The authors wish to thank George Farr and members of the Horwich lab for helpful discussions. This work was supported by the Howard Hughes Medical Institute.

The procedures described here for anesthesia, euthanasia, and cardiac perfusion of mice were performed under a protocol approved by the Yale University Institutional Animal Care and Use Committee.
1. Preparation of RNase-free Instruments and Solutions
<ol>
	<li>RNase is a common contaminant of all laboratory surfaces, including bench tops, micropipettes, and the investigator.
	<ol>
		<li>Change gloves often or regularly wipe with a RNAse decontaminating solution.</li>
		<li>Stainless steel dissection tools and glassware can be made RNase-free by heating at &#62;200 &#176;C for 1 hr or more. Note: Steam sterilization does not destroy RNase. Alternatively, wipe with a RNase decontaminating solution, then with RNase-free 70% ethanol and air dry.</li>
		<li>Wipe bench tops, other lab surfaces and micropipettors with RNase decontaminating solution, then with RNase-free 70% ethanol. Designate a specific lab bench or work area for RNA recovery and analysis. Note: Remove tip ejectors before wiping the shafts of the pipettors and leave them off, if possible.</li>
		<li>Use tubes, microcentrifuge tubes, pipettes, and micropipette tips that are certified by their manufacturer to be RNase-free. Use of very-low binding tips and microtubes is recommended. If possible, use freshly opened boxes or bags of these components and keep them separate from the general lab supply.</li>
		<li>Obtain RNase-free solutions [Dulbecco&#8217;s calcium and magnesium-free PBS (PBS), ethanol, RNase-free 70% ethanol] from commercial sources. Use newly opened bottles for each experiment.</li>
	</ol>
	</li>
	<li>The source of the Azure B dye is critical to successful recovery of intact RNA. Test each batch of dye before committing precious samples to staining and collection. Collect a few thousand neurons from a nonexperimental animal, prepare RNA, and determine the RNA integrity as described below to find one that consistently produces RIN numbers above 8.5.
	<ol>
		<li>Dissolve Azure B dye (1%, wt/vol) in RNase-free 70% ethanol, typically 0.3 g in 30 ml ethanol in a 50 ml centrifuge tube. Mix well on a rocker at RT overnight or until all the particles have dissolved. One tube of this solution can be used to stain multiple slides without affecting the staining intensity.</li>
		<li>As a precaution, use a different tube of stain for each biological replicate.</li>
	</ol>
	</li>
	<li>Use the cryomolds and O.C.T. for embedding cord sections without further treatment.</li>
	<li>Maintain the cryostat at -20 to -24 &#176;C. After sectioning, place the slides in a -80 &#176;C freezer until a sufficient number has been prepared. Start RNA preparation as soon as possible after the slides have been made. For long-term storage, keep unsectioned or partially sectioned OCT blocks, rather than slides, at 80 &#176;C.</li>
	<li>Make the guanidine thiocyanate buffer for RNA preparation from the dissected motor neurons using the solutions provided by the RNA preparation kit manufacturer according to its directions.</li>
</ol>
2. Preparation of Spinal Cord Sections from Mice (Figure 1A)
<ol>
	<li>Clean all the dissection tools, glass slides, razor blades, and dissection platform by baking or wiping with RNase decontaminating solution, followed by RNase-free 70% ethanol. Let dry for 2 min. Keep everything dust-free by covering with lab wipes.</li>
	<li>Animal handling procedures, including anesthesia, cardiac perfusion, and euthanasia, should be carried out according to the requirements of the local institutional animal care and use committee (IACUC), with the goal of rapidly bringing the animal to the point of spinal cord dissection.
	<ol>
		<li>Anesthetize the mouse by intraperitoneal (ip) injection of a lethal dose of Ketamine (450 mg/kg).</li>
		<li>Once a deep level of anesthesia is achieved and confirmed by lack of a toe-pinch response, position the mouse ventral side up on a dissection platform (a Styrofoam board, for example), open the chest cavity to expose the heart, and insert the 27 G butterfly needle of an infusion set into the left ventricle (which is on the investigator&#8217;s right). Nick the right atrium with a sharp forceps, and perfuse with PBS at a rate of 5-7 ml/min for about 2 min using a peristaltic pump. The liquid flowing from the atrium should be largely free of blood at this point.</li>
		<li>Remove the perfusion needle, decapitate the mouse, and turn it over on the dissection board. Open the skin to expose the spinal column, use small scissors and forceps to remove the vertebrae, and lift out the spinal cord while severing the nerve roots with a sharp forceps. Speed and practice are essential in moving from the start of the perfusion to removal of the cord; this should take no more than 7 min.</li>
		<li>Rinse the cord for 10 sec in RNase-free water to wash off any residual blood. Lay the spinal cord on an RNase-free glass slide with a curved forceps very gently but quickly. Divide the spinal cord transversely using a clean razor blade into 9-10 pieces.</li>
		<li>Place the pieces in a cryomold filled with O.C.T. using the same forceps, and align them vertically using a clean needle. Place the mold in a shallow tray containing 2-methylbutane precooled with liquid nitrogen, and then put the tray into a liquid nitrogen bath to fast-freeze the spinal cord pieces to avoid RNA degradation.</li>
		<li>Store the OCT-embedded block at -80 &#176;C for up to 6 months before sectioning. The process from retrieval of the cord through freezing should be done within 5 min to maintain RNA integrity.</li>
	</ol>
	</li>
	<li>Cryosection the O.C.T.-embedded block at -20 &#176;C with a cryostat to produce 20 &#181;m slices, each containing 9-10 spinal cord cross sections, on RNase-free PEN-membrane 2 &#956;m slides kept initially at room temperature to ensure that the sections adhere to the slide. Immediately refreeze the section on a -20 &#176;C surface inside the cryostat. Keep the slides at -80 &#176;C until used.</li>
</ol>
3. Staining of Spinal Cord Sections (Figure 1A)
<ol>
	<li>On a clean rack, arrange six 50 ml conical tubes. Fill all of them with 25-30 ml of RNase-free 70% ethanol, so that the depth is sufficient to cover all the sections on a slide when the slide is immersed. Make 30-35 ml of 1% Azure B solution as described earlier and keep it on the same rack to minimize time between changing solutions during washing or staining. Keep three or four lab wipes in front of the rack to drain extra solution quickly.</li>
	<li>Take the slides out of the -80 &#176;C freezer onto dry ice. Thaw one slide by placing it on a gloved palm. Remove most of the moisture and condensation on the slide by wiping it off with a lab wipe, being careful not to touch the sections. Put the slide on fresh silica gel desiccant in a Petri dish for 30-40 sec&#160;to dry completely. If lab humidity is high, brief treatment in a vacuum dessicator can be used to dry the slide more quickly.</li>
	<li>Washing and staining.
	<ol>
		<li>Dip the dried slide into the first tube of RNase-free 70% ethanol. Soak the slide for 30 sec, then wash the slide to remove the OCT by dipping it up and down for 45-60&#160;sec . Take the slide out of the solution and drain the excess liquid on lab wipes. Repeat the same process by dipping the slide in the second tube of 70% ethanol. If the OCT around the spinal cord sections is not completely gone, repeat the washing in the third tube.</li>
		<li>After draining the excess liquid, submerge the slide in 1% Azure B solution in 70% RNase-free ethanol for 30-45 sec. Drain the excess Azure B on a lab wipe; at this point, the whole slide will be blue.</li>
		<li>Submerge the slide in the next tube of 70% ethanol, and dip up and down quickly 3-4x to remove excess dye and to make the specific motor neuron staining visible. If the sections look very darkly stained, repeat the destaining step in a fresh tube of 70% ethanol. If the staining seems too light, return the slide to the Azure B solution for another 30 sec and repeat the destaining. Wipe off the excess ethanol and air dry the slide for ~40 sec until all the liquid is gone. The gray matter will be light blue, whereas the motor neurons will be stained deep blue, which is easily visible. Start the dissection immediately.</li>
	</ol>
	</li>
</ol>
4. Laser Capture Microdissection (LMD) (Figure 1B)
<ol>
	<li>Turn on the microscope and unload the tube holder to attach the cap of a 0.6 ml microfuge tube for sample collection. Put 30 &#181;l guanidine thiocyanate lysis buffer into the cap of a 0.6 ml microfuge tube. Cover the surface of the cap with liquid by spreading the solution using a pipette tip. In this way, all the collected neurons will be dissolved in solubilizing solution as they are dissected. Align the cap with the hole and the objective with the microscope software. Keep the cap in the covered position until starting laser capture.</li>
	<li>Place the air dried slide on the stage of the LMD microscope upside down, so that the membrane of the PEN slide faces down. The membrane with sections should face the hole, underneath of which is the collection tube.</li>
	<li>Turn on the laser 10 min before starting slide preparation. Focus on a spinal cord section with the 5X objective. Move to the 20X objective for dissection.
	<ol>
		<li>Mark a &#8220;dummy&#8221; region with the light pen and allow the laser to cut it out without collecting it. This relaxes the PEN membrane and makes it possible to mark and cut multiple regions successively.</li>
		<li>Refocus and identify motor neurons in the ventral horn region. These neurons are recognizable by their location, their pyramidal morphology, their large size, and their dark blue staining with Azure B (Figure 2).</li>
		<li>Using the light pen, select the drawing tool and mark along the edge of the motor neurons, making a complete outline. Try to make the outline as close as possible to the motor neuron to avoid contamination from cells other than the motor neuron. (Test some sections beforehand to see how wide the laser cut-line is and adjust the clearance as necessary.) Mark multiple cells before cutting; the software will remember the positions.</li>
		<li>Bring the cap underneath the cutting position by clicking on the cap position. Click the start button to initiate motor neuron dissection with the laser. Collect all the motor neurons from all of the sections on one slide into the cap of one microfuge tube.</li>
		<li>After collection is complete, take the microfuge tube out of the holder by unloading the tray and gently dislodging the tube. Completely dissolve the motor neurons in the buffer by pipetting the solution up and down. Move the solution into the body of the tube by centrifuging at 14,000 x g for 2 min at 4 &#176;C. Freeze the sample immediately in dry ice and store it at -80 &#176;C. This process, from slide staining through motor neuron collection, should be done within 30 min for one slide to minimize RNA degradation.</li>
	</ol>
	</li>
</ol>
5. RNA Preparation from Motor Neurons
Thaw all of the collected neurons from one animal and pool them together to extract RNA. Samples may look pale blue depending on the number of motor neurons (stained with Azure B) in them. Extract RNA using a suitable kit according to the protocol provided for LMD tissue, eluting in the minimum volume possible. Take 1 &#181;l to check the quantity and integrity of the sample. Fast-freeze the remaining RNA on dry ice and store at -80 &#176;C.
6. Determination of RNA Quality and Quantity
Determine the RNA quality with the 1 &#181;l sample on a capillary electrophoresis microfluidics chip according to the manufacturer&#8217;s protocol. Total RNA preparations with an RNA Integrity Number (RIN) above 8.5 can be used for RNA-seq and qRT-PCR. The data output also typically includes the approximate concentration of the sample.

<ol>
	<li>Zhu, J., Nie, S., Wu, J., Lubman, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Target+proteomic+profiling+of+frozen+pancreatic+CD24++adenocarcinoma+tissues+by+immuno-laser+capture+microdissection+and+nano-LC-MS/MS.">Target proteomic profiling of frozen pancreatic CD24+ adenocarcinoma tissues by immuno-laser capture microdissection and nano-LC-MS/MS.</a> J. Proteome. Res. , (2013).</li><li>Bandyopadhyay, U., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA-Seq+profiling+of+spinal+cord+motor+neurons+from+a+presymptomatic+SOD1+ALS+mouse..">RNA-Seq profiling of spinal cord motor neurons from a presymptomatic SOD1 ALS mouse..</a> PLoS ONE. 8 (1), 10-1371 (2013).</li><li>Shea, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+method+for+in+situ+cytophotometric+estimation+of+absolute+amount+of+ribonucleic+acid+using+azure+B1.">A method for in situ cytophotometric estimation of absolute amount of ribonucleic acid using azure B1.</a> J. Histochem. Cytochem. 18 (2), 143-152 (1970).</li><li>Bustin, S. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+MIQE+guidelines:+minimum+information+for+publication+of+quantitative+real-time+PCR+experiments.">The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments.</a> Clin. Chem. 55 (4), 611-622 (2009).</li><li>Schroeder, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+RIN:+an+RNA+integrity+number+for+assigning+integrity+values+to+RNA+measurements.">The RIN: an RNA integrity number for assigning integrity values to RNA measurements.</a> BMC Mol. Biol. 7, (2006).</li><li>Doebler, J. A., Rhoads, R. E., Anthony, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neuronal+RNA+in+Pick's+and+Alzheimer's+diseases.+Comparison+of+disease-susceptible+and+disease-resistant+cortical+areas.">Neuronal RNA in Pick's and Alzheimer's diseases. Comparison of disease-susceptible and disease-resistant cortical areas.</a> Arch. Neurol. 46 (2), 134-137 (1989).</li><li>Lobsiger, C. S., Boill&#233;e, S., Cleveland, D. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Toxicity+from+different+SOD1+mutants+dysregulates+the+complement+system+and+the+neuronal+regenerative+response+in+ALS+motor+neurons.">Toxicity from different SOD1 mutants dysregulates the complement system and the neuronal regenerative response in ALS motor neurons.</a> Proc. Natl. Acad. Sci. U.S.A. 104 (18), (2007).</li><li>Ferraiuolo, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microarray+analysis+of+the+cellular+pathways+involved+in+the+adaptation+to+and+progression+of+motor+neuron+injury+in+the+SOD1+G93A+mouse+model+of+familial+ALS.">Microarray analysis of the cellular pathways involved in the adaptation to and progression of motor neuron injury in the SOD1 G93A mouse model of familial ALS.</a> J. Neurosci. 27 (34), 9201-9219 (2007).</li><li>Sturm, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Improved+protocol+for+laser+microdissection+of+human+pancreatic+islets+from+surgical+specimens.">Improved protocol for laser microdissection of human pancreatic islets from surgical specimens.</a> J. Vis. Exp. 6 (71), (2013).</li><li>Burbach, G. J., Dehn, D., Nagel, B., Del Turco, D., Deller, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Laser+microdissection+of+immunolabeled+astrocytes+allows+quantification+of+astrocytic+gene+expression.">Laser microdissection of immunolabeled astrocytes allows quantification of astrocytic gene expression.</a> J. Neurosci. Methods. 138 (1-2), 141-148 (2004).</li><li>Wang, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Progressive+aggregation+despite+chaperone+associations+of+a+mutant+SOD1-YFP+in+transgenic+mice+that+develop+ALS.">Progressive aggregation despite chaperone associations of a mutant SOD1-YFP in transgenic mice that develop ALS.</a> Proc. Natl. Acad. Sci. U.S.A. 106 (5), 1392-1397 (2009).</li></ol>

The authors declare they have no competing financial interests.

The most significant measure of success of this protocol for producing total RNA by laser microdissection of spinal cord slices is the RIN value5. For RNA samples from higher eukaryotes, values above 8.5 regularly yield high quality sequencing and qRT-PCR data. If yield is low but quality is high, repeat the preparation. If the integrity is lower (even 7.5-8), however, it is better to find the source of the problem and try again. There are many steps where something can go wrong, but really only two sources of the problem -&#160;endogenous RNase contamination or exogenous RNase contamination. The first can be addressed by practice, so that the time from sacrifice of the mouse to freezing its O.C.T-embedded cord is minimized. The other point in the protocol where endogenous RNase can contribute to a poor result is during the preparation of the slices. Each slice should adhere to a room temperature PEN slide quickly, but it will melt (the O.C.T becomes clear). The faster the slice can be refrozen the better. The cryostat we use has flat surfaces inside the chamber that are at -20 &#176;C, which we use to quickly refreeze the slice. Find a similar spot in the cryostat used and make sure the slice becomes opaque again rapidly.
Tracking down sources of exogenous RNase can be difficult, because there are so many possibilities. The only reagents used which are not expressly RNase-free are O.C.T. and the Azure B. If the Azure B has performed satisfactorily before, try a fresh bottle of O.C.T., although this reagent has never been a problem. RNase-free reagents can also be replaced, even from a different supplier. A much more likely source is the investigator. In addition to a thorough cleanup of the working area, it is often useful to have another lab member follow along and observe all the steps in the procedure. Even if this is someone who does not routinely perform this procedure, a fresh set of eyes may pick up an otherwise unnoticed source of contamination.
Extending this protocol to recovering RNA from other spinal cord cells, from spinal cord cells from other species, or from specific cell types in other organs will require modifications in several areas directed at achieving clear identification of the cells of interest while obviating, or at least minimizing, the impact of endogenous RNase. In the protocol here, rapid removal and freezing of the cord, coupled with Azure B staining in 70% ethanol, allowed both minimization of RNA degradation and easy identification of motor neuron cell bodies. Azure B is a well-established histochemical stain for neurons that appears to bind to RNA3 and has been used to evaluate RNA content of neurons in autopsy samples of brain tissue from patients with neurodegenerative disease6. Notably, Azure B staining did not affect either the integrity of the purified RNA or its ability to be reverse-transcribed and analyzed. Other dyes, such as cresyl violet7 and toluidine blue8 have been used in similar LMD protocols. Collecting the cell bodies directly into guanidine thiocyanate solution as they were dissected provided the final step that resulted in the routine recovery of intact RNA.
Similar approaches can be envisioned for other cells and organs, recognizing that identifying the cells of interest while minimizing or, preferably, preventing RNA degradation by endogenous RNases is the critical requirement for successful analysis.&#160;In tissues that have high levels of RNase, such as pancreas, rapid handling and low temperature have been combined to permit recovery of RNA from &#946;-cells, taking advantage of their natural autofluorescence for visualization9.&#160;Procedures using antibody staining for identification have also been reported10, but have not been fully successful in our hands.&#160;Finally, many mouse models are available that express fluorescent fusion proteins (i.e.&#160;GFP, YFP, RFP) in cells of interest, which could be used to identify them in tissue sections on the LMD microscope.&#160;In fact, the mouse strains we have analyzed with this protocol express a fusion protein between SOD1 and YFP11, and their spinal cord motor neurons are highly fluorescent.&#160;We were not able, however, to find a set of ethanol washes and/or dehydration conditions that would simultaneously remove the O.C.T., inhibit RNase activity, and consistently maintain sufficient YFP fluorescence to allow visualization of the motor neurons and their recovery by LMD.&#160;Perhaps a new fluorescent protein or a variant of the available ones that maintains fluorescence in organic solvents can be found to overcome this limitation.&#160;

In mammalian tissues composed of multiple different cell types, the advent of laser capture microdissection (LMD) instrumentation has afforded the possibility to select a specific cell type for analysis at the RNA or protein level.&#160;At present, amplification and next-gen sequencing techniques enable use of a pool of total RNA from a few thousand cells to obtain a relatively thorough inventory of the transcriptome, including assessment of relative levels of RNAs and identification of various spliced forms.&#160;To date, proteomics analyses of a few thousand cells will reach down through only more abundant species.&#160;For example, we have identified &#60;1,000 of the most abundant proteins from 3,000-4,000 motor neuron cell bodies (not shown), and Zhu and coworkers have recently reported identifying 2,665 proteins from ~15,000 tumor cells1.&#160;With further developments of mass spectrometry, however, it is likely that such analyses will extend to far greater depth.&#160;
Here, we present a specific protocol used for LMD of motor neuron cell bodies from spinal cord of mice, followed by preparation of RNA.&#160;This protocol was used in the context of comparing RNAs from motor neurons of presymptomatic transgenic mutant superoxide dismutase (SOD)1 amyotrophic lateral sclerosis (ALS) mice with RNAs prepared from a wild-type SOD1 transgenic strain by both RNA-seq and qRT-PCR validation2.&#160;Notably, motor neurons, in the anterior horn of the gray matter in the spinal cord, comprise &#60;10% of the total cell population, surrounded by a sea of astrocytes, and as such, their transcriptional profile cannot be easily deconvoluted from studies of the entire cord.&#160;A laser capture approach is thus ideal for analyzing RNA expression in these cells, with physiology preserved by rapidly excising and freezing the cord following brief intracardiac saline perfusion.&#160;Motor neuron somata are large and are thus readily detectable, here using a dye that has strong affinity for neurons3.&#160;In addition, with such size, these cells provide a relatively large amount of RNA per cell captured.&#160;The procedure used, as detailed below, could be readily adjusted to obtain other neuronal cell types, as well as potentially other cell types, specifically identified either by dye staining techniques or by antibody staining.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr height="40">
			<td height="40" style="height:40px;width:268px;">Ketamine</td>
			<td style="width:195px;">Webster Veterinary</td>
			<td style="width:155px;">26637041101</td>
			<td style="width:339px;">Any source approved by the institutional veterinary service</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:268px;">Dissection tools (scissors, forceps,&#160;etc.)</td>
			<td></td>
			<td></td>
			<td style="width:339px;">Any convenient source of high-quality dissection instruments</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:268px;">Cryostat&#160;</td>
			<td>Leica Microsystem</td>
			<td>CM3050S</td>
			<td style="width:339px;">Other cryostats should be suitable</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:268px;">LMD6000 B</td>
			<td>Leica Microsystem</td>
			<td></td>
			<td style="width:339px;">Other LMD systems have not been tested</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:268px;">RNase-free PEN-membrane 2 &#956;m slides&#160;</td>
			<td>Leica Microsystem</td>
			<td>11505189</td>
			<td style="width:339px;">Other slide types have been tested and do not perform well</td>
		</tr>
		<tr height="60">
			<td height="60" style="height:60px;width:268px;">RNeasy Micro kit (50)</td>
			<td>Qiagen</td>
			<td>74004</td>
			<td style="width:339px;">Any kit that uses guanidine thiocyanate lysis buffer and has been tested for recovering small quantities of RNA can be used</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:268px;">Agilent 2100 BioAnalyzer</td>
			<td>Agilent Technologies</td>
			<td>G2939A</td>
			<td style="width:339px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:268px;">Azure B Certified&#160;</td>
			<td>MP Biomedicals</td>
			<td>190520</td>
			<td style="width:339px;">Critical! Product from any source has to be tested before use for its ability to maintain RNA integrity</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:268px;">PBS</td>
			<td>Sigma Life Science</td>
			<td>D8537</td>
			<td style="width:339px;">Any reliable source of RNase-free PBS</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:268px;">RNA Ethanol 70% (made with DEPC treated water)</td>
			<td>American Bioanalytical</td>
			<td>AB04010-00500</td>
			<td style="width:339px;">Any reliable source, can be lab-made</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:268px;">Water, RNase-free, Endotoxin tested (treated with DEPC to eliminate RNase)</td>
			<td>American Bioanalytical</td>
			<td>AB02128-00500</td>
			<td style="width:339px;">Any reliable source, can be lab-made</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:268px;">RNase AWAY</td>
			<td>Invitrogen Life Technologies</td>
			<td>10328-011</td>
			<td style="width:339px;">Other similar RNase removal reagents, such as RNaseZAP (also from Invitrogen) can be used</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:268px;">2-Methylbutane&#160;</td>
			<td>Electron Microscopy Sciences</td>
			<td>78-78-4</td>
			<td style="width:339px;">Any source</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:268px;">Maxymum Recovery microfuge tubes (0.6 and 1.5 ml) and pipette tips&#160;</td>
			<td>Axygen&#160;</td>
			<td>311-03-051 &#38; 311-09-051</td>
			<td style="width:339px;">Ultra-low retention, RNase free tubes and tips; test other manufacturer&#39;s products before using</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:268px;">O.C.T. Compound</td>
			<td>Tissue-Tek</td>
			<td>4583</td>
			<td style="width:339px;"></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:268px;">Cryomold Intermediate Size</td>
			<td>Tissue-Tek</td>
			<td>4566</td>
			<td style="width:339px;"></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:268px;">Lab wipes (Kimwipes)</td>
			<td>KIMTECH</td>
			<td>34155</td>
			<td style="width:339px;"></td>
		</tr>
	</tbody>
</table>

production of rna for transcriptomic analysis from mouse spinal cord motor neuron cell bodies by laser capture microdissection

Preparation of high-quality RNA from cells of interest is critical to precise and meaningful analysis of transcriptional differences among cell types or between the same cell type in health and disease or following pharmacologic treatments.&#160;In the spinal cord, such preparation from motor neurons, the target of interest in many neurologic and neurodegenerative diseases, is complicated by the fact that motor neurons represent &#60;10% of the total cell population.&#160;Laser capture microdissection (LMD) has been developed to address this problem.&#160;Here, we describe a protocol to quickly recover, freeze, and section mouse spinal cord to avoid RNA damage by endogenous and exogenous RNases, followed by staining with Azure B in 70% ethanol to identify the motor neurons while keeping endogenous RNase inhibited.&#160;LMD is then used to capture the stained neurons directly into guanidine thiocyanate lysis buffer, maintaining RNA integrity.&#160;Standard techniques are used to recover the total RNA and measure its integrity.&#160;This material can then be used for downstream analysis of the transcripts by RNA-seq and qRT-PCR.

The protocol outlined above and in Figure&#160;1 should produce 50 ng or more of total RNA with a RIN of &#62;8.5 from 3,000-4,000 spinal cord motor neuron cell bodies dissected from the 9-10 20&#160;&#181;m slices on about 20 PEN slides. Because this number of slides represents less than 10% of an O.C.T.-embedded block of a mouse spinal cord, it is possible to return to the block, which has been stored at -80 &#176;C, and cut more slices to go through another round of RNA preparation. If larger amounts of RNA are needed for an analysis, it is better to make only the number of slides (e.g.&#160;20) at one time that can be processed through dissection and RNA preparation in a few days, then make more slides for a second round and combine the products. Be sure to check the RIN of each preparation first to avoid combining a good one with a bad. RNA-seq methods are becoming more sensitive and new PCR technologies are promising higher sensitivity than current ones. Thus, less RNA from fewer neuron cell bodies will be required, allowing greater sequencing depth and more comprehensive validation of interesting hits. On the other hand, full adherence to the MIQE recommendations for qRT-PCR analysis and validation4 may require larger amounts to allow for the necessary control reactions for low-abundance RNAs.
Figure&#160;2 shows a typical series of images of a portion of a spinal cord ventral horn section after Azure B staining and dissection. In panel A, the large, darkly stained cell bodies are motor neurons, confirmed by anti-Chat antibody staining2, and are easily differentiated from smaller neighboring cells. Panel B shows the same region with individual cell bodies outlined with the light pen and numbered by the microscope software. The outlines closely follow the margins of the cell bodies, with a small allowance for the cutting width of the laser. This spacing has to be determined for each laser power setting to minimize the inclusion of extraneous material while avoiding loss of motor neuron cytosol. Panels C and D show the section after the laser has cut and the individual cell bodies have dropped into the collection cap. Notice that the cutting margin does not exactly follow the light pen outline in panel C, but does largely stay outside of it. This irregularity is apparent in panel D, as is the darkened area around each cut, which reflects the heat damage to the tissue caused by the laser. Because of this, if two cell bodies are very close to each other, it is better to outline them for a single cut, rather than trying to cut them separately and losing some RNA to heat damage at their region of near-contact.
Figure&#160;3 shows typical results of an electrophoretic analysis of the RNA integrity of a sample of RNA prepared from ~4,000 mouse motor neuron cell bodies collected by LMD. The upper panel is the electropherogram produced by 1 &#181;l of the total RNA; the inset at the right is an image of the gel. In both, note the prominent ribosomal RNA peaks. The lower panel is the electropherogram of the lane containing RNA size standards. The analysis software calculated an RIN of 9.8 for this sample, with a concentration of 4.9 ng/&#181;l. A total of 13 &#181;l of this solution was available after the analysis, providing 64 ng of RNA for downstream qRT-PCR validation of transcript amounts. For a typical qRT-PCR analysis of moderately abundant transcripts, 0.15-0.20 ng of total RNA is sufficient to produce accurate quantitation2, so the amount of RNA available from this preparation is sufficient to validate a number of transcripts with multiple primer sets, as recommended4. Of course, larger amounts of input RNA can be used to permit validation of rare transcripts. This amount is also more than sufficient to permit library preparation and next-generation RNA-seq.
<img alt="Figure 1" fo:content-width="5in" fo:src="/files/ftp_upload/51168/51168fig1highres.jpg" src="/files/ftp_upload/51168/51168fig1.jpg" /> 
Figure 1.&#160;Overview of spinal cord slice production and laser capture microdissection of spinal cord motor neuron cell bodies.&#160;A)&#160; Major steps in slice production and staining.&#160;B)&#160; Cartoon view of spinal cord section and laser dissection. <a href="https://www.jove.com/files/ftp_upload/51168/51168fig1highres.jpg" target="_blank">Click here to view larger image.</a>
<img alt="Figure 2" fo:content-width="5in" fo:src="/files/ftp_upload/51168/51168fig2highres.jpg" src="/files/ftp_upload/51168/51168fig2.jpg" /> 
Figure 2.&#160;Before-and-after images of a laser dissection of Azure B stained motor neuron cell bodies.&#160;A)&#160; A portion of the ventral horn of a stained section.&#160;Note the four large, darkly stained cells.&#160;There are also a few lightly stained and somewhat smaller cells, which are not motor neurons (confirmed by anti-Chat antibody staining; not shown, but see Bandyopadhyay2) and which will not be selected for dissection.&#160;The many small, dark spots are probably neuronal processes (dendrites and axons), but this has not been confirmed.&#160;B)&#160; The four cell bodies outlined with the light pen.&#160;Note that the outlines closely follow the margins of the cells, with a minimum distance between them.&#160;This spacing should be established empirically for each microscope and laser.&#160;The software numbers the individual neurons, which simplifies keeping track of how many have been collected.&#160;C and D)&#160; After the laser has cut and the pieces containing the cell bodies have dropped into the collection cap.&#160;Note that the hole left behind is somewhat larger than the outline and is irregular.&#160;This reflects the width of the laser beam and its slightly variable cutting efficiency depending on the local composition of the tissue.&#160;Also apparent is the rim of darkened tissue surrounding each hole due to local heating damage caused by the laser. 
<a href="https://www.jove.com/files/ftp_upload/51168/51168fig2highres.jpg" target="_blank">Click here to view larger image.</a>
<img alt="Figure 3" fo:content-width="5in" fo:src="/files/ftp_upload/51168/51168fig3highres.jpg" src="/files/ftp_upload/51168/51168fig3.jpg" /> 
Figure 3. Electrophoretic analysis of the integrity of RNA prepared from LMD samples. A) A 1 &#181;l aliquot of the RNA prepared from ~4,000 motor neuron cell bodies by the above protocol was analyzed by microcapillary electrophoresis on a microfluidics chip. The electropherogram is shown, with prominent ribosomal RNA peaks. On the right is an image of the gel itself. B) The electropherogram of the size standards is shown, with the corresponding gel lane to the right. The instrument software calculated a RIN of 9.8 for this sample and a concentration of 4.9 ng/&#181;l. <a href="https://www.jove.com/files/ftp_upload/51168/51168fig3highres.jpg" target="_blank">Click here to view larger image.</a>

Watch this Scientific Journal Video about Production of RNA for Transcriptomic Analysis from Mouse Spinal Cord Motor Neuron Cell Bodies by Laser Capture Microdissection at JoVE.com

Production of RNA for Transcriptomic Analysis from Mouse Spinal Cord Motor Neuron Cell Bodies by Laser Capture Microdissection

High-quality total RNA has been prepared from cell bodies of mouse spinal cord motor neurons by laser capture microdissection after staining spinal cord sections with Azure B in 70% ethanol.&#160;Sufficient RNA (~40-60 ng) is recovered from 3,000-4,000 motor neurons to allow downstream RNA analysis by RNA-seq and qRT-PCR.

Preparation of high-quality RNA from cells of interest is critical to precise and meaningful analysis of transcriptional differences among cell types or ...

production-rna-for-transcriptomic-analysis-from-mouse-spinal-cord

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Neuroscience

10.6K Views.  Yale School of Medicine. High-quality total RNA has been prepared from cell bodies of mouse spinal cord motor neurons by laser capture microdissection after staining spinal cord sections with Azure B in 70% ethanol. Sufficient RNA (~40-60 ng) is recovered from 3,000-4,000 motor neurons to allow downstream RNA analysis by RNA-seq and qRT-PCR.

Video: Production of RNA for Transcriptomic Analysis from Mouse Spinal Cord Motor Neuron Cell Bodies by Laser Capture Microdissection

Laser Capture Microdissection of Drosophila Peripheral Neurons

The dendritic arborization (da) neurons of the Drosophila peripheral nervous system (PNS) provide an excellent model system in which to investigate the molecular mechanisms underlying class-specific dendrite morphogenesis1,2. To facilitate molecular analyses of class-specific da neuron development, it is vital to obtain these cells in a pure population. Although a range of different cell, and tissue-specific RNA isolation techniques exist for Drosophila cells, including magnetic bead based cell purification3,4, Fluorescent Activated Cell Sorting (FACS)5-8, and RNA binding protein based strategies9, none of these methods can be readily utilized for isolating single or multiple class-specific Drosophila da neurons with a high degree of spatial precision. Laser Capture Microdissection (LCM) has emerged as an extremely powerful tool that can be used to isolate specific cell types from tissue sections with a high degree of spatial resolution and accuracy. RNA obtained from isolated cells can then be used for analyses including qRT-PCR and microarray expression profiling within a given cell type10-16. To date, LCM has not been widely applied in the analysis of Drosophila tissues and cells17,18, including da neurons at the third instar larval stage of development. 
Here we present our optimized protocol for isolation of Drosophila da neurons using the infrared (IR) class of LCM. This method allows for the capture of single, class-specific or multiple da neurons with high specificity and spatial resolution. Age-matched third instar larvae expressing a UAS-mCD8::GFP19 transgene under the control of either the class IV da neuron specific ppk-GAL420 driver or the pan-da neuron specific 21-7-GAL421 driver were used for these experiments. RNA obtained from the isolated da neurons is of very high quality and can be directly used for downstream applications, including qRT-PCR or microarray analyses. Furthermore, this LCM protocol can be readily adapted to capture other Drosophila cell types a various stages of development dependent upon the cell type specific, GAL4-driven expression pattern of GFP.

Laser Capture Microdissection of Drosophila Peripheral Neurons

In this video-article we present a method for isolating single or multiple Drosophila da neurons from third instar larvae using the infrared capture (IR) class of Laser Capture Microdissection (LCM). RNA obtained from the isolated neurons can be readily used for downstream applications including qRT-PCR or microarray analyses.

The dendritic arborization (da) neurons of the Drosophila peripheral nervous system (PNS) provide an excellent model system in which to investigate the ...

Non-Laser Capture Microscopy Approach for the Microdissection of Discrete Mouse Brain Regions for Total RNA Isolation and Downstream Next-Generation Sequencing and Gene Expression Profiling

As technological platforms, approaches such as next-generation sequencing, microarray, and qRT-PCR have great promise for expanding our understanding of the breadth of molecular regulation. Newer approaches such as high-resolution RNA sequencing (RNA-Seq)1 provides new and expansive information about tissue- or state-specific expression such as relative transcript levels, alternative splicing, and micro RNAs2-4. Prospects for employing the RNA-Seq method in comparative whole transcriptome profiling5 within discrete tissues or between phenotypically distinct groups of individuals affords new avenues for elucidating molecular mechanisms involved in both normal and abnormal physiological states. Recently, whole transcriptome profiling has been performed on human brain tissue, identifying gene expression differences associated with disease progression6. However, the use of next-generation sequencing has yet to be more widely integrated into mammalian studies.
Gene expression studies in mouse models have reported distinct profiles within various brain nuclei using laser capture microscopy (LCM) for sample excision7,8. While LCM affords sample collection with single-cell and discrete brain region precision, the relatively low total RNA yields from the LCM approach can be prohibitive to RNA-Seq and other profiling approaches in mouse brain tissues and may require sub-optimal sample amplification steps. Here, a protocol is presented for microdissection and total RNA extraction from discrete mouse brain regions. Set-diameter tissue corers are used to isolate 13 tissues from 750-&mu;m serial coronal sections of an individual mouse brain. Tissue micropunch samples are immediately frozen and archived. Total RNA is obtained from the samples using magnetic bead-enabled total RNA isolation technology. Resulting RNA samples have adequate yield and quality for use in downstream expression profiling. This microdissection strategy provides a viable option to existing sample collection strategies for obtaining total RNA from discrete brain regions, opening possibilities for new gene expression discoveries.

Non-Laser Capture Microscopy Approach for the Microdissection of Discrete Mouse Brain Regions for Total RNA Isolation and Downstream Next-Generation Sequencing and Gene Expression Profiling  |

RNA expression profiling of discrete mouse brain regions requires a precise and repeatable tissue collection strategy. A protocol that uses both coronal brain sectioning and tissue corer-assisted microdissection is described here. The yield and quality of total RNA obtained from the resulting samples confirms the utility of the outlined method.

As technological platforms, approaches such as next-generation sequencing, microarray, and qRT-PCR have great promise for expanding our understanding of ...

Laser Capture Microdissection of Enriched Populations of Neurons or Single Neurons for Gene Expression Analysis After Traumatic Brain Injury

Long-term cognitive disability after TBI is associated with injury-induced neurodegeneration in the hippocampus-a region in the medial temporal lobe that is critical for learning, memory and executive function.1,2 Hence our studies focus on gene expression analysis of specific neuronal populations in distinct subregions of the hippocampus. The technique of laser capture microdissection (LCM), introduced in 1996 by Emmert-Buck, et al.,3 has allowed for significant advances in gene expression analysis of single cells and enriched populations of cells from heterogeneous tissues such as the mammalian brain that contains thousands of functional cell types.4 We use LCM and a well established rat model of traumatic brain injury (TBI) to investigate the molecular mechanisms that underlie the pathogenesis of TBI. Following fluid-percussion TBI, brains are removed at pre-determined times post-injury, immediately frozen on dry ice, and prepared for sectioning in a cryostat. The rat brains can be embedded in OCT and sectioned immediately, or stored several months at -80 &deg;C before sectioning for laser capture microdissection. Additionally, we use LCM to study the effects of TBI on circadian rhythms. For this, we capture neurons from the suprachiasmatic nuclei that contain the master clock of the mammalian brain. Here, we demonstrate the use of LCM to obtain single identified neurons (injured and degenerating, Fluoro-Jade-positive, or uninjured, Fluoro-Jade-negative) and enriched populations of hippocampal neurons for subsequent gene expression analysis by real time PCR and/or whole-genome microarrays. These LCM-enabled studies have revealed that the selective vulnerability of anatomically distinct regions of the rat hippocampus are reflected in the different gene expression profiles of different populations of neurons obtained by LCM from these distinct regions. The results from our single-cell studies, where we compare the transcriptional profiles of dying and adjacent surviving hippocampal neurons, suggest the existence of a cell survival rheostat that regulates cell death and survival after TBI.

We describe how to use laser capture microdissection (LCM) to obtain enriched populations of hippocampal neurons or single neurons from frozen sections of the injured rat brain for subsequent gene expression analysis using quantitative real time PCR and/or whole-genome microarrays.

Long-term cognitive disability after TBI is associated with injury-induced neurodegeneration in the hippocampus-a region in the medial temporal lobe that ...

Laser Capture Microdissection of Neurons from Differentiated Human Neuroprogenitor Cells in Culture

Neuroprogenitor cells (NPCs) isolated from the human fetal brain were expanded under proliferative conditions in the presence of epidermal growth factor (EGF) and fibroblast growth factor (FGF) to provide an abundant supply of cells. NPCs were differentiated in the presence of a new combination of nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), dibutyryl cAMP (DBC) and retinoic acid on dishes coated with poly-L-lysine and mouse laminin to obtain neuron-rich cultures. NPCs were also differentiated in the absence of neurotrophins, DBC and retinoic acid and in the presence of ciliary neurotrophic factor (CNTF) to yield astrocyte-rich cultures. Differentiated NPCs were characterized by immunofluorescence staining for a panel of neuronal markers including NeuN, synapsin, acetylcholinesterase, synaptophysin and GAP43. Glial fibrillary acidic protein (GFAP) and STAT3, astrocyte markers, were detected in 10-15% of differentiated NPCs. To facilitate cell-type specific molecular characterization, laser capture microdissection was performed to isolate neurons cultured on polyethylene naphthalate (PEN) membrane slides. The methods described in this study provide valuable tools to advance our understanding of the molecular mechanism of neurodegeneration.

Human neuroprogenitor cells (NPCs) were expanded under proliferating conditions. NPCs were differentiated into neuron-rich cultures in the presence of a combination of neurotrophins. Neuronal markers were detected by immunofluorescence staining. To isolate a pure population of neurons, NPCs were differentiated on PEN membrane slides and laser capture microdissection was performed.

Neuroprogenitor cells (NPCs) isolated from the human fetal brain were expanded under proliferative conditions in the presence of epidermal growth factor ...

RNA-Seq Analysis of Differential Gene Expression in Electroporated Chick Embryonic Spinal Cord

In ovo electroporation of the chick neural tube is a fast and inexpensive method for identification of gene function during neural development. Genome wide analysis of differentially expressed transcripts after such an experimental manipulation has the potential to uncover an almost complete picture of the downstream effects caused by the transfected construct. This work describes a simple method for comparing transcriptomes from samples of transfected embryonic spinal cords comprising all steps between electroporation and identification of differentially expressed transcripts. The first stage consists of guidelines for electroporation and instructions for dissection of transfected spinal cord halves from HH23 embryos in ribonuclease-free environment and extraction of high-quality RNA samples suitable for transcriptome sequencing. The next stage is that of bioinformatic analysis with general guidelines for filtering and comparison of RNA-Seq datasets in the Galaxy public server, which eliminates the need of a local computational structure for small to medium scale experiments. The representative results show that the dissection methods generate high quality RNA samples and that the transcriptomes obtained from two control samples are essentially the same, an important requirement for detection of differential expression genes in experimental samples. Furthermore, one example is provided where experimental overexpression of a DNA construct can be visually verified after comparison with control samples. The application of this method may be a powerful tool to facilitate new discoveries on the function of neural factors involved in spinal cord early development.

This video shows the basic steps for performing whole transcriptome analysis on dissected chick embryonic spinal cord samples after transfection with in ovo electroporation.

In ovo electroporation of the chick neural tube is a fast and inexpensive method for identification of gene function during neural development. Genome ...

An Ex Vivo Laser-induced Spinal Cord Injury Model to Assess Mechanisms of Axonal Degeneration in Real-time

Injured CNS axons fail to regenerate and often retract away from the injury site. Axons spared from the initial injury may later undergo secondary axonal degeneration. Lack of growth cone formation, regeneration, and loss of additional myelinated axonal projections within the spinal cord greatly limits neurological recovery following injury. To assess how central myelinated axons of the spinal cord respond to injury, we developed an ex vivo living spinal cord model utilizing transgenic mice that express yellow fluorescent protein in axons and a focal and highly reproducible laser-induced spinal cord injury to document the fate of axons and myelin (lipophilic fluorescent dye Nile Red) over time using two-photon excitation time-lapse microscopy. Dynamic processes such as acute axonal injury, axonal retraction, and myelin degeneration are best studied in real-time. However, the non-focal nature of contusion-based injuries and movement artifacts encountered during in vivo spinal cord imaging make differentiating primary and secondary axonal injury responses using high resolution microscopy challenging. The ex vivo spinal cord model described here mimics several aspects of clinically relevant contusion/compression-induced axonal pathologies including axonal swelling, spheroid formation, axonal transection, and peri-axonal swelling providing a useful model to study these dynamic processes in real-time. Major advantages of this model are excellent spatiotemporal resolution that allows differentiation between the primary insult that directly injures axons and secondary injury mechanisms; controlled infusion of reagents directly to the perfusate bathing the cord; precise alterations of the environmental milieu (e.g., calcium, sodium ions, known contributors to axonal injury, but near impossible to manipulate in vivo); and murine models also offer an advantage as they provide an opportunity to visualize and manipulate genetically identified cell populations and subcellular structures. Here, we describe how to isolate and image the living spinal cord from mice to capture dynamics of acute axonal injury.

An Ex Vivo Laser-induced Spinal Cord Injury Model to Assess Mechanisms of Axonal Degeneration in Real-time

We present a protocol utilizing two-photon excitation time-lapse microscopy to simultaneously visualize the dynamics of axon and myelin injuries in real time. This proposed protocol permits studies of both intrinsic and extrinsic factors which can influence central myelinated axon fate after injury and contribute to permanent clinical disability.

Injured CNS axons fail to regenerate and often retract away from the injury site. Axons spared from the initial injury may later undergo secondary axonal ...

Zebrafish In Situ Spinal Cord Preparation for Electrophysiological Recordings from Spinal Sensory and Motor Neurons

Zebrafish, first introduced as a developmental model, have gained popularity in many other fields. The ease of rearing large numbers of rapidly developing organisms, combined with the embryonic optical clarity, served as initial compelling attributes of this model. Over the past two decades, the success of this model has been further propelled by its amenability to large-scale mutagenesis screens and by the ease of transgenesis. More recently, gene-editing approaches have extended the power of the model.
For neurodevelopmental studies, the zebrafish embryo and larva provide a model to which multiple methods can be applied. Here, we focus on methods that allow the study of an essential property of neurons, electrical excitability. Our preparation for the electrophysiological study of zebrafish spinal neurons involves the use of veterinarian suture glue to secure the preparation to a recording chamber. Alternative methods for recording from zebrafish embryos and larvae involve the attachment of the preparation to the chamber using a fine tungsten pin1,2,3,4,5. A tungsten pin is most often used to mount the preparation in a lateral orientation, although it has been used to mount larvae dorsal-side up4. The suture glue has been used to mount embryos and larvae in both orientations. Using the glue, a minimal dissection can be performed, allowing access to spinal neurons without the use of an enzymatic treatment, thereby avoiding any resultant damage. However, for larvae, it is necessary to apply a brief enzyme treatment to remove the muscle tissue surrounding the spinal cord. The methods described here have been used to study the intrinsic electrical properties of motor neurons, interneurons, and sensory neurons at several developmental stages6,7,8,9.

Zebrafish In Situ Spinal Cord Preparation for Electrophysiological Recordings from Spinal Sensory and Motor Neurons

This manuscript describes methods for electrophysiological recordings from spinal neurons of zebrafish embryos and larvae. The preparation maintains neurons in situ and often involves minimum dissection. These methods allow for the electrophysiological study of a variety of spinal neurons, from the initial electrical excitability acquisition through the early larval stages.

Zebrafish, first introduced as a developmental model, have gained popularity in many other fields. The ease of rearing large numbers of rapidly developing ...

Stereotactic Atlas-Guided Laser Capture Microdissection of Brain Regions Affected by Traumatic Injury

The ability to isolate specific brain regions of interest can be impeded in tissue disassociation techniques that do not preserve their spatial distribution. Such techniques also potentially skew gene expression analysis because the process itself can alter expression patterns in individual cells. Here we describe a laser capture microdissection (LCM) method to selectively collect specific brain regions affected by traumatic brain injury (TBI) by using a modified Nissl (cresyl violet) staining protocol and the guidance of a rat brain atlas. LCM provides access to brain regions in their native positions and the ability to use anatomical landmarks for identification of each specific region. To this end, LCM has been used previously to examine brain region specific gene expression in TBI. This protocol allows examination of TBI-induced alterations in gene and microRNA expression in distinct brain areas within the same animal. The principles of this protocol can be amended and applied to a wide range of studies examining genomic expression in other disease and/or animal models.

We describe the use of laser capture microdissection to obtain samples of distinct cell populations from different brain regions for gene and microRNA analysis. This technique allows the study of differential effects of traumatic brain injury in specific regions of the rat brain.

The ability to isolate specific brain regions of interest can be impeded in tissue disassociation techniques that do not preserve their spatial ...

Optimization of Laser-Capture Microdissection for the Isolation of Enteric Ganglia from Fresh-Frozen Human Tissue

The purpose of this method is to obtain high-integrity RNA samples from enteric ganglia collected from unfixed, freshly-resected human intestinal tissue using laser capture microdissection (LCM). We have identified five steps in the workflow that are crucial for obtaining RNA isolates from enteric ganglia with sufficiently high quality and quantity for RNA-seq. First, when preparing intestinal tissue, each sample must have all excess liquid removed by blotting prior to flattening the serosa as much as possible across the bottom of large base molds. Samples are then quickly frozen atop a slurry of dry ice and 2-methylbutane. Second, when sectioning the tissue, it is important to position cryomolds so that intestinal sections parallel the full plane of the myenteric plexus, thereby yielding the greatest surface area of enteric ganglia per slide. Third, during LCM, polyethylene napthalate (PEN)-membrane slides offer the greatest speed and flexibility in outlining the non-uniform shapes of enteric ganglia when collecting enteric ganglia. Fourth, for distinct visualization of enteric ganglia within sections, ethanol-compatible dyes, like Cresyl Violet, offer excellent preservation of RNA integrity relative to aqueous dyes. Finally, for the extraction of RNA from captured ganglia, we observed differences between commercial RNA extraction kits that yielded superior RNA quantity and quality, while eliminating DNA contamination. Optimization of these factors in the current protocol greatly accelerates the workflow and yields enteric ganglia samples with exceptional RNA quality and quantity.

The goal of this protocol is to obtain high-integrity RNA samples from enteric ganglia isolated from unfixed, freshly-resected human intestinal tissue using laser capture microdissection (LCM). This protocol involves preparing flash-frozen samples of human intestinal tissue, cryosectioning, ethanolic staining and dehydration, LCM, and RNA extraction.

The purpose of this method is to obtain high-integrity RNA samples from enteric ganglia collected from unfixed, freshly-resected human intestinal tissue ...

Isolation of Adult Spinal Cord Nuclei for Massively Parallel Single-nucleus RNA Sequencing

Probing an individual cell&#39;s gene expression enables the identification of cell type and cell state. Single-cell RNA sequencing has emerged as a powerful tool for studying transcriptional profiles of cells, particularly in heterogeneous tissues such as the central nervous system. However, dissociation methods required for single cell sequencing can lead to experimental changes in the gene expression and cell death. Furthermore, these methods are generally restricted to fresh tissue, thus limiting studies on archival and bio-bank material. Single nucleus RNA sequencing (snRNA-Seq) is an appealing alternative for transcriptional studies, given that it accurately identifies cell types, permits the study of tissue that is frozen or difficult to dissociate, and reduces dissociation-induced transcription. Here, we present a high-throughput protocol for rapid isolation of nuclei for downstream snRNA-Seq. This method enables isolation of nuclei from fresh or frozen spinal cord samples and can be combined with two massively parallel droplet encapsulation platforms.

Here, we present a protocol to rapidly isolate high-quality nuclei from the fresh or frozen tissue for downstream massively parallel RNA sequencing. We include detergent-mechanical and hypotonic-mechanical tissue disruption and cell lysis options, both of which can be used for isolation of nuclei.

Probing an individual cell&#39;s gene expression enables the identification of cell type and cell state. Single-cell RNA sequencing has emerged as a ...

Production of RNA for Transcriptomic Analysis from Mouse Spinal Cord Motor Neuron Cell Bodies by Laser Capture Microdissection

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Chapters in this video

Laser Capture Microdissection of Drosophila Peripheral Neurons

Non-Laser Capture Microscopy Approach for the Microdissection of Discrete Mouse Brain Regions for Total RNA Isolation and Downstream Next-Generation Sequencing and Gene Expression Profiling

Laser Capture Microdissection of Enriched Populations of Neurons or Single Neurons for Gene Expression Analysis After Traumatic Brain Injury

Laser Capture Microdissection of Neurons from Differentiated Human Neuroprogenitor Cells in Culture

RNA-Seq Analysis of Differential Gene Expression in Electroporated Chick Embryonic Spinal Cord

An Ex Vivo Laser-induced Spinal Cord Injury Model to Assess Mechanisms of Axonal Degeneration in Real-time

Zebrafish In Situ Spinal Cord Preparation for Electrophysiological Recordings from Spinal Sensory and Motor Neurons

Stereotactic Atlas-Guided Laser Capture Microdissection of Brain Regions Affected by Traumatic Injury

Optimization of Laser-Capture Microdissection for the Isolation of Enteric Ganglia from Fresh-Frozen Human Tissue

Isolation of Adult Spinal Cord Nuclei for Massively Parallel Single-nucleus RNA Sequencing