We would like to acknowledge Dr. Bradley Schulte for comments on this protocol. This work was supported by National Institutes of Health grant R00 (5R00DC010220). This project was performed in a renovated laboratory space supported by Grant C06RR014516.

NOTE: All protocols using live animals must be reviewed and approved by an Institutional Animal Care and Use Committee (IACUC) and must follow officially approved methods for the care and use of the laboratory animals. All the dissections should be performed using sterile technique on a clean laminar flow bench. Gloves and a mask, if desired, should be worn during this procedure.
1. Dissection of the Embryonic Mouse Inner Ear
<ol>
	<li>Setting up for organ of Corti explant cultures:
	<ol>
		<li>Sterilize the laminar flow tissue culture hood by turning on UV light for about 30 min and disinfect the surface with 70% ethanol prior to use. In addition, sterilize all dissection instruments including fine dissection tools and Sylgard-coated dishes for embryo dissection via autoclave or by soaking in 70% ethanol for at least 20 min before use. Pour off 70% ethanol and allow the dishes and instruments to air dry in a clean laminar flow clean bench prior to use.</li>
		<li>Prepare sterile Hank&#8217;s Balanced Salt Solution (HBSS)/(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) (HEPES) mixture by adding 10% of 10x HBSS and 0.5% HEPES and adjust the pH to approximately 7.2 and filter sterilize the final solution and store at 4 &#176;C. Carry out all dissections in chilled HBSS/HEPES solution to better preserve the tissue throughout the procedure.</li>
		<li>Coat glass bottom dishes with basement membrane matrix by adding 5 ml of cold (4 &#176;C) sterile Dulbecco&#8217;s Modified Eagle Medium (DMEM) to a 300 &#181;l aliquot of basement membrane matrix in a sterile 15 ml polypropylene tube. Mix by vortexing the contents and add 150 &#181;l of the basement membrane matrix-DMEM mixture to the center of each culture dish so that it covers the entire culture well present in the center of the dish. Cover the dishes and store in a 37 &#176;C incubator for at least 45 min before use.</li>
		<li>Pour 4-5 ml chilled HBSS into three sterile polystyrene petri dishes and leave closed in the hood.</li>
		<li>Prepare culture medium in a sterile 15 ml polypropylene tube by adding 9 ml of DMEM, 100 &#181;l of N2 supplements, 10 g/ml Cipro and 1 ml of FBS.</li>
	</ol>
	</li>
	<li>Isolation of embryos: 
	NOTE: In this procedure for culturing cochlear explants from embryonic mice, harvest inner ears from embryonic day (E) 13 temporal bones with the day after fertilization being considered as E19. The protocol can also be used with embryonic mouse inner ears beginning from E12 to E18.
	<ol>
		<li>Euthanize a timed-pregnant mouse with CO2 and sacrifice animal by cervical dislocation or appropriate approved protocols. Carry out euthanization away from laminar-flow tissue culture hood to maintain sterility in the tissue culture room.</li>
		<li>Place euthanized mouse on paper towel with abdomen facing up and disinfect abdomen with 70% ethanol.</li>
		<li>Open the abdominal cavity by grabbing skin with curved forceps with one hand and cut epidermis and muscle along the midline with scissors using another hand. Make two perpendicular cuts on both sides and pull out the uterus carefully by lifting up bilateral uterine horns with forceps and detach it from underneath connective tissue using scissors.</li>
		<li>Place the embryonic chain in a petri dish containing chilled dissection solution (HBSS/HEPES mixture) and transfer to the laminar-flow clean bench.</li>
		<li>Remove embryos carefully from placenta and place them into one of the sterile Petri dishes containing dissection solution. If the solution turns bloody, move them to a new Petri dish. 
		NOTE: At this point, embryos can be staged using a Theiler staging guide.</li>
		<li>Decapitate embryos by pinching at the neck region with a pair of clean forceps or scissors and place the heads in a fresh Petri dish containing chilled dissection solution.</li>
	</ol>
	</li>
	<li>Dissection of the inner ears:
	<ol>
		<li>Place one embryo head in a sterile sylgard dish containing cold dissecting</li>
		<li>solution. Working under a dissecting microscope at a magnification of ~1.6X, immobilize the embryo head by placing Minutien pins around or closer to eye region (Figure 1A).</li>
		<li>Using two pairs of sterile forceps carefully remove the skin and open up the skull on the dorsal side along the midline (Figure 1B). Remove brain from cranial cavity and inner ears located within temporal bones can be identified at this stage (Figure 1C, D). The lining of the blood vessel, which is usually present around the inner ears, can be used as a landmark for identifying the inner ear at this stage (Figure 1D).</li>
		<li>Dissect the inner ear from the temporal bones by placing the forceps underneath the tissue and isolating the inner ear from base of the skull and transfer to a new dish containing cold dissecting solution (Figure 1E, F).</li>
	</ol>
	</li>
</ol>
2. Generation of Organ of Corti Explant Cultures
NOTE: At this stage of development, the tissue is cartilaginous and can be easily dissected using forceps.
<ol>
	<li>Orient the inner ear so that ventral side is facing up (Figure 2A) and stabilize the inner ear by gently inserting the sharp end of Minutien pins through the vestibular portion of the inner ear (Figure 2B).</li>
	<li>Using ultrafine forceps cut open the overlying cartilage by making an incision using one end of forceps near the oval window and carefully remove the cartilage from the cochlea (Figure 2C). 
	NOTE: It is important to make sure that forceps are not inserted too deeply into the cartilage as overlying cartilage is sometimes fused with the cochlear duct in which case it is helpful to use closed forceps to release cartilage from the underlying cochlear duct by scraping below the surface of the cartilage. At this stage of development, the cochlear spiral is only three quarters of a turn in length.</li>
	<li>Next, expose the sensory epithelium by placing the forceps at the preferred region of the cochlear duct, either the base or at the very apex, and gently pulling out the roof of the cochlea (Figure 2D). 
	NOTE: The roof of the cochlea must be removed completely as it can mask the sensory epithelium hindering the analysis. 
	NOTE: This procedure must be done gently as it is easy to tear the sensory epithelium.</li>
	<li>As a last step, carefully remove the underlying connective tissue from the exposed sensory epithelium so that the base of the cochlear explant is uniformly flat.</li>
	<li>Isolate the dissected cochlea from the vestibular portion of the inner ear using forceps. This can be performed before or after step 2.4 (Figure 2E).</li>
	<li>Transfer the dissected cochlear sensory epithelium into a basement membrane matrix-coated culture well using a 1.5 mm sterile scooper (Figure 2F).</li>
	<li>Orient the cochlear explant with the lumenal surface of the epithelium facing up and aspirate the basement membrane matrix-DMEM solution to carefully flatten the tissue and replace it with 150 &#181;l of fresh culture medium by gently adding to the dish. Care should be taken to make sure that each explant adheres well to the coated glass coverslip and is not floating in the culture medium. Ensure that the tip of the forceps is pointed up while affixing to the glass well to avoid damaging the cochlear explant.</li>
	<li>Gently transfer the culture dish into a sterile 150 mm culture dish and place in a tissue culture incubator at 37 &#176;C with 5% CO2 for desired period of time, usually 3-6 days in vitro (DIV). After 1 DIV, examine the cultures under a dissecting microscope to make sure that the cochlear explant has adhered well to the culture dish.</li>
	<li>After incubation in vitro for desired lengths of time, cultures are processed for immunohistochemistry. 
	NOTE: The explant cultures usually are incubated for 6 DIV which is equivalent to developmental stage, P0. After incubation in vitro, cultures can be processed for further downstream applications like immunohistochemistry (Figure 3B), RT-PCR, in situ hybridization, and/or western blot.</li>
</ol>
3. Electroporation-mediated Gene Transfer
<ol>
	<li>Setting up for electroporation:
	<ol>
		<li>Sterilize one 100 mm Sylgard-coated glass dish by autoclaving or soaking in 70% ethanol for about 20 min and allow to air dry in a clean bench prior to use.</li>
		<li>Prepare DNA from an expression vector of choice using appropriate maxi- or midi-prep kits. The expression vectors used in this protocol are pIRES2-Atoh1.EGFP and pCLIG-NeuroD1.EGFP. The final concentration of DNA should be at least 1 &#181;g/&#181;l in sterile DNA/RNAse-free water.</li>
	</ol>
	</li>
	<li>Electroporating DNA into embryonic cochlear explants:
	<ol>
		<li>Add 10 &#181;l of plasmid DNA solution to a fresh 100 mm Sylgard coated dish and transfer a fully dissected cochlear explant (obtained from step 2.5) into the DNA solution.</li>
		<li>With lumenal surface of the epithelium facing up, tilt the cochlea slightly so that it&#8217;s perpendicular to the plane of the dish.</li>
		<li>Place the electrode paddles on either side of the cochlea with negative paddle (cathode) towards the sensory epithelium and the positive paddle (anode) located adjacent to the base of the cochlea. 
		NOTE: Since DNA is negatively charged, it migrates from negative to positive electrode and by placing the cathode end of the probe adjacent to the sensory epithelium; the DNA will mostly go through the surface of the sensory epithelium.</li>
		<li>Using electroporator, deliver 9 to 10 pulses of 24 mV, 30 msec pulse duration with the foot pedal switch on the electroporator, and then add 100 &#181;l of warm culture medium to the electroporated cochlea.</li>
		<li>Repeat steps 3.2.1-4 for all the cochlear explants and for DNA of all genes of interest and transfer the electroporated cochleae into the basement membrane matrix-coated dish for plating (step 2.7). Culture all the electroporated cochleae in a 37 &#176;C, 5% CO2 humidified incubator for desired lengths of time which will then be processed for immunocytochemistry. 
		NOTE: The cochlea from an entire litter of CD1 mouse (approximately 8-12 pups) can be isolated, microdissected, electroporated and plated in &#60;4 hr.</li>
	</ol>
	</li>
</ol>
4. Analysis of Cochlear Explant Cultures
NOTE: The cultures are usually incubated for 6 DIV which is equivalent to developmental stage, P0. After incubation in vitro, the cultures are fixed and processed for immunocytochemistry.
<ol>
	<li>After desired length of incubation, remove culture medium and quickly rinse the cochlear explant in phosphate-buffered saline (PBS) and incubate in 4% paraformaldehyde (prepared in PBS) for 15 min at room temperature.</li>
	<li>Wash the fixative by adding PBS and rinse in PBS three times for 15 min.</li>
	<li>Permeabilize using PBS-T (PBS + 0.5% Tween) for 30 min before blocking with PBS-T containing 10% goat serum.</li>
	<li>Incubate in primary antibody solution containing primary antibody in PBS-T with 1% goat serum overnight at 4 &#176;C.</li>
	<li>Wash the cochlea three times at room temperature using PBS-T 15 min each before adding appropriate Alexa-conjugated secondary antibodies.</li>
	<li>Since the cochlear explant is cultured on glass coverslip it can be handled individually by isolating the coverslip from the dish and mounting on a slide. This can be achieved by soaking the culture dish in OS30 solvent for at least 1 hr at room temperature. Using the sterile razor blade, detach the coverslip from the dish and mount on a slide and visualize under a fluorescent microscope.</li>
</ol>

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No conflicts of interest declared.

All the cells within the membranous labyrinth of the mouse inner ear including sensory, nonsensory and the spiral ganglion neurons are all derived from placodally-derived otocyst located adjacent to the hindbrain of the ectoderm, around E810-14. At E11, the ventral region of the otocyst extends to form the cochlear duct and as development continues, a group of epithelial cells within the cochlea, as well as in other regions of the otocyst, become specified as prosensory patches that will subsequently give rise...

The mammalian organ of Corti is comprised of a mosaic of specialized cell types, including two types of mechanosensory hair cells as well as at least four types of nonsensory supporting cells making it an ideal model system to study normal cellular processes like proliferation, fate specification, differentiation and patterning. In addition, the normal development of these different cell types is essential for normal hearing function. Hence, it is crucial to understand the factors, both molecular and cellular, that regulate their development. However, the small size of the mouse cochlea as well as its inaccessibility poses a particular challenge for gene expression studies. Moreover, most of the cell fate specification and patterning events occur during embryonic time periods and are mostly completed before birth. Therefore, identification and characterization of signaling events during embryonic time periods is essential to gain insight into the molecular basis of cochlear morphogenesis. 
Here, we demonstrate a method to culture intact cochlea in vitro from embryonic mouse inner ears. The rationale behind the use of this technique is that cultured cochleae maintain their molecular and morphological characteristics thereby providing a valuable model for investigating potential candidate genes and exploring the mechanisms involved in cochlear morphogenesis. Although transgenic mice can be used for gene expression studies, an in vitro system is often needed for monitoring specific gene functions. Moreover, cochlear cultures can be established from transgenic mouse embryos so that their in vitro development and response to various soluble factors and antagonists can be studied. Although embryos at day 13 (E13) are used in this protocol, cultures from E12 or E14 to early postnatal inner ears can give similar results. 
We also present a gene transfer technique in cultured embryonic cochlear explants using square wave electroporation. Following the isolation of the cochlear explants, electroporation can be used to express DNA plasmids of gene(s) of interest in individual cells within the cochlear duct. This technique serves as a complementary approach to studies utilizing transgenic mice to gain insight into the molecular pathways underlying cellular phenotype. Using this method of gene transfer, a variety of epithelial cell types within the embryonic cochlea are transfected, thereby enabling loss-and gain-of-function analyses at the single-cell level. In addition, electrophysiological studies can also be performed in cochlear explant cultures8. This method of in vitro electroporation is relatively simple and straightforward, combined with minimal damage to the tissue, has resulted in a rapid expansion of this technique.

<table border="0" cellpadding="0" cellspacing="0" width="836">
	<tbody>
		<tr height="43">
			<td height="43" style="height:43px;width:316px;">HBSS</td>
			<td style="width:192px;">Gibco</td>
			<td style="width:161px;">14065-056</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:316px;">HEPES</td>
			<td>Gibco</td>
			<td style="width:161px;">15630-080</td>
			<td></td>
		</tr>
		<tr height="43">
			<td dir="LTR" height="43" style="height:43px;width:316px;">Dulbecco&#8217;s Modified Medium</td>
			<td dir="LTR" style="width:192px;">Gibco</td>
			<td dir="LTR" style="width:161px;">12430-054</td>
			<td></td>
		</tr>
		<tr height="43">
			<td dir="LTR" height="43" style="height:43px;width:316px;">Fetal Bovine Serum</td>
			<td dir="LTR" style="width:192px;">Gibco</td>
			<td dir="LTR" style="width:161px;">10082</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td dir="LTR" height="43" style="height:43px;width:316px;">N-2 Supplement (100X)</td>
			<td dir="LTR" style="width:192px;">Gibco</td>
			<td dir="LTR" style="width:161px;">17502-048</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td dir="LTR" height="43" style="height:43px;width:316px;">Ciprofloxacin Hydrochloride</td>
			<td dir="LTR" style="width:192px;">Cellgro</td>
			<td dir="LTR" style="width:161px;">61-277-RF</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td dir="LTR" height="43" style="height:43px;width:316px;">Glass Dish 60mm</td>
			<td dir="LTR" style="width:192px;">Kimble Chase</td>
			<td dir="LTR" style="width:161px;">23062-6015/23064-6015</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:316px;">Glass Dish 100 mm</td>
			<td dir="LTR">Kimble Chase</td>
			<td style="width:161px;">23064-10015/23062-10015</td>
			<td></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:316px;">Minutien Pins</td>
			<td dir="LTR" style="width:192px;">Fine Science Tools</td>
			<td style="width:161px;">26002-15</td>
			<td></td>
		</tr>
		<tr height="43">
			<td dir="LTR" height="43" style="height:43px;width:316px;">Dumont # 5 Forceps</td>
			<td dir="LTR" style="width:192px;">Fine Science Tools</td>
			<td dir="LTR" style="width:161px;">11251-10</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:316px;">Pulse Generator&#160;</td>
			<td dir="LTR">Protech International Inc</td>
			<td style="width:161px;">CUY21Vivo-SQ</td>
			<td></td>
		</tr>
		<tr height="43">
			<td dir="LTR" height="43" style="height:43px;width:316px;">Glass Bottom Culture Dishes</td>
			<td dir="LTR" style="width:192px;">MatTek</td>
			<td dir="LTR" style="width:161px;">P35G-0-10-C</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td dir="LTR" height="43" style="height:43px;width:316px;">Matrigel Matrix</td>
			<td dir="LTR" style="width:192px;">BD Biosciences</td>
			<td dir="LTR" style="width:161px;">356237</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:316px;">Culture Dish, 60 X 15 mm</td>
			<td dir="LTR" style="width:192px;">Becton Dickinson</td>
			<td style="width:161px;">353037</td>
			<td></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:316px;">Tissue&#160; Culture Dishes</td>
			<td dir="LTR" style="width:192px;">Greiner Bio-one</td>
			<td style="width:161px;">639160</td>
			<td></td>
		</tr>
		<tr height="43">
			<td dir="LTR" height="43" style="height:43px;width:316px;">Phosphate Buffered Saline</td>
			<td dir="LTR" style="width:192px;">Gibco</td>
			<td dir="LTR" style="width:161px;">10010-023</td>
			<td></td>
		</tr>
		<tr height="43">
			<td dir="LTR" height="43" style="height:43px;width:316px;">OS-30</td>
			<td dir="LTR" style="width:192px;">Dow Corning</td>
			<td dir="LTR" style="width:161px;">4021768</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td dir="LTR" height="43" style="height:43px;width:316px;">Fluoromount</td>
			<td dir="LTR" style="width:192px;">Southern Biotech</td>
			<td dir="LTR" style="width:161px;">0100-01</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:316px;">Conical Tubes, 15ml</td>
			<td style="width:192px;">Greiner Bio-one</td>
			<td style="width:161px;">188261</td>
			<td></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:316px;">Myosin 6</td>
			<td>Proteus Biosciences Inc</td>
			<td style="width:161px;">25-6791</td>
			<td></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:316px;">Myosin 7a</td>
			<td style="width:192px;">Proteus Biosciences Inc</td>
			<td style="width:161px;">25-6790</td>
			<td></td>
		</tr>
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			<td height="43" style="height:43px;width:316px;">TuJ1</td>
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culture of embryonic mouse cochlear explants and gene transfer by electroporation

Auditory hair cells located within the mouse organ of Corti detect and transmit sound information to the central nervous system. The mechanosensory hair cells are aligned in one row of inner hair cells and three rows of outer hair cells that extend along the basal to apical axis of the cochlea. The explant culture technique described here provides an efficient method to isolate and maintain cochlear explants from the embryonic mouse inner ear. Also, the morphology and molecular characteristics of sensory hair cells and nonsensory supporting cells within the cochlear explant cultures resemble those observed in vivo and can be studied within its intrinsic cellular environment. The cochlear explants can serve as important experimental tools for the identification and characterization of molecular and genetic pathways that are involved in cellular specification and patterning. Although transgenic mouse models provide an effective approach for gene expression studies, a considerable number of mouse mutants die during embryonic development thereby hindering the analysis and interpretation of developmental phenotypes. The organ of Corti from mutant mice that die before birth can be cultured so that their in vitro development and responses to different factors can be analyzed. Additionally, we describe a technique for electroporating embryonic cochlear explants ex vivo which can be used to downregulate or overexpress specific gene(s) and analyze their potential endogenous function and test whether specific gene product is necessary or sufficient in a given context to influence mammalian cochlear development1-8.

We describe a method to isolate cochlea from embryonic inner ears and micro-dissect to expose the sensory epithelium. Once dissected, it may be plated and cultured as an intact cochlear duct (Figure 3) and analyzed by immunohistochemistry. The cultured cochlear explants provide a useful assay to examine the effect of variety of soluble factors and pharmacological drugs on cochlear development. Following dissection of cochlear explants, electroporation technique can be used to misexpress genes of interest...

Watch this Scientific Journal Video about Culture of Embryonic Mouse Cochlear Explants and Gene Transfer by Electroporation at JoVE.com

Culture of Embryonic Mouse Cochlear Explants and Gene Transfer by Electroporation

We present a method that describes isolation and culture of cochlear explants from embryonic mouse inner ear. We also demonstrate a method for gene transfer into cochlear explants via square-wave electroporation. The in vitro explant culture coupled with gene transfer technique enables researchers to study the effects of altering gene expression during development.

Auditory hair cells located within the mouse organ of Corti detect and transmit sound information to the central nervous system. The mechanosensory hair ...

culture-embryonic-mouse-cochlear-explants-gene-transfer

Research

JoVE Journal

Developmental Biology

12.8K Views.  Medical University of South Carolina, College of Medicine. We present a method that describes isolation and culture of cochlear explants from embryonic mouse inner ear. We also demonstrate a method for gene transfer into cochlear explants via square-wave electroporation. The in vitro explant culture coupled with gene transfer technique enables researchers to study the effects of altering gene expression during development. 

Video: Culture of Embryonic Mouse Cochlear Explants and Gene Transfer by Electroporation

Efficient Gene Transfer in Chick Retinas for Primary Cell Culture Studies: An Ex-ovo Electroporation Approach

The cone photoreceptor-enriched cultures derived from embryonic chick retinas have become an indispensable tool for researchers around the world studying the biology of retinal neurons, particularly photoreceptors. The applications of this system go beyond basic research, as they can easily be adapted to high throughput technologies for drug development. However, genetic manipulation of retinal photoreceptors in these cultures has proven to be very challenging, posing an important limitation to the usefulness of the system. We have recently developed and validated an ex&#160;ovo plasmid electroporation technique that increases the rate of transfection of retinal cells in these cultures by five-fold compared to other currently available protocols1. In this method embryonic chick eyes are enucleated at stage 27, the RPE is removed, and the retinal cup is placed in a plasmid-containing solution and electroporated using easily constructed custom-made electrodes. The retinas are then dissociated and cultured using standard procedures. This technique can be applied to overexpression studies as well as to the downregulation of gene expression, for example via the use of plasmid-driven RNAi technology, commonly achieving transgene expression in 25% of the photoreceptor population. The video format of the present publication will make this technology easily accessible to researchers in the field, enabling the study of gene function in primary retinal cultures. We have also included detailed explanations of the critical steps of this procedure for a successful outcome and reproducibility.

Efficient Gene Transfer in Chick Retinas for Primary Cell Culture Studies: An Ex-ovo Electroporation Approach

Embryonic chick retinal cell cultures constitute valuable tools for the study of photoreceptor biology. We have developed an efficient gene transfer technique based on ex&#160;ovo plasmid electroporation of the retinas prior to culture. This technique considerably increases transfection efficiencies over currently available protocols, making genetic manipulation feasible for this system.

The cone photoreceptor-enriched cultures derived from embryonic chick retinas have become an indispensable tool for researchers around the world studying ...

Ex Utero Electroporation and Organotypic Slice Culture of Mouse Hippocampal Tissue

Mouse genetics offers a powerful tool determining the role of specific genes during development. Analyzing the resulting phenotypes by immunohistochemical and molecular methods provides information of potential target genes and signaling pathways. To further elucidate specific regulatory mechanisms requires a system allowing the manipulation of only a small number of cells of a specific tissue by either overexpression, ablation or re-introduction of specific genes and follow their fate during development. To achieve this ex utero electroporation of hippocampal structures, especially the dentate gyrus, followed by organotypic slice culture provides such a tool. Using this system to generate mosaic deletions allows determining whether the gene of interest regulates cell-autonomously developmental processes like progenitor cell proliferation or neuronal differentiation. Furthermore it facilitates the rescue of phenotypes by re-introducing the deleted gene or its target genes. In contrast to in utero electroporation the ex utero approach improves the rate of successfully targeting deeper layers of the brain like the dentate gyrus. Overall ex utero electroporation and organotypic slice culture provide a potent tool to study regulatory mechanisms in a semi-native environment mirroring endogenous conditions.

Ex Utero Electroporation and Organotypic Slice Culture of Mouse Hippocampal Tissue

Here we present a protocol providing a tool to examine regulatory mechanisms of specific genes during hippocampal development. Employing ex utero electroporation and organotypic slice culture allows the up- and down-regulation of the expression of genes of interest in single cells and follow their fate during development.

Mouse genetics offers a powerful tool determining the role of specific genes during development. Analyzing the resulting phenotypes by immunohistochemical ...

Neural Differentiation of Mouse Embryonic Stem Cells in Serum-free Monolayer Culture

The ability to differentiate mouse embryonic stem cells (ESC) to neural progenitors allows the study of the mechanisms controlling neural specification as well as the generation of mature neural cell types for further study. In this protocol we describe a method for the differentiation of ESC to neural progenitors using serum-free, monolayer culture. The method is scalable, efficient and results in production of ~70% neural progenitor cells within 4 - 6 days. It can be applied to ESC from various strains grown under a variety of conditions. Neural progenitors can be allowed to differentiate further into functional neurons and glia or analyzed by microscopy, flow cytometry or molecular techniques. The differentiation process is amenable to time-lapse microscopy and can be combined with the use of reporter lines to monitor the neural specification process. We provide detailed instructions on media preparation and cell density optimization to allow the process to be applied to most ESC lines and a variety of cell culture vessels.

This protocol describes in detail the method for generating neural progenitors from embryonic stem cells using a serum-free monolayer method. These progenitors can be used to derive mature neural cell types or to study the process of neural specification and is amenable to multiwell format scaling for compound screening.

The ability to differentiate mouse embryonic stem cells (ESC) to neural progenitors allows the study of the mechanisms controlling neural specification as ...

Whole Retinal Explants from Chicken Embryos for Electroporation and Chemical Reagent Treatments

The retina is a good model for the developing central nervous system. The large size of the eye and most importantly the accessibility for experimental manipulations in ovo/in vivo makes the chicken embryonic retina a versatile and very efficient experimental model. Although the chicken retina is easy to target in ovo by intraocular injections or electroporation, the effective and exact concentration of the reagents within the retina may be difficult to fully control. This may be due to variations of the exact injection site, leakage from the eye or uneven diffusion of the substances. Furthermore, the frequency of malformations and mortality after invasive manipulations such as electroporation is rather high.
This protocol describes an ex ovo technique for culturing whole retinal explants from chicken embryos and provides a method for controlled exposure of the retina to reagents. The protocol describes how to dissect, experimentally manipulate, and culture whole retinal explants from chicken embryos. The explants can be cultured for approximately 24 hr and be subjected to different manipulations such as electroporation. The major advantages are that the experiment is not dependent on the survival of the embryo and that the concentration of the introduced reagent can be varied and controlled in order to determine and optimize the effective concentration. Furthermore, the technique is rapid, cheap and together with its high experimental success rate, it ensures reproducible results. It should be emphasized that it serves as an excellent complement to experiments performed in ovo.

This protocol describes a method to dissect, experimentally manipulate and culture whole retinal explants from chicken embryos. The explant cultures are useful when high success rate, efficacy and reproducibility are needed to test the effects of plasmids for electroporation and/or reagent substances, i.e., enzymatic inhibitors.

The retina is a good model for the developing central nervous system. The large size of the eye and most importantly the accessibility for experimental ...

Gene Transfer into the Chicken Auditory Organ by In Ovo Micro-electroporation

Chicken embryos are ideal model systems for studying embryonic development as manipulations of gene function can be conducted with relative ease in ovo. The inner ear auditory sensory organ is critical for our ability to hear. It houses a highly specialized sensory epithelium that consists of mechano-transducing hair cells (HCs) and surrounding glial-like supporting cells (SCs). Despite structural differences in the auditory organs, molecular mechanisms regulating the development of the auditory organ are evolutionarily conserved between mammals and aves. In ovo electroporation is largely limited to early stages at E1 - E3. Due to the relative late development of the auditory organ at E5, manipulations of the auditory organ by in ovo electroporation past E3 are difficult due to the advanced development of the chicken embryo at later stages. The method presented here is a transient gene transfer method for targeting genes of interest at stage E4 - E4.5 in the developing chicken auditory sensory organ via in ovo micro-electroporation. This method is applicable for gain- and loss-of-functions with conventional plasmid DNA-based expression vectors and can be combined with in ovo cell proliferation assay by adding EdU (5-ethynyl-2&#180;-deoxyuridine) to the whole embryo at the time of electroporation. The use of green or red fluorescent protein (GFP or RFP) expression plasmids allows the experimenter to quickly determine whether the electroporation successfully targeted the auditory portion of the developing inner ear. In this method paper, representative examples of GFP electroporated specimens are illustrated; embryos were harvested 18 - 96 hr&#160;after electroporation and targeting of GFP to the pro-sensory area of the auditory organ was confirmed by RNA in situ hybridization. The method paper also provides an optimized protocol for the use of the thymidine analog EdU to analyze cell proliferation; an example of an EdU based cell proliferation assay that combines immuno-labeling and click EdU chemistry is provided.

Gene Transfer into the Chicken Auditory Organ by In Ovo Micro-electroporation

The auditory organ mediates hearing. Here we present a modified in ovo micro-electroporation method optimized for studying auditory progenitor cell proliferation and differentiation in the developing chicken auditory organ.

Chicken embryos are ideal model systems for studying embryonic development as manipulations of gene function can be conducted with relative ease in ovo. ...

Culture of Murine Embryonic Metatarsals: A Physiological Model of Endochondral Ossification

The fundamental process of endochondral ossification is under tight regulation in the healthy individual so as to prevent disturbed development and/or longitudinal bone growth. As such, it is imperative that we further our understanding of the underpinning molecular mechanisms involved in such disorders so as to provide advances towards human and animal patient benefit. The mouse metatarsal organ explant culture is a highly physiological ex vivo model for studying endochondral ossification and bone growth as the growth rate of the bones in culture mimic that observed in vivo. Uniquely, the metatarsal organ culture allows the examination of chondrocytes in different phases of chondrogenesis and maintains cell-cell and cell-matrix interactions, therefore providing conditions closer to the in vivo situation than cells in monolayer or 3D culture. This protocol describes in detail the intricate dissection of embryonic metatarsals from the hind limb of E15 murine embryos and the subsequent analyses that can be performed in order to examine endochondral ossification and longitudinal bone growth.

We present a protocol to dissect and culture embryonic day 15 (E15) murine metatarsal bones. This highly physiological ex vivo model of endochondral ossification provides conditions closer to the in vivo situation than cells in monolayer or 3D culture and is a vital tool for investigating bone growth and development.

The fundamental process of endochondral ossification is under tight regulation in the healthy individual so as to prevent disturbed development and/or ...

Culture of Adult Transgenic Zebrafish Retinal Explants for Live-cell Imaging by Multiphoton Microscopy

An endogenous regeneration program is initiated by M&#252;ller glia in the adult zebrafish (Danio rerio) retina following neuronal damage and death. The M&#252;ller glia re-enter the cell cycle and produce neuronal progenitor cells that undergo subsequent rounds of cell divisions and differentiate into the lost neuronal cell types. Both M&#252;ller glia and neuronal progenitor cell nuclei replicate their DNA and undergo mitosis in distinct locations of the retina, i.e. they migrate between the basal Inner Nuclear Layer (INL) and the Outer Nuclear Layer (ONL), respectively, in a process described as Interkinetic Nuclear Migration (INM). INM has predominantly been studied in the developing retina. To examine the dynamics of INM in the adult regenerating zebrafish retina in detail, live-cell imaging of fluorescently-labeled M&#252;ller glia/neuronal progenitor cells is required. Here, we provide the conditions to isolate and culture dorsal retinas from Tg[gfap:nGFP]mi2004 zebrafish that were exposed to constant intense light for 35 h. We also show that these retinal cultures are viable to perform live-cell imaging experiments, continuously acquiring z-stack images throughout the thickness of the retinal explant for up to 8 h using multiphoton microscopy to monitor the migratory behavior of gfap:nGFP-positive cells. In addition, we describe the details to perform post-imaging analysis to determine the velocity of apical and basal INM. To summarize, we established conditions to study the dynamics of INM in an adult model of neuronal regeneration. This will advance our understanding of this crucial cellular process and allow us to determine the mechanisms that control INM.

Zebrafish retinal regeneration has mostly been studied using fixed retinas. However, dynamic processes such as interkinetic nuclear migration occur during the regenerative response and require live-cell imaging to investigate the underlying mechanisms. Here, we describe culture and imaging conditions to monitor Interkinetic Nuclear Migration (INM) in real-time using multiphoton microscopy.

An endogenous regeneration program is initiated by M&#252;ller glia in the adult zebrafish (Danio rerio) retina following neuronal damage and death. The ...

Dissection and Culture of Mouse Embryonic Kidney

The goal of this protocol is to describe a method for the dissection, isolation, and culture of mouse metanephric rudiments. 
During mammalian kidney development, the two progenitor tissues, the ureteric bud and the metanephric mesenchyme, communicate and reciprocally induce cellular mechanisms to eventually form the collecting system and the nephrons of the kidney. As mammalian embryos grow intrauterine and therefore are inaccessible to the observer, an organ culture has been developed. With this method, it is possible to study epithelial-mesenchymal interactions and cellular behavior during kidney organogenesis. Furthermore, the origin of congenital kidney and urogenital tract malformations can be investigated. After careful dissection, the metanephric rudiments are transferred onto a filter that floats on culture medium and can be kept in a cell culture incubator for several days. However, one must be aware that the conditions are artificial and could influence the metabolism in the tissue. Also, the penetration of test substances could be limited due to the extracellular matrix and basal membrane present in the explant.
One main advantage of organ culture is that the experimenter can gain direct access to the organ. This technology is cheap, simple, and allows a large number of modifications, such as the addition of biologically active substances, the study of genetic variants, and the application of advanced imaging techniques.

This protocol describes a method for isolating and culturing metanephric rudiments from mouse embryos.

The goal of this protocol is to describe a method for the dissection, isolation, and culture of mouse metanephric rudiments. 
During mammalian kidney ...

CRISPR-mediated Loss of Function Analysis in Cerebellar Granule Cells Using In Utero Electroporation-based Gene Transfer

Brain malformation is often caused by genetic mutations. Deciphering the mutations in patient-derived tissues has identified potential causative factors of the diseases. To validate the contribution of a dysfunction of the mutated genes to disease development, the generation of animal models carrying the mutations is one obvious approach. While germline genetically engineered mouse models (GEMMs) are popular biological tools and exhibit reproducible results, it is restricted by time and costs. Meanwhile, non-germline GEMMs often enable exploring gene function in a more feasible manner. Since some brain diseases (e.g., brain tumors) appear to result from somatic but not germline mutations, non-germline chimeric mouse models, in which normal and abnormal cells coexist, could be helpful for disease-relevant analysis. In this study, we report a method for the induction of CRISPR-mediated somatic mutations in the cerebellum. Specifically, we utilized conditional knock-in mice, in which Cas9 and GFP are chronically activated by the CAG (CMV enhancer/chicken &#223;-actin) promoter after Cre-mediated recombination of the genome. The self-designed single-guide RNAs (sgRNAs) and the Cre recombinase sequence, both encoded in a single plasmid construct, were delivered into cerebellar stem/progenitor cells at an embryonic stage using in utero electroporation. Consequently, transfected cells and their daughter cells were labeled with green fluorescent protein (GFP), thus facilitating further phenotypic analyses. Hence, this method is not only showing electroporation-based gene delivery into embryonic cerebellar cells but also proposing a novel quantitative approach to assess CRISPR-mediated loss-of-function phenotypes.

CRISPR-mediated Loss of Function Analysis in Cerebellar Granule Cells Using In Utero Electroporation-based Gene Transfer

Conventional loss-of-function studies of genes using knockout animals have often been costly and time-consuming. Electroporation-based CRISPR-mediated somatic mutagenesis is a powerful tool to understand gene functions in vivo. Here, we report a method to analyze knockout phenotypes in proliferating cells of the cerebellum.

Brain malformation is often caused by genetic mutations. Deciphering the mutations in patient-derived tissues has identified potential causative factors ...

Isolation and Differentiation of Primary Myoblasts from Mouse Skeletal Muscle Explants

Primary myoblasts are undifferentiated proliferating precursors of skeletal muscle. They can be cultured and studied as muscle precursors or induced to differentiate into later stages of muscle development. The protocol provided here describes a robust method for the isolation and culture of a highly proliferative population of myoblast cells from young adult mouse skeletal muscle explants. These cells are useful for the study of the metabolic properties of skeletal muscle of different mouse models, as well as in other downstream applications such as transfection with exogenous DNA or transduction with viral expression vectors. The level of differentiation and metabolic profile of these cells depends on the length of exposure, and composition of the media used to induce myoblast differentiation. These methods provide a robust system for the study of mouse muscle cell metabolism ex vivo. Importantly, unlike in vivo models, the methods described here provide a cell population that can be expanded and studied with high levels of reproducibility.

Myoblasts are proliferating precursor cells that differentiate to form polynucleated myotubes and eventually skeletal muscle myofibers. Here, we present a protocol for efficient isolation and culture of primary myoblasts from young adult mouse skeletal muscles. The method enables molecular, genetic, and metabolic studies of muscle cells in culture.

Primary myoblasts are undifferentiated proliferating precursors of skeletal muscle. They can be cultured and studied as muscle precursors or induced to ...