This work was supported by a Pilot and Feasibility Grants from the Indiana University School of Medicine Center (IUSM) for Excellence in Molecular Hematology (NIDDK, 5P30DK090948). Additional funding was provided by a Biomedical Enhancement Grant from IUSM. We would like to thank Dr. Karen Cowden Dahl for commenting on the manuscript.

1. Embryoid Body (EB) Formation
<ol>
	<li>Gelatin-adapt ESCs that have been maintained on mouse embryo fibroblasts (MEFs). Passage ESCs 3 times on 6 well tissue culture plate coated with 0.1% gelatin to remove MEFs.
	<ol>
		<li>Grow cells in ESC maintenance media with LIF to keep the cells undifferentiated (Table 1). Make sure cells never exceed 80% confluence. Use low passage (10 or less passages after removing from MEFs) cells for differentiation.</li>
	</ol>
	</li>
	<li>On the day before ESCs are cultured for EB differentiation, passage the cells so they will be approximately 50-70% confluent the next day. Continue culturing cells in ESC maintenance medium to retain cell pluripotency.</li>
	<li>On the day of the differentiation, aspirate ESC maintenance media and wash with 1 ml Phosphate Buffered Saline (PBS: 137 mM NaCl, 2.7 mM KCl, and 11.9 mM phosphate buffer, pH 7.4) per well of a 6-well plate.
	<ol>
		<li>Add 200 &#181;l of 0.25% trypsin/EDTA to each well and incubate at 37 &#176;C for 3 min.</li>
		<li>Inactivate the trypsin/EDTA with 800 &#181;l of differentiation media. Pipet up and down in a 2 ml serological pipet with a p200 tip to break-up the cells into a single cell suspension. Ensure that the p200 tip fits snugly on the end so media does not go up between the pipet and tip interface.</li>
		<li>Pipet up and down approximately 5-10 times. Take care not to create bubbles during the pipetting.</li>
	</ol>
	</li>
	<li>Transfer cells to a 15 ml conical tube. Bring up the volume to 10 ml with PBS. Centrifuge at 315 x g for 5 min at room temperature.</li>
	<li>Remove supernatant. Wash twice with 5 ml PBS to remove remaining media containing LIF. Centrifuge as in step 1.4 for each wash.
	<ol>
		<li>Resuspend the final cell pellet in 2 ml of differentiation media (Table 2).</li>
	</ol>
	</li>
	<li>Count cells with a hemocytometer or cell counter and plate 6,000-10,000 cells/ml in a 10 cm Petri plate (non-tissue culture treated).
	<ol>
		<li>Determine the exact cells/ml empirically for each ESC line. Use sterile Petri plates normally used for bacterial work or low adherence plates. 
		NOTE: For best differentiation results, the EBs should form spheres that remain in suspension without attaching to the plate. Test several brands of plates to find ones with the least adherence.</li>
		<li>Incubate the differentiating ESCs in a 37 &#176;C tissue culture incubator with 5% CO2.</li>
	</ol>
	</li>
</ol>
<table border="0" cellpadding="0" cellspacing="0">
	<colgroup>
		<col />
		<col span="2" />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr>
			<td>Reagent</td>
			<td>Stock</td>
			<td>Final Concentration</td>
			<td>Volume</td>
			<td>Company</td>
			<td>Catalog Number</td>
		</tr>
		<tr>
			<td>DMEM</td>
			<td>1x</td>
			<td></td>
			<td>410 ml</td>
			<td>Sigma/Aldrich</td>
			<td>D5796</td>
		</tr>
		<tr>
			<td>FBS (ES Screened)</td>
			<td>100%</td>
			<td>15%</td>
			<td>75 ml</td>
			<td>Hyclone</td>
			<td>SH30070.03E</td>
		</tr>
		<tr>
			<td>Non-essential Amino Acids</td>
			<td>100x</td>
			<td>1x</td>
			<td>5 ml</td>
			<td>Life Technologies</td>
			<td>11140</td>
		</tr>
		<tr>
			<td>L-Glutamine</td>
			<td>100x</td>
			<td>1x</td>
			<td>5 ml</td>
			<td>Life Technologies</td>
			<td>35050</td>
		</tr>
		<tr>
			<td>Penncillin/Streptomycin</td>
			<td>100x</td>
			<td>1x</td>
			<td>5 ml</td>
			<td>Life Technologies</td>
			<td>15070</td>
		</tr>
		<tr>
			<td>&#946;-mercaptoethanol</td>
			<td>14.3 M</td>
			<td>114 &#181;M</td>
			<td>4 &#181;l</td>
			<td>Sigma/Aldrich</td>
			<td>M3148</td>
		</tr>
		<tr>
			<td>Leukemia Inhibitory Factor (LIF)</td>
			<td>107 units/ml</td>
			<td>1,000 units/ml</td>
			<td>50 &#181;l</td>
			<td>Millipore</td>
			<td>ESG1107</td>
		</tr>
	</tbody>
</table>
Table 1: ESC Maintenance Media.
<table border="0" cellpadding="0" cellspacing="0">
	<colgroup>
		<col />
		<col span="2" />
		<col />
		<col span="2" />
	</colgroup>
	<tbody>
		<tr>
			<td>Reagent</td>
			<td>Stock</td>
			<td>Final Concentration</td>
			<td>Volume</td>
			<td>Company</td>
			<td>Catalog Number</td>
		</tr>
		<tr>
			<td>DMEM</td>
			<td>1x</td>
			<td></td>
			<td>410 ml</td>
			<td>Sigma/Aldrich</td>
			<td>D5796</td>
		</tr>
		<tr>
			<td>FBS (User Screened for optimal differentiation)</td>
			<td>100%</td>
			<td>15%</td>
			<td>75 ml</td>
			<td>Hyclone</td>
			<td>SH30070.03E</td>
		</tr>
		<tr>
			<td>Non-essential Amino Acids</td>
			<td>100x</td>
			<td>1x</td>
			<td>5 ml</td>
			<td>Life Technologies</td>
			<td>11140</td>
		</tr>
		<tr>
			<td>L-Glutamine</td>
			<td>100x</td>
			<td>1x</td>
			<td>5 ml</td>
			<td>Life Technologies</td>
			<td>35050</td>
		</tr>
		<tr>
			<td>Penncillin/Streptomycin</td>
			<td>100x</td>
			<td>1x</td>
			<td>5 ml</td>
			<td>Life Technologies</td>
			<td>15070</td>
		</tr>
		<tr>
			<td>&#946;-mercaptoethanol</td>
			<td>14.3 M</td>
			<td>114 &#181;M</td>
			<td>4 &#181;l</td>
			<td>Sigma/Aldrich</td>
			<td>M3148</td>
		</tr>
	</tbody>
</table>
Table 2: Differentiation Media.
2. Preparing EB Cells for Virus Infection
<ol>
	<li>At the desired stage of development (between day 2 and day 3), transfer the EBs from the 10 cm Petri dish to 15 ml conical tube. Wash the plate with 5 ml PBS and add the wash to the conical tube.</li>
	<li>Pellet the EBs at 315 x g at room temperature for 5 min. Wash the EB cells with 5 ml PBS.</li>
	<li>Add 1 ml of thawed cell detachment solution (Containing proteolytic and collagenolytic enzymes) and place the tubes in a 37 &#176;C water bath (or incubator) for 30 min with occasional agitation (from flicking or light vortexing).</li>
	<li>Add 1 ml of differentiation media. Pipet up and down with a 2 ml pipet with a p200 pipet tip. Place the tube in 37 &#176;C water bath again for 30-60 min.</li>
	<li>Spin down the cells at 315 x g for 5 min and wash the cells with PBS.</li>
</ol>
3. Virus Infection
<ol>
	<li>Resuspend the cells in 1.5 ml of differentiation media. Transfer the cell suspension to a 6-well non-tissue culture treated plate.</li>
	<li>Prepare the retrovirus by standard techniques ahead of time. Add 5 to 100 &#181;l of viral supernatant to cells depending on viral titer. Do not add polybrene to enhance infection as this inhibits the subsequent reformation of EBs.</li>
	<li>Spinoculate the cells with virus by centrifuging at 2,120 x g for 90 min at room temperature.</li>
</ol>
4. Differentiating Viral Infected EB Cells in Hanging Drops
<ol>
	<li>Add 2 ml of differentiation media to each well of infected EB cell suspension.</li>
	<li>Pipet 3.5 ml of infected EB cell suspension into a sterile reagent reservoir for multipipettors. Use the multipipettor to pipet 15-20 rows of eight 20 &#181;l drops onto the inverted lid of the 15 cm Petri plate.</li>
	<li>Add 10 ml of sterile PBS or water to the bottom half of the Petri plate. Then invert the lid with the drops and place onto the Petri plate. Ensure that the drops are hanging upside down from lid with PBS or water below to keep the chamber humidified.</li>
	<li>Place the dishes in the 37 &#176;C tissue culture incubator with 5.0% CO2.</li>
	<li>After 2 days, collect EBs formed in the hanging drops by inverting lid and washing with 4.5 ml of differentiation media.
	<ol>
		<li>Transfer media and EBs to a new 10 cm non-tissue culture Petri plate. Wash the lid once more with 3 ml of differentiation media and transfer to the 10 cm plate.</li>
	</ol>
	</li>
	<li>Harvest cells for analysis by flow cytometry after a total of 8 days culture starting from the initial transfer of cells to differentiation media (-LIF).</li>
</ol>
5. Preparing Cells for Flow Cytometer Analysis
<ol>
	<li>Transfer cells to a 15 ml conical tube with a 10 ml pipet. Wash the plate with 5 ml PBS and transfer to the same conical tube.</li>
	<li>Pellet cells at 315 x g. Wash pellets with 10 ml PBS.</li>
	<li>Add 1 ml of thawed cell detachment solution and place the tubes in a 37 &#176;C water bath for 30 min with occasional agitation. For detection of some cell surface antigens, trypsin may be used instead.</li>
	<li>Add 1 ml differentiation media and pipet up and down with a 2 ml pipet. Use a p200 tip to the end of the pipet to help break-up digested EB into single cell suspension.
	<ol>
		<li>Place the tube in a 37 &#176;C water bath again for 60 min in order for the integral membrane proteins to recycle to the cell surface.</li>
	</ol>
	</li>
	<li>Pellet cells at 315 x g for 5 min.</li>
	<li>Wash the cells with 0.1% Bovine Serum Albumin Fraction V (BSA) prepared in PBS (PBS/BSA) and incubate the cells with specific fluorescently tagged antibodies.</li>
</ol>
6. Flow Cytometry Analysis for Hematopoietic Progenitors
<ol>
	<li>Place 106 EB derived cells in a 5 ml 12 x 75 mm round bottom tube. For adjusting flow cytometer compensation settings, use compensation beads according to manufacturer instructions.</li>
	<li>Pellet cells at 315 x g. Pour off supernatant and resuspend pellet in residual PBS/BSA solution in the tube.</li>
	<li>For detecting ESC HPCs, incubate the cells with fluorescent labeled antibodies: anti-mouse CD41-PE (R-Phycoerytherin) and anti-mouse CD117 (cKit)-APC/CY7 (Allophycocyanin Cyanine 7).
	<ol>
		<li>Dilute antibodies 1:100 in PBS/BSA. Add 100 &#181;l of diluted antibody to each sample. Determine the correct dilution of antibody for each vendor, clone, and lot or antibody. Determine optimal dilution for labeling cells individually.</li>
	</ol>
	</li>
	<li>Incubate samples on ice in the dark for 30 min.</li>
	<li>Add 2 ml PBS/ BSA and pellet cells at 315 x g for 5 min.</li>
	<li>Aspirate supernatant and resuspend pellet in 300 &#181;l of PBS or another isotonic buffer.</li>
	<li>Filter resuspended cells through a cell strainer cap (0.35 &#181;M) to remove large cell aggregates.</li>
	<li>Analyze cells on a flow cytometer.</li>
</ol>

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The authors have no competing financial interests to disclose.

As discussed above, ESC clones that inducibly express a gene of interest can be generated using doxycycline systems, however, generation of these lines is time-consuming and labor intensive. Described in this protocol is a method to express a gene of interest in single cell suspension prepared from ESC derived EBs. These infected cells are then reformed into EBs by hanging drop to examine subsequent differentiation. In the example (Figure 3), it is shown that expression of the mirn23a cluster en...

Murine embryonic stem cells (ESCs) are pluripotent, remaining undifferentiated and self-renewing in the presence of the cytokine Leukemia Inhibitory Factor (LIF)1. Upon withdrawal of LIF they will spontaneously differentiate into 3-dimensional (3D) structures called embryoid bodies (EBs)2. The 3D architecture allows for the development of the three germ layers ectoderm, endoderm, and mesoderm, which then later give rise to mature tissue types3. ESCs are an exceptional model for elucidating the molecular mechanisms of cellular differentiation, particularly the investigation of the development of early hematopoietic progenitor cells (HPCs)4. 
Gene expression in ESCs can be manipulated by several techniques that allow for the determination of a role for individual molecules in development. One of the most common techniques is to use homologous recombination to generate ESC lines, which lack a gene of interest5,6. There are also a number of techniques that have been used to overexpress genes. The first technique used to modify gene expression in ESCs was to infect them with recombinant retroviruses7,8. The gene of interest however is often silenced as the ESCs differentiate into progenitor and mature cell types. Use of lentiviruses has been successful in limiting the silencing of virally expressed genes9. Other viral vectors used for overexpression include adenovirus and adeno-associated virus10. In addition standard transfection techniques to stably introduce expression plasmids are widely used for ESC transgene expression11. One difficulty with these systems is that often expression of a specific gene has different effects depending on its temporal expression. For example, the Smad1 protein affects the development of hematopoietic cells differently during different stages of EB development12,13. 
This problem can be circumvented by the generation of ESCs that inducibly express a gene of interest. The most common system for inducibly expressing transgenes in ESCs uses the tetracycline resistance operon from E. Coli (Escherichia coli). Several different tetracycline systems have been developed. One of the more popular strategies was developed by Kyba and colleagues14. They generated an ESC line (Ainv15), which has the reverse tetracycline transactivator gene inserted into the constitutively active ROSA26 locus. A tetracycline response element (TRE), a downstream LoxP site (locus of X-over P1 from bacteriophage P1), and a promoterless neomycin cassette were introduced into the HPRT (Hypoxanthine-guanine phosphoribosyltransferase) locus on the X chromosome. Using a CRE recombination approach a gene of interest along with a eukaryotic promoter to drive the expression of the neomycin resistance gene can be inserted into the LoxP site. Correctly targeted ESCs are isolated by G418 selection. These targeted clones then must be tested for doxycycline (or tetracycline) inducible expression of the transgene. This approach has successfully generated ESC lines that inducibly express HoxB4, Stat5, SCL, and Smad714-17. However, generation of these inducible cell lines is time consuming. Described here is a method to disaggregate ESC-derived embryoid bodies (EBs) into single cell suspensions, retrovirally infect the cell suspensions at different days of development, and then reform the EBs by hanging drop. Downstream differentiation is later evaluated by flow cytometry. In this article an example of how miRNA expression in EB-derived cells effects hematopoietic differentiation is shown. This method is useful for investigating the role of genes after specific germ layer tissue is derived.

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retroviral infection of murine embryonic stem cell derived embryoid body cells for analysis of hematopoietic differentiation

Embryonic stem cells (ESCs) are an outstanding model for elucidating the molecular mechanisms of cellular differentiation. They are especially useful for investigating the development of early hematopoietic progenitor cells (HPCs). Gene expression in ESCs can be manipulated by several techniques that allow the role for individual molecules in development to be determined. One difficulty is that expression of specific genes often has different phenotypic effects dependent on their temporal expression. This problem can be circumvented by the generation of ESCs that inducibly express a gene of interest using technology such as the doxycycline-inducible transgene system. However, generation of these inducible cell lines is costly and time consuming. Described here is a method for disaggregating ESC-derived embryoid bodies (EBs) into single cell suspensions, retrovirally infecting the cell suspensions, and then reforming the EBs by hanging drop. Downstream differentiation is then evaluated by flow cytometry. Using this protocol, it was demonstrated that exogenous expression of a microRNA gene at the beginning of ESC differentiation blocks HPC generation. However, when expressed in EB derived cells after nascent mesoderm is produced, the microRNA gene enhances hematopoietic differentiation. This method is useful for investigating the role of genes after specific germ layer tissue is derived.

In these studies gelatinized RW4 (Derived from 129X1/SvJ mouse strain) ESCs were used. EBs were isolated at 3 days of differentiation. For best results the EBs should be spherical and non-adherent (Figure 1A, B). After spinoculation with virus co-expressing the fluorescent marker GFP along with a gene of interest, EBs were reformed by the hanging drop method. EBs were successfully reformed from cell suspensions prepared from 2.0, 2.5, and 3.0 day EBs. However, EBs could not be reformed from cell suspensi...

Watch this Scientific Journal Video about Retroviral Infection of Murine Embryonic Stem Cell Derived Embryoid Body Cells for Analysis of Hematopoietic Differentiation at JoVE.com

Retroviral Infection of Murine Embryonic Stem Cell Derived Embryoid Body Cells for Analysis of Hematopoietic Differentiation

Manipulating temporal gene expression in differentiating embryonic stem cells (ESCs) can be achieved using inducible gene systems. However, generation of these cell lines is costly and time consuming. This protocol achieves rapid expression of a transgene in differentiating ES-derived cells and subsequent analysis of downstream hematopoietic differentiation.

Embryonic stem cells (ESCs) are an outstanding model for elucidating the molecular mechanisms of cellular differentiation. They are especially useful for ...

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8.4K Views.  Harper Cancer Research Institute. Manipulating temporal gene expression in differentiating embryonic stem cells (ESCs) can be achieved using inducible gene systems. However, generation of these cell lines is costly and time consuming. This protocol achieves rapid expression of a transgene in differentiating ES-derived cells and subsequent analysis of downstream hematopoietic differentiation. 