The authors would like to acknowledge Lynn Opdenaker at the University of Delaware Center for Translational Research at the Helen F. Graham Cancer Center for technical assistance, as well as Nancy Martin from the Duke University Cancer Institute Flow Cytometry Shared Resource, and Dr. Susan H. Smith for guidance in methods and data collection.

1. Preparation for Tissue Collection (15 &#8211; 30 min)
<ol>
	<li>Fire polish three sets of glass Pasteur pipettes in decreasing diameters and number them &#8220;1&#8221; = approximately 1 mm diameter, &#8220;2&#8221; = approximately 0.75 mm diameter, and &#8220;3&#8221; = approximately 0.50 mm diameter.</li>
	<li>Resuspend lyophilized Enzyme A with all of Buffer A according to the protocol provided with the Neural Dissociation Kit (see Table of Materials). Do not vortex. Aliquot the solution into 50 &#181;l&#160;aliquots and store at -20 &#186;C for later use.</li>
	<li>Make 1 L of myelin removal buffer and vacuum filter for sterilization [myelin removal buffer = 1,000 ml of 0.1 M phosphate-buffered saline (PBS), 2 ml of 500 mM Ethylenediaminetetraacetic acid (EDTA), and 10 g of Bovine Serum Albumin (BSA)].</li>
	<li>Cut nylon mesh sheet into small 1&#160; x 1 inch (2.5 x 2.5 cm) squares that will be used for filtering cellular debris and autoclave in a small beaker covered with aluminum foil.</li>
	<li>Prepare 1 L of wash buffer [wash buffer = 1,000 ml of 0.1 M PBS, 2 ml of 500 mM EDTA, and 10 g BSA].</li>
</ol>
2. Tissue Collection
<ol>
	<li>Turn on water bath to 37 &#186;C.</li>
	<li>Prepare Buffer X from the Neural Dissociation Kit by adding beta-mercaptoethanol to Buffer X to a final concentration of 0.067 mM (for 4 samples, add 13.5 &#181;l of 50 mM beta-mercaptoethanol to 10 ml of Buffer X).</li>
	<li>Prepare Enzyme Mix 1 by mixing 50 &#181;l of Enzyme P with 1,900 &#181;l of Buffer X for each sample as described in the protocol for the Neural Dissociation Kit For Example, for 4 samples, mix 200 &#181;l of Enzyme P with 7,600 &#181;l of Buffer X.</li>
	<li>Place Buffer X in the water bath at 37 &#186;C.</li>
	<li>Place 2 ml of cold Hank&#8217;s Buffered Salt Solution (HBSS) (without Ca++ and Mg++) into one well of a sterile 6-well culture plate for each sample that will be collected and keep on ice for tissue dissection.</li>
</ol>
3. Tissue Dissection (45 min &#8211; 1 hr)
<ol>
	<li>Inject the animal with appropriate volume of euthanasia solution (commercial barbiturate solution, e.g., Euthasol), according to Institutional Animal Care and Use Committee (IACUC) guidelines, and perfuse out all blood with cold 0.9% saline solution.
	<ol>
		<li>Administer Rats with an overdose of euthanasia solution.</li>
		<li>Monitor anesthesia via breathing and via toe-pinch. When the animal is sufficiently anesthetized (no response to the toe-pinch and deep, slow breathing), the rat can be perfused.</li>
		<li>To perfuse the rat, cut the chest cavity open with a pair of heavy-duty scissors. Cut the diaphragm to allow access up to the heart. Cut the ribs along both sides up to towards the top of the chest, to allow full access to the heart. At that point, the rib cage can be held off to the side using a pair of hemostats.</li>
		<li>Perform cardiac perfusion by inserting an 18 G needle (for adult rats) attached to an electric pump into the left ventricle of the heart. The pump is drawing up cold 0.9% saline solution.</li>
		<li>Then cut open the right atrium with a small pair of scissors to allow for the blood and liquid perfusate to drain from the body.</li>
		<li>Perfuse rats with approximately 10 ml (for adult rats) of 0.9% saline to remove all peripheral immune cells and factors.</li>
	</ol>
	</li>
	<li>Dissect the desired part of the brain region using sterile razor blades and appropriate dissection, then place the tissue pieces into the cold HBSS without Ca2+ and Mg2+. 
	NOTE: The protocol requires HBSS without Ca2+ and Mg2+ in the early steps of the protocol as these ions may interfere with the enzymes required for neural dissociation.</li>
	<li>After all tissue samples have been collected, return to the clean bench or sterile culture hood for tissue processing.</li>
</ol>
4. Neural Dissociation (1 hr)
<ol>
	<li>Dice each tissue sample into small pieces using sterile razor blades on the lid of the 6-well culture plate. This protocol has been used for tissue samples of approximately 30 - 100 mg, but is approved for tissue samples of up to 400 mg. For tissue samples larger than 400 mg, the reagent volumes must be scaled up appropriately.</li>
	<li>Use 1 ml of fresh HBSS without Ca2+ and Mg2+ to transfer the diced pieces of tissue with a pipette into a sterile 2 ml centrifuge tube. Repeat steps 4.1 and 4.2 for all sample until all samples have been transferred into a 2ml centrifuge tube.</li>
	<li>Centrifuge the samples at 300 x g for 2 min at RT and aspirate supernatant.</li>
	<li>Add 1,900 &#181;l of warm Enzyme Mix 1, as prepared in Steps 2.2 and 2.3, to each sample and close the tubes.</li>
	<li>Incubate the samples for 15 min in the 37 &#186;C water bath, inverting the tubes several times every 5 min to re-suspend the settled pieces of tissue.</li>
	<li>Meanwhile, prepare Enzyme Mix 2 by mixing 20 &#181;l of Buffer Y with 10 &#181;l of thawed Enzyme A (for 4 samples, mix 80 &#181;l of Buffer Y with 40 &#181;l of thawed Enzyme A).</li>
	<li>Add 30 &#181;l of Enzyme Mix 2 to each sample and invert gently. Do not vortex.</li>
	<li>Dissociate each tissue sample with Pasteur pipette &#8220;1&#8221;, triturating up and down 30 times.</li>
	<li>Incubate the samples for 15 min in the 37 &#186;C water bath; invert the tubes several times every 5 min to re-suspend the settled pieces of tissue.</li>
	<li>Dissociate each tissue sample with Pasteur pipette &#8220;2&#8221;, triturating up and down 30 times. Avoid generating bubbles.</li>
	<li>Dissociate each tissue sample with Pasteur pipette &#8220;3&#8221;, triturating up and down 30 times. Avoid generating bubbles.</li>
	<li>Incubate the samples for 10 min in the 37 &#186;C water bath; invert the tubes several times every 5 min to re-suspend the settled cells.</li>
	<li>Apply single-cell suspension to an 80 micron cell strain placed on top of a 15 ml falcon tube to remove any large pieces of debris and wash the filter and cells with 10 ml of HBSS (with Ca2+ and Mg2+) to stop the enzyme reactions. Repeat until each sample is transferred into a clean 15 ml falcon tube.</li>
	<li>Centrifuge the samples at 300 x g for 10 min at RT and aspirate off the supernatant.</li>
</ol>
5. Myelin Depletion (45 min)
<ol>
	<li>Thoroughly re-suspend the pellet of cells with 400 &#181;l of myelin removal buffer.</li>
	<li>Add specified amount of the myelin removal beads and pipette up and down to thoroughly mix. 
	NOTE: The volume of myelin removal beads that is used will depend upon the size of the tissue, the age of the animal, and the amount of myelin expected in that particular brain region. e.g.,&#160;for an adult rat hippocampus sample (approximately 300 mg), incubate the sample with 100 &#181;l of myelin removal beads.
	
	</li>
	<li>Incubate for 15 min in the refrigerator at 4 &#186;C.</li>
	<li>Wash each sample with 5 ml of myelin removal buffer.</li>
	<li>Centrifuge the samples at 300 x g for 10 min at RT.</li>
	<li>While centrifuging the samples, place 1 column for each sample in the magnetic field of the magnetic sorter and place a clean 80 micron filter on top of each column.</li>
	<li>Prepare the columns and filter by rinsing each column with 1 ml of myelin removal buffer, 3 times (3 ml total). Collect all flow-through in a waste container such as the bottom of an empty tip box.</li>
	<li>Position 5 ml polystyrene round bottom tube directly underneath each column in preparation of sample collection.</li>
	<li>When cells have finished centrifugation, aspirate supernatant and thoroughly re-suspend in 500 &#181;l of myelin removal buffer. Immediately apply cell suspension to the column and collect the cells in the tube below.</li>
	<li>Wash the filter and column with 1 ml myelin removal buffer, 4 times (4 ml total).</li>
	<li>Centrifuge the cell collection at 300 x g for 10 min at RT.</li>
	<li>Aspirate the supernatant and the cells are now ready for staining.</li>
</ol>
6. Staining Live Cells for FACS (1 hr for staining)
<ol>
	<li>Briefly vortex (2 sec) the cells to separate the pellet and immediately add 5 &#181;l of Fc block (anti- clusters of differentiation 32, CD32), vortex again, and incubate in the refrigerator at 4 &#186;C for 5 min.</li>
	<li>Meanwhile, prepare the primary antibody mixture by adding the three primary antibodies in wash buffer as follows: 0.125 &#181;l of allophycocyanin (APC) -conjugated CD11b antibody (1:800), 1 &#181;l of anti-GLT1 antibody (1:100), and 0.4 &#181;l of Fluorescein isothiocyanate (FITC) &#8211; conjugated Thy1 antibody (1:250) for every 100 &#181;l of wash buffer. Each sample will receive 100 &#181;l of primary antibody mixture for incubation; however, if your sample is much larger than 400 mg of tissue, you may want to consider increasing the volume of your primary antibody mixture accordingly</li>
	<li>Prepare tubes for single staining controls by removing just 2 &#181;l of cells from each sample tube and adding it to each single stain control tube. The &#8220;single stain&#8221; controls include: APC-CD11b only, GLT1 only, FITC-Thy1 only, PE secondary antibody only, and the &#8220;blank&#8221; or unstained control. 
	NOTE: All samples should be represented in all staining controls, thus 2 &#181;l of cells from each sample should be added to each staining control tube.</li>
	<li>Briefly vortex the tubes (2 sec) and add 100 &#181;l of primary antibody mixture to each sample tube and 100 &#181;l of appropriate primary antibody to each staining control tube, vortex the tubes again, cover the tubes with aluminum foil to protect the fluorescent antibodies from any light, and incubate the tubes in the refrigerator at 4 &#186;C for 20 min. The samples should be kept cool (at 4 &#186;C) for the remainder of the procedure to maintain the integrity of the samples and the antibodies.</li>
	<li>Briefly vortex the tubes and add 2 ml of wash buffer to each tube.</li>
	<li>Centrifuge tubes at 350 x g for 5 min at 4 &#186;C.</li>
	<li>Meanwhile, prepare the secondary antibody mixture by adding 0.2 &#181;l of PE-conjugated anti-rabbit secondary antibody for every 100 &#181;l of wash buffer. Each sample will get 100 &#181;l of secondary antibody mixture; however, if your sample is much larger than 400 mg of tissue, you may want to consider increasing the volume of your primary antibody mixture accordingly.</li>
	<li>When the centrifugation is complete, dump the supernatant off of each sample into the sink and blot the tubes upside-down on a paper towel.</li>
	<li>Briefly vortex the tubes and add 100 &#181;l of secondary antibody mixture to each sample tube and the appropriate secondary antibody to each staining control, vortex the tubes again, cover the tubes with aluminum foil, and incubate the tubes in the refrigerator at 4 &#186;C for 15 min. 
	NOTE: The GLT1-only staining control tube should get the secondary antibody mixture.
	
	</li>
	<li>After the incubation, briefly vortex the tubes and add 2 ml of wash buffer to each tube.</li>
	<li>Centrifuge the tubes at 350 x g for 5 min at 4 &#186;C.</li>
	<li>When the centrifugation is complete, dump the supernatant off of each sample into the sink and blot the tubes upside-down on a paper towel.</li>
	<li>Vortex the tubes and add 0.25 ml of sterile PBS to each tube. The samples are ready for sorting. 
	NOTE: More cells may require 0.5 ml of sterile PBS; however it is best to begin with a lower volume as the sample can always be diluted if it is too concentrated with cells. 
	NOTE: Optionally add DNase to the tube to prevent clumping of the cells and thus clogging of the sorter. Samples can also be filtered using a sterile 80 micron filter just prior to sorting in order to avoid clogging the sorter.
	
	</li>
	<li>Take cells to the sorter on ice. Collect the cell populations in 2 ml nuclease-free centrifuge tubes with 0.5 ml of sterile PBS in each tube.</li>
	<li>After the sort, spin the cells down at 300 x g for 2 min at 4 &#186;C. Aspirate off most of the PBS and flash freeze the cells in the -80 &#186;C freezer until further processing for either RNA extraction (see 1 for further protocol details), DNA extraction (see 2 for further protocol details) or cell lysis for protein analysis.</li>
</ol>

<ol>
	<li>Schwarz, J. M., Smith, S. H., Bilbo, S. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=FACS+analysis+of+neuronal-glial+interactions+in+the+nucleus+accumbens+following+morphine+administration.">FACS analysis of neuronal-glial interactions in the nucleus accumbens following morphine administration.</a> Psychopharmacology. 230 (4), 525-535 (2013).</li><li>Schwarz, J. M., Hutchinson, M. R., Bilbo, S. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Early-life+experience+decreases+drug-induced+reinstatement+of+morphine+CPP+in+adulthood+via+microglial-specific+epigenetic+programming+of+anti-inflammatory+IL-10+expression.">Early-life experience decreases drug-induced reinstatement of morphine CPP in adulthood via microglial-specific epigenetic programming of anti-inflammatory IL-10 expression.</a> J Neurosci. 31 (49), 17835-1523 (2011).</li><li>Herzenberg, L. A., Tung, J., Moore, W. A., Herzenberg, L. A., Parks, D. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Interpreting+flow+cytometry+data:+a+guide+for+the+perplexed.">Interpreting flow cytometry data: a guide for the perplexed.</a> Nature Immunology. 7 (7), 681-685 (2006).</li><li>Guez-Barber, 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=FACS+identifies+unique+cocaine-induced+gene+regulation+in+selectively+activated+adult+striatal+neurons.">FACS identifies unique cocaine-induced gene regulation in selectively activated adult striatal neurons.</a> J Neurosci. 31 (11), 4251-4259 (2011).</li><li>Fanous, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Unique+gene+alterations+are+induced+in+FACS-purified+Fos-positive+neurons+activated+during+cue-induced+relapse+to+heroin+seeking.">Unique gene alterations are induced in FACS-purified Fos-positive neurons activated during cue-induced relapse to heroin seeking.</a> J Neurochem. 124 (1), 100-108 (2013).</li><li>Liu, Q. R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Detection+of+molecular+alterations+in+methamphetamine-activated+Fos-expressing+neurons+from+single+rat+dorsal+striatum+using+fluorescence-activated+cell+sorting+(FACS).">Detection of molecular alterations in methamphetamine-activated Fos-expressing neurons from single rat dorsal striatum using fluorescence-activated cell sorting (FACS).</a> J Neurochem. 128 (1), 173-185 (2013).</li><li>Guez-Barber, 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=FACS+purification+of+immunolabeled+cell+types+from+adult+rat+brain.">FACS purification of immunolabeled cell types from adult rat brain.</a> J Neurosci Methods. 203 (1), 10-18 (2012).</li><li>Nolte, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=GFAP+promoter-controlled+EGFP-expressing+transgenic+mice:+a+tool+to+visualize+astrocytes+and+astrogliosis+in+living+brain+tissue.">GFAP promoter-controlled EGFP-expressing transgenic mice: a tool to visualize astrocytes and astrogliosis in living brain tissue.</a> Glia. 33 (1), 72-86 (2000).</li><li>Okana, M., Bell, D. W., Haber, D. A., Li, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+methyltransferases+Dnmt3a+and+Dnmt3b+are+essential+for+de+novo+methylation+and+mammalian+development.">DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development.</a> Cell. 99 (3), 247-257 (1999).</li><li>Bogdanovi&#263;, O., Veenstra, G. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+methylation+and+methyl-CpG+binding+proteins:+developmental+requirements+and+function.">DNA methylation and methyl-CpG binding proteins: developmental requirements and function.</a> Chromosoma. 118 (5), 549-565 (2009).</li><li>Iwamoto, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neurons+show+distinctive+DNA+methylation+profile+and+higher+inter-individual+variations+compared+with+non-neurons.">Neurons show distinctive DNA methylation profile and higher inter-individual variations compared with non-neurons.</a> Genome Res. 21 (5), 688-696 (2011).</li><li>Nishioka, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neuronal+cell-type+specific+DNA+methylation+patterns+of+the+Cacna1c+gene.">Neuronal cell-type specific DNA methylation patterns of the Cacna1c gene.</a> Int J Dev Neurosci. 31 (2), 89-95 (2013).</li><li>Kozlenkov, 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=Differences+in+DNA+methylation+between+human+neuronal+and+glial+cells+are+concentrated+in+enhancers+and+non-CpG+sites.">Differences in DNA methylation between human neuronal and glial cells are concentrated in enhancers and non-CpG sites.</a> Nucleic Acid Res. 42 (1), 109-127 (2014).</li><li>Russo, S. 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=Nuclear+factor+kappa+B+signaling+regulates+neuronal+morphology+and+cocaine+reward.">Nuclear factor kappa B signaling regulates neuronal morphology and cocaine reward.</a> J Neurosci. 29 (11), 3529-3537 (2009).</li><li>Bhatt, D., Ghosh, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regulation+of+the+NF-&#954;B-Mediated+Transcription+of+Inflammatory+Genes.">Regulation of the NF-&#954;B-Mediated Transcription of Inflammatory Genes.</a> Front Immunol. 5, 71 (2014).</li><li>Okada, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Flow+cytometric+sorting+of+neuronal+and+glial+nuclei+from+central+nervous+system+tissue.">Flow cytometric sorting of neuronal and glial nuclei from central nervous system tissue.</a> J Cell Physiol. 226 (2), 552-558 (2011).</li></ol>

The authors declare that they have no competing financial interests.

Similar to many other tissues and systems, the brain is comprised of a heterogeneous cell population that functions together to impact behavior. The analysis of gene expression, protein expression, or epigenetic modifications from individual cells within that heterogeneous population has the potential to reveal information about the function of the system as a whole, to identify cellular processes regulating both normal behavior and disease processes, and to provide cell-type-specific targets for potential therapies. It ...

The purpose of the protocol described below is to isolate individual cell types from a heterogeneous population of neural tissue for the subsequent analysis of cell-type-specific gene expression, protein expression, or even epigenetic markers. The brain is comprised of many cell types that are derived from distinct progenitor cells and that have cell-type-specific properties and functions. Despite these differences, these distinct neural cell types can express similar receptors and intracellular signaling molecules which make the analysis of these more ubiquitous proteins difficult to measure or interpret in a cell-type-specific manner using conventional methods. Neuroscientists must identify the function and activation of these distinct cell types in the brain and how they can individually impact behavior as this will ultimately be the first step to identifying more specific drugs and therapeutic targets for neurological and neuropsychiatric diseases. Despite this overarching goal of neuroscience research, it can been difficult to isolate individual neural cell types from the brain for the analysis of gene or protein expression, the activation of signaling molecules, or the modification of epigenetic markers on DNA. Of the techniques that are currently used, immunohistochemistry can identify the expression of proteins in a cell-type-specific manner when combined with additional staining of a cell-type-specific marker, though this relies on specific antibodies that can properly stain for the proteins of interest and it can be difficult to quantify. In situ hybridization can identify the specific localization of messenger ribonucleic acid (mRNA) in individual cells in the brain, but this is a laborious process that also limits the co-analysis of specific cell types and only allows for the analysis of one or maybe a few genes of interest. Laser capture micro-dissection uses a laser to isolate subpopulations of cells that are visualized via microscopy; however the time-consuming nature of this process and the relatively low yield can significantly limit the subsequent analysis of proteins or mRNA levels, particularly if the expression of these molecules is low to begin with. Fluorescence activated cell sorting (FACS) is a relatively novel technique in the field of neuroscience to isolate individual cell types from the brain for subsequent analysis of gene expression1 and/or epigenetic targets2. This process can also be used to sort specific types of neural cells for subsequent analysis of cell-type-specific gene expression, protein expression, or epigenetic markers. FACS has been used in a number of medical research fields such as cancer and immunology for decades to count and sort different cells based on either physical or biochemical characteristics3. In addition, flow cytometry has classically been used to analyze protein expression on a per cell basis, using specific antibodies. The procedure described below, takes advantage of classical flow cytometry techniques to isolate individual cell types for subsequent analysis of molecular biology endpoints. The flow cytometer can analyze several thousand cells in a second, which makes it a quick and efficient alternative to the techniques described above. In addition, cells can be isolated based on the cellular expression of a specific protein (for example a neurotransmitter receptor) or a combination of two or more proteins (colocalization of multiple proteins in a specific cell type). This allows the user to isolate very selective neural cell types based on their molecular properties to identify their function in the brain.
To perform FACS, neural cells are prepared into a single-cell suspension which is passed through a flow cell that carries and aligns the cells so that they pass single-file through a light beam and lasers for analysis. A computer acquires the data from each cell and plots it on a histogram for analysis of specified parameters (size, granularity, and fluorescence). Based on these parameters, the cells can immediately be sorted into separate tubes for their recollection and subsequent analysis of any endpoint desired. The protocol described below utilizes three antibodies to sort neurons (using a Thymocyte antigen 1, Thy1 antibody), astrocytes (using a glial glutamate transporter, GLT1 antibody), and microglia (using a cluster of differentiation molecule 11B, CD11b antibody). This protocol can be used as described below or modified with different antibodies depending on the cell type that one would like to isolate for his own experiments.
There are a few caveats to consider when determining whether this protocol is appropriate for specific experiments. One major caveat may concern the specific cell type that one would like to isolate. In this protocol, the three antibodies that are used are extracellular antibodies, which allow the experimenter to keep the cell types intact during the staining procedure, thus preserving the integrity of the RNA, DNA and proteins inside. It is possible that one may wish to isolate a specific neural cell type using an antibody that identifies a protein that is only expressed inside that particular cell. For example, one might want to isolate dopaminergic neurons using an antibody to tyrosine hydroxylase or isolate acetylcholine neurons using an antibody for choline acetyltransferase. These proteins are intracellular and thus would require fixation and permeabilization of the cell membrane for subsequent staining with the appropriate antibodies. While this has been done before 4,5, this process may significantly decrease the yield of RNA or DNA from these permeabilized cells. Another caveat may be that not all antibodies are appropriate for FACS. For example, one may currently use an antibody that works very well for western blot, a technique that requires the denaturation of proteins. This antibody may not necessarily be suitable for identification of these cell types using FACS given that the proteins are not denatured at any point in this protocol and thus the antibody may have no way to bind to its inherent antigen. Companies provide specification sheets which identify the applications for which an antibody has been approved. If an antibody has not been approved for flow cytometry, it should not discourage one from trying this protocol with a particular antibody; however, one should be aware that it isn&#8217;t guaranteed to work for FACS. A third caveat of this protocol has to do with the number of cells that one is trying to isolate. FACS is an excellent technique to yield the most cells possible from even a small piece of tissue, but it is also possible that if one would like to isolate a relatively sparse population of cells from a relatively small brain region, the yield from one animal will be inherently low. In this case, it may be necessary to pool the brain tissue from a few animals in the same treatment group in order to yield the number of cells necessary for subsequent analysis; however, a recent publication has used gene-targeted pre-amplification of cDNA for subsequent analysis of gene expression from a small number of activated neurons (5-6%) from a larger set sorted neurons, indicating that it is possible to analyze gene expression from even small subsets of neural cells without pooling large numbers of animals6A final caveat of this technique is that one should have access to a cell sorter that is not too far away. The cell sorter is a complicated machine that requires significant training in order to use it properly. Thus these machines are often run by a qualified technician in a core facility. In addition, the goal of this procedure is to dissociate the neural tissue, stain it for specific antibodies, and immediately take those samples to a sorter within a short period of time (perhaps a half day). This timeframe will help to increase the survival and yield of isolated cells and maintain the integrity of the cells for subsequent processing and analysis. If all of these parameters described above are met, FACS is an excellent method to analyze cell-type specific expression of genes and proteins from neural tissue.
All experiments were performed in accordance with the Institutional Animal Care and Use Committee (IACUC) of the University of Delaware and the National Institutes of Health Guide for the Care and Use of Laboratory Animals.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>Neural Dissociation Kit (P)</td>
			<td>Miltenyi Biotec</td>
			<td>130-092-628</td>
			<td></td>
		</tr>
		<tr>
			<td>Myelin Removal Beads II</td>
			<td>Miltenyi Biotec</td>
			<td>130-096-733</td>
			<td></td>
		</tr>
		<tr>
			<td>LS Columns</td>
			<td>Miltenyi Biotec</td>
			<td>130-042-401</td>
			<td></td>
		</tr>
		<tr>
			<td>QuadroMACS Separator</td>
			<td>Miltenyi Biotec</td>
			<td>130-090-976</td>
			<td></td>
		</tr>
		<tr>
			<td>MACS MultiStand</td>
			<td>Miltenyi Biotec</td>
			<td>130-042-303</td>
			<td></td>
		</tr>
		<tr>
			<td>Nylon Mesh Sheet</td>
			<td>Amazon</td>
			<td>CMN-0074-10YD</td>
			<td>40 inch width, 80 micron size mesh</td>
		</tr>
		<tr>
			<td>Fc Block / anti-CD32</td>
			<td>BD Biosciences</td>
			<td>BDB550270</td>
			<td>reactivity for rat</td>
		</tr>
		<tr>
			<td>APC-conjugated CD11b antibody</td>
			<td>Biolegend</td>
			<td>201809</td>
			<td>reactivity for rat</td>
		</tr>
		<tr>
			<td>Rabbit anti-GLT1</td>
			<td>Novus Biologicals</td>
			<td>NBP1-20136</td>
			<td>reactivity for rat or human</td>
		</tr>
		<tr>
			<td>PE-conjugated anti-rabbit secondary antibody</td>
			<td>eBioscience</td>
			<td>1037259</td>
			<td>secondary antibody for anti-GLT1</td>
		</tr>
		<tr>
			<td>FITC-conjugated anti-rat CD90 (Thy1) mouse antibody</td>
			<td>Biolegend</td>
			<td>202504</td>
			<td>reactivity for rat</td>
		</tr>
	</tbody>
</table>

using fluorescence activated cell sorting to examine cell-type-specific gene expression in rat brain tissue

The brain is comprised of four primary cell types including neurons, astrocytes, microglia and oligodendrocytes. Though they are not the most abundant cell type in the brain, neurons are the most widely studied of these cell types given their direct role in impacting behaviors. Other cell types in the brain also impact neuronal function and behavior via the signaling molecules they produce. Neuroscientists must understand the interactions between the cell types in the brain to better understand how these interactions impact neural function and disease. To date, the most common method of analyzing protein or gene expression utilizes the homogenization of whole tissue samples, usually with blood, and without regard for cell type. This approach is an informative approach for examining general changes in gene or protein expression that may influence neural function and behavior; however, this method of analysis does not lend itself to a greater understanding of cell-type-specific gene expression and the effect of cell-to-cell communication on neural function. Analysis of behavioral epigenetics has been an area of growing focus which examines how modifications of the deoxyribonucleic acid (DNA) structure impact long-term gene expression and behavior; however, this information may only be relevant if analyzed in a cell-type-specific manner given the differential lineage and thus epigenetic markers that may be present on certain genes of individual neural cell types. The Fluorescence Activated Cell Sorting (FACS) technique described below provides a simple and effective way to isolate individual neural cells for the subsequent analysis of gene expression, protein expression, or epigenetic modifications of DNA. This technique can also be modified to isolate more specific neural cell types in the brain for subsequent cell-type-specific analysis.

The Importance of Myelin Depletion and Tissue Perfusion
Figure 1 depicts the importance of myelin depletion. Myelin depletion (Steps 5.1 through 5.12 of the protocol above) occurs when the single-cell suspension is incubated in the Myelin Removal Beads, washed, and subsequently passed through the column on the magnetic sorter. The purpose of these steps is to reduce the amount of cellular debris present in each sample. As neurons are dissociated and triturated, it can shear of...

Watch this Scientific Journal Video about Using Fluorescence Activated Cell Sorting to Examine Cell-Type-Specific Gene Expression in Rat Brain Tissue at JoVE.com

Using Fluorescence Activated Cell Sorting to Examine Cell-Type-Specific Gene Expression in Rat Brain Tissue

The goal of this protocol is to use the fluorescence activated cell sorting (FACS) technique to sort specific types of neural cells for subsequent analysis of cell-type-specific gene expression, epigenetic markers, and or protein expression.

The brain is comprised of four primary cell types including neurons, astrocytes, microglia and oligodendrocytes. Though they are not the most abundant ...

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Research

JoVE Journal

Neuroscience

16.8K Views.  University of Delaware. The goal of this protocol is to use the fluorescence activated cell sorting (FACS) technique to sort specific types of neural cells for subsequent analysis of cell-type-specific gene expression, epigenetic markers, and or protein expression.

Video: Using Fluorescence Activated Cell Sorting to Examine Cell-Type-Specific Gene Expression in Rat Brain Tissue

Spinal Cord Electrophysiology II: Extracellular Suction Electrode Fabrication

Development of neural circuitries and locomotion can be studied using neonatal rodent spinal cord central pattern generator (CPG) behavior. We demonstrate a method to fabricate suction electrodes that are used to examine CPG activity, or fictive locomotion, in dissected rodent spinal cords. The rodent spinal cords are placed in artificial cerebrospinal fluid and the ventral roots are drawn into the suction electrode. The electrode is constructed by modifying a commercially available suction electrode. A heavier silver wire is used instead of the standard wire given by the commercially available electrode. The glass tip on the commercial electrode is replaced with a plastic tip for increased durability. We prepare hand drawn electrodes and electrodes made from specific sizes of tubing, allowing consistency and reproducibility. Data is collected using an amplifier and neurogram acquisition software. Recordings are performed on an air table within a Faraday cage to prevent mechanical and electrical interference, respectively.

A demonstration of the fabrication and use of an extracellular suction electrode used to measure electrophysiological recordings of neonatal rodent spinal cords in vitro

Development of neural circuitries and locomotion can be studied using neonatal rodent spinal cord central pattern generator (CPG) behavior. We demonstrate ...

GABA-activated Single-channel and Tonic Currents in Rat Brain Slices

The GABAA channels are present in all neurons and are located both at synapses and outside of synapses where they generate phasic and tonic currents, respectively 4,5,6,7 The GABAA channel is a pentameric GABA-gated chloride channel. The channel subunits are grouped into 8 families (&alpha;1-6, &beta;1-3, &gamma;1-3, &delta;, &#949;, &theta;, &pi; and &rho;). Two alphas, two betas and one 3rd subunit form the functional channel 8. By combining studies of sub-type specific GABA-activated single-channel molecules with studies including all populations of GABAA channels in the neuron it becomes possible to understand the basic mechanism of neuronal inhibition and how it is modulated by pharmacological agents.
We use the patch-clamp technique 9,10 to study the functional properties of the GABAA channels in alive neurons in hippocampal brain slices and record the single-channel and whole-cell currents. We further examine how the channels are affected by different GABA concentrations, other drugs and intra and extracellular factors. For detailed theoretical and practical description of the patch-clamp method please see The Single-Channel Recordings edited by B Sakman and E Neher 10.

We use the patch-clamp technique to measure GABA-activated single-channel currents (GABAA channels, GABAA receptors) and the synaptic and tonic currents they generate in neurons. Activation of the channels decreases neuronal excitability in health and disease 1,2,3,4.

The GABAA channels are present in all neurons and are located both at synapses and outside of synapses where they generate phasic and tonic currents, ...

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

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

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

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

Micromanipulation of Gene Expression in the Adult Zebrafish Brain Using Cerebroventricular Microinjection of Morpholino Oligonucleotides

Manipulation of gene expression in tissues is required to perform functional studies. In this paper, we demonstrate the cerebroventricular microinjection (CVMI) technique as a means to modulate gene expression in the adult zebrafish brain. By using CVMI, substances can be administered into the cerebroventricular fluid and be thoroughly distributed along the rostrocaudal axis of the brain. We particularly focus on the use of antisense morpholino oligonucleotides, which are potent tools for knocking down gene expression in vivo. In our method, when applied, morpholino molecules are taken up by the cells lining the ventricular surface. These cells include the radial glial cells, which act as neurogenic progenitors. Therefore, knocking down gene expression in the radial glial cells is of utmost importance to analyze the widespread neurogenesis response in zebrafish, and also would provide insight into how vertebrates could sustain adult neurogenesis response. Such an understanding would also help the efforts for clinical applications in human neurodegenerative disorders and central nervous system regeneration. Thus, we present the cerebroventricular microinjection method as a quick and efficient way to alter gene expression and neurogenesis response in the adult zebrafish forebrain. We also provide troubleshooting tips and other useful information on how to carry out the CVMI procedure.

In this article, we demonstrate a method for manipulation of gene expression in the ventricular cells of the adult zebrafish telencephalon using antisense morpholino oligonucleotides. We present this method as an efficient and quick protocol that can be used for functional studies in the adult vertebrate brain.

Manipulation of gene expression in tissues is  required to perform functional studies. In this paper, we demonstrate the  cerebroventricular ...

Analysis of Gene Expression Changes in the Rat Hippocampus After Deep Brain Stimulation of the Anterior Thalamic Nucleus

Deep brain stimulation (DBS) surgery, targeting various regions of the brain such as the basal ganglia, thalamus, and subthalamic regions, is an effective treatment for several movement disorders that have failed to respond to medication. Recent progress in the field of DBS surgery has begun to extend the application of this surgical technique to other conditions as diverse as morbid obesity, depression and obsessive compulsive disorder. Despite these expanding indications, little is known about the underlying physiological mechanisms that facilitate the beneficial effects of DBS surgery. One approach to this question is to perform gene expression analysis in neurons that receive the electrical stimulation. Previous studies have shown that neurogenesis in the rat dentate gyrus is elicited in DBS targeting of the anterior nucleus of the thalamus1. DBS surgery targeting the ATN is used widely for treatment refractory epilepsy. It is thus of much interest for us to explore the transcriptional changes induced by electrically stimulating the ATN. In this manuscript, we describe our methodologies for stereotactically-guided DBS surgery targeting the ATN in adult male Wistar rats. We also discuss the subsequent steps for tissue dissection, RNA isolation, cDNA preparation and quantitative RT-PCR for measuring gene expression changes. This method could be applied and modified for stimulating the basal ganglia and other regions of the brain commonly clinically targeted. The gene expression study described here assumes a candidate target gene approach for discovering molecular players that could be directing the mechanism for DBS.

The mechanism underlying the therapeutic effects of Deep Brain Stimulation (DBS) surgery needs investigation. The methods presented in this manuscript describe an experimental approach to examine the cellular events triggered by DBS by analyzing the gene expression profile of candidate genes that can facilitate neurogenesis post DBS surgery.

Deep brain stimulation (DBS) surgery, targeting various regions of the brain such as the basal ganglia, thalamus, and subthalamic regions, is an effective ...

Fluorescence Activated Cell Sorting (FACS) and Gene Expression Analysis of Fos-expressing Neurons from Fresh and Frozen Rat Brain Tissue

The study of neuroplasticity and molecular alterations in learned behaviors is switching from the study of whole brain regions to the study of specific sets of sparsely distributed activated neurons called neuronal ensembles that mediate learned associations. Fluorescence Activated Cell Sorting (FACS) has recently been optimized for adult rat brain tissue and allowed isolation of activated neurons using antibodies against the neuronal marker NeuN and Fos protein, a marker of strongly activated neurons. Until now, Fos-expressing neurons and other cell types were isolated from fresh tissue, which entailed long processing days and allowed very limited numbers of brain samples to be assessed after lengthy and complex behavioral procedures. Here we found that yields of Fos-expressing neurons and Fos mRNA from dorsal striatum were similar between freshly dissected tissue and tissue frozen at -80 &#186;C for 3 - 21 days. In addition, we confirmed the phenotype of the NeuN-positive and NeuN-negative sorted cells by assessing gene expression of neuronal (NeuN), astrocytic (GFAP), oligodendrocytic (Oligo2) and microgial (Iba1) markers, which indicates that frozen tissue can also be used for FACS isolation of glial cell types. Overall, it is possible to collect, dissect and freeze brain tissue for multiple FACS sessions. This maximizes the amount of data obtained from valuable animal subjects that have often undergone long and complex behavioral procedures.

Fluorescence Activated Cell Sorting FACS and Gene Expression Analysis of Fos-expressing Neurons from Fresh and Frozen Rat Brain Tissue

Here we present a Fluorescence Activated Cell Sorting (FACS) protocol to study molecular alterations in Fos-expressing neuronal ensembles from both fresh and frozen brain tissue. The use of frozen tissue allows FACS isolation of many brain areas over multiple sessions to maximize the use of valuable animal subjects.

The study of neuroplasticity and molecular alterations in learned behaviors is switching from the study of whole brain regions to the study of specific ...

In Vivo Monitoring of Circadian Clock Gene Expression in the Mouse Suprachiasmatic Nucleus Using Fluorescence Reporters

This technique combines optical fiber mediated fluorescence recordings with the precise delivery of recombinant adeno-associated virus based gene reporters. This new and easy to use in vivo fluorescence monitoring system was developed to record the transcriptional rhythm of the clock gene, Cry1, in the suprachiasmatic nucleus (SCN) of freely moving mice. To do so, a Cry1 transcription fluorescence reporter was designed and packaged into Adeno-associated virus. Purified, concentrated virus was injected into the mouse SCN followed by the insertion of an optic fiber, which was then fixed onto the surface of the brain. The animals were returned to their home cages and allowed a 1-month post-operative recovery period to ensure sufficient reporter expression. Fluorescence was then recorded in freely moving mice via an in vivo monitoring system that was constructed at our institution. For the in vivo recording system, a 488 nm laser was coupled with a 1 &#215; 4 beam-splitter that divided the light into four laser excitation outputs of equal power. This setup enabled us to record from four animals simultaneously. Each of the emitted fluorescence signals was collected via a photomultiplier tube and a data acquisition card. In contrast to the previous bioluminescence in vivo circadian clock recording technique, this fluorescence in vivo recording system allowed the recording of circadian clock gene expression during the light cycle.

In Vivo Monitoring of Circadian Clock Gene Expression in the Mouse Suprachiasmatic Nucleus Using Fluorescence Reporters

This newly developed fluorescence-based technology enables long-term monitoring of the transcription of circadian clock genes in the suprachiasmatic nucleus (SCN) of freely moving mice in real-time and at a high temporal resolution.

This technique combines optical fiber mediated fluorescence recordings with the precise delivery of recombinant adeno-associated virus based gene ...

Primary Cell Culture of Purified GABAergic or Glutamatergic Neurons Established through Fluorescence-activated Cell Sorting

The overall goal of this protocol is to generate purified neuronal cultures derived from either GABAergic or glutamatergic neurons. Purified neurons can be cultured in defined media for 16 days in vitro and are amenable to any analyses typically performed on dissociated cultures, including electrophysiological, morphological and survival analyses. The major advantage of these cultures is that specific cell types can be selectively studied in the absence of complex external influences, such as those arising from glial cells or other neuron types. When planning experiments with purified cells, however, it is important to note that neurons strongly depend on glia-conditioned media for their growth and survival. In addition, glutamatergic neurons further depend on glia-secreted factors for the establishment of synaptic transmission. We therefore also describe a method for co-culturing neurons and glial cells in a non-contact arrangement. Using these methods, we have identified major differences between the development of GABAergic and glutamatergic neuronal networks. Thus, studying cultures of purified neurons has great potential for furthering our understanding of how the nervous system develops and functions. Moreover, purified cultures may be useful for investigating the direct action of pharmacological agents, growth factors or for exploring the consequences of genetic manipulations on specific cell types. As more and more transgenic animals become available, labeling additional specific cell types of interest, we expect that the protocols described here will grow in their applicability and potential.

This protocol describes a cell sorting based method for the purification and culture of fluorescent GABAergic or glutamatergic neurons from the neocortex and hippocampus of postnatal mice or rats.

The overall goal of this protocol is to generate purified neuronal cultures derived from either GABAergic or glutamatergic neurons. Purified neurons can ...

Using Near-infrared Fluorescence and High-resolution Scanning to Measure Protein Expression in the Rodent Brain

Neuroscience is the study of how cells in the brain mediate various functions. Measuring protein expression in neurons and glia is critical for the study of neuroscience as cellular function is determined by the composition and activity of cellular proteins. In this article, we describe how immunocytochemistry can be combined with near-infrared high-resolution scanning to provide a semi-quantitative measure of protein expression in distinct brain regions. This technique can be used for single or double protein expression in the same brain region. Measuring proteins in this fashion can be used to obtain a relative change in protein expression with an experimental manipulation, molecular signature of learning and memory, activity in molecular pathways, and neural activity in multiple brain regions. Using the correct proteins and statistical analysis, functional connectivity among brain regions can be determined as well. Given the ease of implementing immunocytochemistry in a laboratory, using immunocytochemistry with near-infrared high-resolution scanning can expand the ability of the neuroscientist to examine neurobiological processes at a systems level.

Here, we present a protocol that uses near-infrared dyes in conjunction with immunohistochemistry and high-resolution scanning to assay proteins in brain regions.

Neuroscience is the study of how cells in the brain mediate various functions. Measuring protein expression in neurons and glia is critical for the study ...

A Hydrophobic Tissue Clearing Method for Rat Brain Tissue

Hydrophobic tissue clearing methods are easily adjustable, fast, and low-cost procedures that allows for the study of a molecule of interest in unaltered tissue samples. Traditional immunolabeling procedures require cutting the sample into thin sections, which restricts the ability to label and examine intact structures. However, if brain tissue can remain intact during processing, structures and circuits can remain intact for the analysis. Previously established clearing methods take significant time to completely clear the tissue, and the harsh chemicals can often damage sensitive antibodies. The iDISCO method quickly and completely clears tissue, is compatible with many antibodies, and requires no special lab equipment. This technique was initially validated for the use in mice tissue, but the current protocol adapts this method to image hemispheres of control and transgenic rat brains. In addition to this, the present protocol also makes several adjustments to preexisting protocol to provide clearer images with less background staining. Antibodies for Iba-1 and tyrosine hydroxylase were validated in the HIV-1 transgenic rat and in F344/N control rats using the present hydrophobic tissue clearing method. The brain is an interwoven network, where structures work together more often than separately of one another. Analyzing the brain as a whole system as opposed to a combination of individual pieces is the greatest benefit of this whole brain clearing method.

Here we present a hydrophobic tissue clearing method that allows for the viewing of target molecules as part of intact brain structures. This technique has now been validated for F344/N control and HIV-1 transgenic rats of both sexes.

Hydrophobic tissue clearing methods are easily adjustable, fast, and low-cost procedures that allows for the study of a molecule of interest in unaltered ...