiated hiPSCs that captures aspects of the early development of the cortex.
The potential of SFEBs to model network aberrations in neurological disorders is a strength of this system. The hiPSCs derived from patient tissue can be grown into cells of the nervous system that are subject to assays relating to cell biology as well as concomitant gene expression. Human iPSCs are being used to ascertain the genetic profile of large groups of individuals with varying neurological disorders with complex etiologies such as autism spectrum disorder (ASD), schizophrenia9, Rett Syndrome10, and Alzheimer&#39;s disease11,12. Until recently, iPSC models were typically monolayer preparations that, while proficient in evaluating molecular interactions, were inadequate in deciphering the complex cellular interactions seen in vivo. Animal models have been the default substitute for recreating the whole-organ platform. These animal models are plagued by poor translation of findings and have limited ability to replicate human genetic profiles identified by large genetic screening studies. Thus, the development of 3-D systems from iPSCs adds a needed layer of complexity in human disease modeling13,14. The next step for 3D hiPSC platforms is to accommodate the large scale requirements of high throughput screening using cell based assays15.

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			<td height="22" style="height:22px;width:573px;">SFEB Neuronal Differentiation Cell culture Media. Reagents. Components&#160;</td>
			<td style="width:183px;"></td>
			<td style="width:164px;"></td>
			<td style="width:253px;"></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">STEMdiff Neural Induction Medium (hiPSC Media)</td>
			<td>STEMCELL Technologies</td>
			<td>0-5835</td>
			<td>250ml</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">PluriQ ES-DMEM Medium (MEF Media)</td>
			<td>GlobalStem</td>
			<td>GSM-2001</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Name</td>
			<td>Company&#160;</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">DM1 Media Components</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">D-MEM/F-12 (1X), Glutamax liquid, 1:1</td>
			<td>Invitrogen</td>
			<td align="right">10565018</td>
			<td>385ml</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Knockout Serum Replacement</td>
			<td>Invitrogen</td>
			<td align="right">10828028</td>
			<td>20% 100ml</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Pen/Strep</td>
			<td>Invitrogen</td>
			<td align="right">15140122</td>
			<td>5ml</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Glutamax 200mM</td>
			<td>Invitrogen</td>
			<td align="right">35050061</td>
			<td>5ml</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">MEM Non-Essential Amino Acids Solution 10 mM (100X), liquid</td>
			<td>Invitrogen</td>
			<td align="right">11140050</td>
			<td>5ml</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">2-Mercaptoethanol (1,000X), liquid</td>
			<td>Invitrogen</td>
			<td align="right">21985023</td>
			<td>900ul</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Name</td>
			<td>Company&#160;</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">DM2 Media Components</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">D-MEM/F-12 (1X), Glutamax liquid, 1:1</td>
			<td>Invitrogen</td>
			<td align="right">10565018</td>
			<td>500ml</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Glutamax 200mM</td>
			<td>Invitrogen</td>
			<td align="right">35050061</td>
			<td>5ml</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Pen/Strep</td>
			<td>Invitrogen</td>
			<td align="right">15140122</td>
			<td>5ml</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">N-2 Supplement (100X), liquid</td>
			<td>Invitrogen</td>
			<td align="right">17502048</td>
			<td>10ml</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Name</td>
			<td>Company&#160;</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">DM3 Media Components</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">NEUROBASAL Medium (1X), liquid</td>
			<td>Invitrogen</td>
			<td align="right">21103049</td>
			<td>500ml</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">B-27 Supplement Minus Vitamin A (50X), liquid</td>
			<td>Invitrogen</td>
			<td align="right">12587010</td>
			<td>10ml</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Glutamax 200mM</td>
			<td>Invitrogen</td>
			<td align="right">35050061</td>
			<td>5ml</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Pen/Strep</td>
			<td>Invitrogen</td>
			<td align="right">15140122</td>
			<td>5ml</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Name</td>
			<td>Company&#160;</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Small Molecules</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Thiazovivin</td>
			<td>Stemgent</td>
			<td>04-0017</td>
			<td>2uM</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">SB431542</td>
			<td>Stemgent</td>
			<td>04-0010-10</td>
			<td>1:1000 (10uM)</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Dorsomorphin</td>
			<td>Stemgent</td>
			<td>04-0024</td>
			<td>1uM</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">LDN-193189</td>
			<td>Stemgent</td>
			<td>04-0074-10</td>
			<td>250nM</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Y27632 (ROCKi)</td>
			<td>Stemgent</td>
			<td>04-0012-10</td>
			<td>10uM</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Name</td>
			<td>Company&#160;</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Recombinant Protiens</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">DKK-1</td>
			<td>Peprotech</td>
			<td>120-30</td>
			<td>200ng/ml</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Name</td>
			<td>Company&#160;</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Components/Materials</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Cell Culture inserts 0.4uM, 30mm Diameter</td>
			<td>Millicell</td>
			<td>PICM0RG50</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Mouse Embryonic Fibroblasts</td>
			<td>GlobalStem</td>
			<td>GSC-6301G</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">96 well V bottom w/Lids</td>
			<td>Evergreen</td>
			<td>222-8031-01V</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">StemPro Accutase Cell Dissociation Reagent</td>
			<td>ThermoFisher</td>
			<td>A1110501</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">TritonX-100</td>
			<td>ThermoFisher</td>
			<td align="right">85111</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Phosphate Buffered Saline (PBS)</td>
			<td>ThermoFisher</td>
			<td align="right">10010023</td>
			<td>500 mL</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Normal Donkey Serum</td>
			<td>Jackson Labs</td>
			<td>017-000-121</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Leibovitz&#39;s L-15 Medium</td>
			<td>ThermoFisher</td>
			<td align="right">11415114</td>
			<td>500 mL</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">DRAQ5 (Nuclear Marker)&#160;</td>
			<td>ThermoFisher</td>
			<td>65-0880-96</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">MEA Plates</td>
			<td>Axion Biosystems</td>
			<td>M768-GL1-30Pt200</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">6 well flat bottom</td>
			<td>Falcon</td>
			<td align="right">353046</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Name</td>
			<td>Company&#160;</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Antibody</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Nestin</td>
			<td>Millipore</td>
			<td>MAB5326</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Brn-2</td>
			<td>Protein tech</td>
			<td>14596-1-AP</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">VGLUT1&#160;</td>
			<td>Synaptic Systems&#160;</td>
			<td>135 303</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Pax6</td>
			<td>abcam</td>
			<td>ab5790</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Calretinin&#160;</td>
			<td>abcam</td>
			<td>ab702</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Calbindin</td>
			<td>abcam</td>
			<td>ab11426</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">CoupTFII</td>
			<td>R&#38;D Systems</td>
			<td>PPH714700</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Nkx 2.1</td>
			<td>abcam</td>
			<td>ab12650</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Tuj1</td>
			<td>abcam</td>
			<td>ab41489</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Reelin</td>
			<td>Millipore</td>
			<td>MAB5364</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Tbr1</td>
			<td>Millipore</td>
			<td>MAB2261</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">NFH</td>
			<td>Dako</td>
			<td>M0762</td>
			<td></td>
		</tr>
	</tbody>
</table>

developing hipsc derived serum free embryoid bodies for the interrogation of 3-d stem cell cultures using physiologically relevant assays

Although a number of in vitro disease models have been developed using hiPSCs, one limitation is that these two-dimensional (2-D) systems may not represent the underlying cytoarchitectural and functional complexity of the affected individuals carrying suspected disease variants. Conventional 2-D models remain incomplete representations of in vivo-like structures and do not adequately capture the complexity of the brain. Thus, there is an emerging need for more 3-D hiPSC-based models that can better recapitulate the cellular interactions and functions seen in an in vivo system.
Here we report a protocol to develop a 3-D system from undifferentiated hiPSCs based on the serum free embryoid body (SFEB). This 3-D model mirrors aspects of a developing ventralized neocortex and allows for studies into functions integral to living neural cells and intact tissue such as migration, connectivity, communication, and maturation. Specifically, we demonstrate that the SFEBs using our protocol can be interrogated using physiologically relevant and high-content cell based assays such as calcium imaging, and multi-electrode array (MEA) recordings without cryosectioning. In the case of MEA recordings, we demonstrate that SFEBs increase both spike activity and network-level bursting activity during long-term culturing. This SFEB protocol provides a robust and scalable system for the study of developing network formation in a 3-D model that captures aspects of early cortical development.

SFEBs grown using our technique yielded tissue with morphological characteristics that resemble an early developing cortical subventricular zone replete with extensive Tuj1-positive neurons, as well as neural progenitors (Figure 3A). Numerous developing cortical rosettes were observed in the outer layers and inner layers of the SFEB (Figure 3B). The outer edge of the SFEB resembles a developing cortical plate containing postmitot...

Watch this Scientific Journal Video about Developing HiPSC Derived Serum Free Embryoid Bodies for the Interrogation of 3-D Stem Cell Cultures Using Physiologically Relevant Assays at JoVE.com

Developing HiPSC Derived Serum Free Embryoid Bodies for the Interrogation of 3-D Stem Cell Cultures Using Physiologically Relevant Assays

Here we report a protocol to develop a three-dimensional (3-D) system from human induced-pluripotent stem cells (hiPSCs) called the serum free embryoid body (SFEB). This 3-D model can be used like an organotypic slice culture to model human cortical development and for the physiological interrogation of developing neural circuits.

Although a number of in vitro disease models have been developed using hiPSCs, one limitation is that these two-dimensional (2-D) systems may not ...

developing-hipsc-derived-serum-free-embryoid-bodies-for-interrogation

Research

JoVE Journal

Neuroscience

8.8K Views.  The Hussman Institute for Autism. Here we report a protocol to develop a three-dimensional (3-D) system from human induced-pluripotent stem cells (hiPSCs) called the serum free embryoid body (SFEB). This 3-D model can be used like an organotypic slice culture to model human cortical development and for the physiological interrogation of developing neural circuits.

Video: Developing HiPSC Derived Serum Free Embryoid Bodies for the Interrogation of 3-D Stem Cell Cultures Using Physiologically Relevant Assays

Scalable Fluidic Injector Arrays for Viral Targeting of Intact 3-D Brain Circuits

Our understanding of neural circuits--how they mediate the computations that subserve sensation, thought, emotion, and action, and how they are corrupted in neurological and psychiatric disorders--would be greatly facilitated by a technology for rapidly targeting genes to complex 3-dimensional neural circuits, enabling fast creation of "circuit-level transgenics." We have recently developed methods in which viruses encoding for light-sensitive proteins can sensitize specific cell types to millisecond-timescale activation and silencing in the intact brain. We here present the design and implementation of an injector array capable of delivering viruses (or other fluids) to dozens of defined points within the 3-dimensional structure of the brain (Figure. 1A, 1B). The injector array comprises one or more displacement pumps that each drive a set of syringes, each of which feeds into a polyimide/fused-silica capillary via a high-pressure-tolerant connector. The capillaries are sized, and then inserted into, desired locations specified by custom-milling a stereotactic positioning board, thus allowing viruses or other reagents to be delivered to the desired set of brain regions. To use the device, the surgeon first fills the fluidic subsystem entirely with oil, backfills the capillaries with the virus, inserts the device into the brain, and infuses reagents slowly (&lt;0.1 microliters/min). The parallel nature of the injector array facilitates rapid, accurate, and robust labeling of entire neural circuits with viral payloads such as optical sensitizers to enable light-activation and silencing of defined brain circuits. Along with other technologies, such as optical fiber arrays for light delivery to desired sets of brain regions, we hope to create a toolbox that enables the systematic probing of causal neural functions in the intact brain. This technology may not only open up such systematic approaches to circuit-focused neuroscience in mammals, and facilitate labeling of brain regions in large animals such as non-human primates, but may also open up a clinical translational path for cell-specific optical control prosthetics, whose precision may enable improved treatment of intractable brain disorders. Finally, such devices as described here may facilitate precisely-timed fluidic delivery of other payloads, such as stem cells and pharmacological agents, to 3-dimensional structures, in an easily user-customizable fashion.

Controlling and analyzing neural circuits in vivo would be facilitated by a technology for delivery of viruses and other reagents to desired 3-dimensional sets of brain regions. We demonstrate customized fluidic injector array fabrication, and delivery of virally-encoded optical sensitizers, enabling optical manipulation of complex brain circuits.

Our understanding of neural circuits--how they mediate the computations that subserve sensation, thought, emotion, and action, and how they are corrupted ...

The Neuroblast Assay: An Assay for the Generation and Enrichment of Neuronal Progenitor Cells from Differentiating Neural Stem Cell Progeny Using Flow Cytometry

Neural stem cells (NSCs) can be isolated and expanded in large-scale, using the neurosphere assay and differentiated into the three major cell types of the central nervous system (CNS); namely, astrocytes, oligodendrocytes and neurons. These characteristics make neural stem and progenitor cells an invaluable renewable source of cells for in vitro studies such as drug screening, neurotoxicology and electrophysiology and also for cell replacement therapy in many neurological diseases. In practice, however, heterogeneity of NSC progeny, low production of neurons and oligodendrocytes, and predominance of astrocytes following differentiation limit their clinical applications. Here, we describe a novel methodology for the generation and subsequent purification of immature neurons from murine NSC progeny using fluorescence activated cell sorting (FACS) technology. Using this methodology, a highly enriched neuronal progenitor cell population can be achieved without any noticeable astrocyte and bona fide NSC contamination. The procedure includes differentiation of NSC progeny isolated and expanded from E14 mouse ganglionic eminences using the neurosphere assay, followed by isolation and enrichment of immature neuronal cells based on their physical (size and internal complexity) and fluorescent properties using flow cytometry technology. Overall, it takes 5-7 days to generate neurospheres and 6-8 days to differentiate NSC progeny and isolate highly purified immature neuronal cells.

This video protocol demonstrates a novel method for the generation and subsequent purification of neuronal progenitor cells from a renewable source of neural stem cells (NSCs) based on their physical (size and internal granularity) and fluorescent properties using flow cytometry technology.

Neural stem cells (NSCs) can be isolated and expanded in large-scale, using the neurosphere assay and differentiated into the three major cell types of ...

High-resolution Live Imaging of Cell Behavior in the Developing Neuroepithelium

The embryonic spinal cord consists of cycling neural progenitor cells that give rise to a large percentage of the neuronal and glial cells of the central nervous system (CNS). Although much is known about the molecular mechanisms that pattern the spinal cord and elicit neuronal differentiation1, 2, we lack a deep understanding of these early events at the level of cell behavior. It is thus critical to study the behavior of neural progenitors in real time as they undergo neurogenesis.
In the past, real-time imaging of early embryonic tissue has been limited by cell/tissue viability in culture as well as the phototoxic effects of fluorescent imaging. Here we present a novel assay for imaging such tissue for long periods of time, utilizing a novel ex vivo slice culture protocol and wide-field fluorescence microscopy (Fig. 1). This approach achieves long-term time-lapse monitoring of chick embryonic spinal cord progenitor cells with high spatial and temporal resolution.
This assay may be modified to image a range of embryonic tissues3, 4 In addition to the observation of cellular and sub-cellular behaviors, the development of novel and highly sensitive reporters for gene activity (for example, Notch signaling5) makes this assay a powerful tool with which to understand how signaling regulates cell behavior during embryonic development.

Imaging embryonic tissue in real-time is challenging over long periods of time. Here we present an assay for monitoring cellular and sub-cellular changes in chick spinal cord for long periods with high spatial and temporal resolution. This technique can be adapted for other regions of the nervous system and developing embryo.

The embryonic spinal cord consists of cycling neural progenitor cells that give rise to a large percentage of the neuronal and glial cells of the central ...

Live Imaging of Mitosis in the Developing Mouse Embryonic Cortex

Although of short duration, mitosis is a complex and dynamic multi-step process fundamental for development of organs including the brain. In the developing cerebral cortex, abnormal mitosis of neural progenitors can cause defects in brain size and function. Hence, there is a critical need for tools to understand the mechanisms of neural progenitor mitosis. Cortical development in rodents is an outstanding model for studying this process. Neural progenitor mitosis is commonly examined in fixed brain sections. This protocol will describe in detail an approach for live imaging of mitosis in ex vivo embryonic brain slices. We will describe the critical steps for this procedure, which include: brain extraction, brain embedding, vibratome sectioning of brain slices, staining and culturing of slices, and time-lapse imaging. We will then demonstrate and describe in detail how to perform post-acquisition analysis of mitosis. We include representative results from this assay using the vital dye Syto11, transgenic mice (histone H2B-EGFP and centrin-EGFP), and in utero electroporation (mCherry-&#945;-tubulin). We will discuss how this procedure can be best optimized and how it can be modified for study of genetic regulation of mitosis. Live imaging of mitosis in brain slices is a flexible approach to assess the impact of age, anatomy, and genetic perturbation in a controlled environment, and to generate a large amount of data with high temporal and spatial resolution. Hence this protocol will complement existing tools for analysis of neural progenitor mitosis.

Neural progenitor mitosis is a critical parameter of neurogenesis. Much of our understanding of neural progenitor mitosis is based on analysis of fixed tissue. Live imaging in embryonic brain slices is a versatile technique to assess mitosis with high temporal and spatial resolution in a controlled environment.

Although of short duration, mitosis is a complex and dynamic multi-step process fundamental for development of organs including the brain. In the ...

Feeder-free Derivation of Neural Crest Progenitor Cells from Human Pluripotent Stem Cells

Human pluripotent stem cells (hPSCs) have great potential for studying human embryonic development, for modeling human diseases in the dish and as a source of transplantable cells for regenerative applications after disease or accidents. Neural crest (NC) cells are the precursors for a large variety of adult somatic cells, such as cells from the peripheral nervous system and glia, melanocytes and mesenchymal cells. They are a valuable source of cells to study aspects of human embryonic development, including cell fate specification and migration. Further differentiation of NC progenitor cells into terminally differentiated cell types offers the possibility to model human diseases in vitro, investigate disease mechanisms and generate cells for regenerative medicine. This article presents the adaptation of a currently available in vitro differentiation protocol for the derivation of NC cells from hPSCs. This new protocol requires 18 days of differentiation, is feeder-free, easily scalable and highly reproducible among human embryonic stem cell (hESC) lines as well as human induced pluripotent stem cell (hiPSC) lines. Both old and new protocols yield NC cells of equal identity.

Neural crest (NC) cells derived from human pluripotent stem cells (hPSC) have great potential for modeling human development and disease and for cell replacement therapies. Here, a feeder-free adaptation of the currently widely used in vitro differentiation protocol for the derivation of NC cells from hPSCs is presented.

Human pluripotent stem cells (hPSCs) have great potential for studying human embryonic development, for modeling human diseases in the dish and as a ...

Functional Evaluation of Biological Neurotoxins in Networked Cultures of Stem Cell-derived Central Nervous System Neurons

Therapeutic and mechanistic studies of the presynaptically targeted clostridial neurotoxins (CNTs) have been limited by the need for a scalable, cell-based model that produces functioning synapses and undergoes physiological responses to intoxication. Here we describe a simple and robust method to efficiently differentiate murine embryonic stem cells (ESCs) into defined lineages of synaptically active, networked neurons. Following an 8 day differentiation protocol, mouse embryonic stem cell-derived neurons (ESNs) rapidly express and compartmentalize neurotypic proteins, form neuronal morphologies and develop intrinsic electrical responses. By 18 days after differentiation (DIV 18), ESNs exhibit active glutamatergic and &#947;-aminobutyric acid (GABA)ergic synapses and emergent network behaviors characterized by an excitatory:inhibitory balance. To determine whether intoxication with CNTs functionally antagonizes synaptic neurotransmission, thereby replicating the in vivo pathophysiology that is responsible for clinical manifestations of botulism or tetanus, whole-cell patch clamp electrophysiology was used to quantify spontaneous miniature excitatory post-synaptic currents (mEPSCs) in ESNs exposed to tetanus neurotoxin (TeNT) or botulinum neurotoxin (BoNT) serotypes /A-/G. In all cases, ESNs exhibited near-complete loss of synaptic activity within 20 hr. Intoxicated neurons remained viable, as demonstrated by unchanged resting membrane potentials and intrinsic electrical responses. To further characterize the sensitivity of this approach, dose-dependent effects of intoxication on synaptic activity were measured 20 hr after addition of BoNT/A. Intoxication with 0.005 pM BoNT/A resulted in a significant decrement in mEPSCs, with a median inhibitory concentration (IC50) of 0.013 pM. Comparisons of median doses indicate that functional measurements of synaptic inhibition are faster, more specific and more sensitive than SNARE cleavage assays or the mouse lethality assay. These data validate the use of synaptically coupled, stem cell-derived neurons for the highly specific and sensitive detection of CNTs.

A custom protocol is described to differentiate mouse ES cells into defined populations of highly pure neurons exhibiting functioning synapses and emergent network behavior. Electrophysiological analysis demonstrates the loss of synaptic transmission following exposure to botulinum neurotoxin serotypes /A-/G and tetanus neurotoxin.

Therapeutic and mechanistic studies of the presynaptically targeted clostridial neurotoxins (CNTs) have been limited by the need for a scalable, ...

Enumeration of Neural Stem Cells Using Clonal Assays

Neural stem cells (NSCs) have the ability to self-renew and generate the three major neural lineages &#8212; astrocytes, neurons and oligodendrocytes. NSCs and neural progenitors (NPs) are commonly cultured in vitro as neurospheres. This protocol describes in detail how to determine the NSC frequency in a given cell population under clonal conditions. The protocol begins with the seeding of the cells at a density that allows for the generation of clonal neurospheres. The neurospheres are then transferred to chambered coverslips and differentiated under clonal conditions in conditioned medium, which maximizes the differentiation potential of the neurospheres. Finally, the NSC frequency is calculated based on neurosphere formation and multipotency capabilities. Utilities of this protocol include the evaluation of candidate NSC markers, purification of NSCs, and the ability to distinguish NSCs from NPs. This method takes 13 days to perform, which is much shorter than current methods to enumerate NSC frequency.

Neural stem cells (NSCs) refer to cells&#160;which can self-renew and differentiate into the three neural lineages. Here, we describe a protocol to determine NSC frequency in a given cell population using neurosphere formation and differentiation under clonal conditions.

Neural stem cells (NSCs) have the ability to self-renew and generate the three major neural lineages &#8212; astrocytes, neurons and oligodendrocytes. ...

Modelling Zika Virus Infection of the Developing Human Brain In Vitro Using Stem Cell Derived Cerebral Organoids

The recent emergence of Zika virus (ZIKV) in susceptible populations has led to an abrupt increase in microcephaly and other neurodevelopmental conditions in newborn infants. While mosquitos are the main route of viral transmission, it has also been shown to spread via sexual contact and vertical mother-to-fetus transmission. In this latter case of transmission, due to the unique viral tropism of ZIKV, the virus is believed to predominantly target the neural progenitor cells (NPCs) of the developing brain.
Here a method for modeling ZIKV infection, and the resulting microcephaly, that occur when human cerebral organoids are exposed to live ZIKV is described. The organoids display high levels of virus within their neural progenitor population, and exhibit severe cell death and microcephaly over time. This three-dimensional cerebral organoid model allows researchers to conduct species-matched experiments to observe and potentially intervene with ZIKV infection of the developing human brain. The model provides improved relevance over standard two-dimensional methods, and contains human-specific cellular architecture and protein expression that are not possible in animal models.

Modelling Zika Virus Infection of the Developing Human Brain In Vitro Using Stem Cell Derived Cerebral Organoids

This protocol describes a technique used to model Zika virus infection of the developing human brain. Using wildtype or engineered stem cell lines, researchers may use this technique to uncover the various mechanisms or treatments that may affect early brain infection and resulting microcephaly in Zika virus-infected embryos.

The recent emergence of Zika virus (ZIKV) in susceptible populations has led to an abrupt increase in microcephaly and other neurodevelopmental conditions ...

Generation of 3-D Collagen-based Hydrogels to Analyze Axonal Growth and Behavior During Nervous System Development

This protocol uses natural type I collagen to generate three-dimensional (3-D) hydrogel for monitoring and analyzing the axonal growth. The protocol is centered on culturing small pieces of embryonic or early postnatal rodent brains inside a 3-D hydrogel formed by the rat tail tendon-derived type I collagen with specific porosity. Tissue pieces are cultured inside the hydrogel and confronted to specific brain fragments or genetically-modified cell aggregates to produce and secrete molecules suitable for creating a gradient inside the porous matrix. The steps of this protocol are simple and reproducible but include critical steps to be considered carefully during its development. Moreover, the behavior of growing axons can be monitored and analyzed directly using a phase-contrast microscope or mono/multiphoton fluorescence microscope after fixation by immunocytochemical methods.

Here, we provide a method for analyzing the behavior of growing axons in 3D matrices, mimicking their natural development.

This protocol uses natural type I collagen to generate three-dimensional (3-D) hydrogel for monitoring and analyzing the axonal growth. The protocol is ...

Migration, Chemo-Attraction, and Co-Culture Assays for Human Stem Cell-Derived Endothelial Cells and GABAergic Neurons

Role of brain vasculature in nervous system development and etiology of brain disorders is increasingly gaining attention. Our recent studies have identified a special population of vascular cells, the periventricular endothelial cells, that play a critical role in the migration and distribution of forebrain GABAergic interneurons during embryonic development. This, coupled with their cell-autonomous functions, alludes to novel roles of periventricular endothelial cells in the pathology of neuropsychiatric disorders like schizophrenia, epilepsy, and autism. Here, we have described three different in vitro assays that collectively evaluate the functions of periventricular endothelial cells and their interaction with GABAergic interneurons. Use of these assays, particularly in a human context, will allow us to identify the link between periventricular endothelial cells and brain disorders. These assays are simple, low cost, and reproducible, and can be easily adapted to any adherent cell type.

We present three simple in vitro assays-the long-distance migration assay, the co-culture migration assay, and chemo-attraction assay-that collectively evaluate the functions of human stem cell derived periventricular endothelial cells and their interaction with GABAergic interneurons.

Developing HiPSC Derived Serum Free Embryoid Bodies for the Interrogation of 3-D Stem Cell Cultures Using Physiologically Relevant Assays

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Functional Evaluation of Biological Neurotoxins in Networked Cultures of Stem Cell-derived Central Nervous System Neurons

Enumeration of Neural Stem Cells Using Clonal Assays

Modelling Zika Virus Infection of the Developing Human Brain In Vitro Using Stem Cell Derived Cerebral Organoids

Generation of 3-D Collagen-based Hydrogels to Analyze Axonal Growth and Behavior During Nervous System Development

Migration, Chemo-Attraction, and Co-Culture Assays for Human Stem Cell-Derived Endothelial Cells and GABAergic Neurons