Work in the authors' laboratories was supported by the UK Biotechnology and Biological Sciences Research Council (BB/J006602/1 and BB/L003236/1), the Wellcome Trust (WT100269MA) and the European Research Council (ERC, "Ideas" Programme 293544). SJ was supported by an EMBO long-term fellowship. The authors thank Stephen Grant for his technical assistance.

Ethics Statement: 
Mouse husbandry and handling are in accordance with UK Home Office regulations and UCL ethics committee guidelines, complying with the Animals (Scientific Procedures) Act 1986 of the United Kingdom and its Amendment Regulations 2012.
NOTE: All solutions should be made with diethyl pyrocarbonate (DEPC)- treated water to destroy any residual RNase. For DEPC treatment, add DEPC (1 ml per litre), shake vigorously until all the DEPC globules have disappeared then autoclave to degrade the DEPC.
1. RNA Probe Synthesis
<ol>
	<li>CAUTION: When handling formamide, wear Personal Protective Equipment (PPE) and use a safety cabinet. Prepare hybridization buffer: DEPC-treated deionized water with 50% (v/v) deionized formamide, 200 mM NaCl, 5 mM EDTA, 10 mM Tris-HCl pH 7.5, 5 mM NaH2PO4, 5 mM Na2HPO4, 0.01 mg/ml yeast tRNA, 1&#215; Denhardt&#39;s solution, and 10% w/v dextran sulfate.</li>
	<li>Choose a DNA clone that contains the cDNA sequence of the gene of interest in a plasmid with RNA polymerase promoters. For this example, use a pCMV-SPORT6 clone, IRAVp968C0654D (Genbank accessionBC024934), with T7 and Sp6 RNA polymerase promoters for Aspa (Supplementary Figure 1).</li>
	<li>Prepare linearized plasmid DNA as template.
	<ol>
		<li>Grow the DNA clone, extract the plasmid with a small-scale plasmid purification kit according to the manufacturer&#39;s protocol and sequence with the T7 and Sp6 universal primers.</li>
		<li>Digest 1,020 &#181;g plasmid DNA with a restriction enzyme that cuts at the 5&#39; end of the sense strand of the cDNA. For this example, use 100 unit SalI to digest the pCMV-SPORT6-Aspa plasmid. Incubate for 1.5 hr at 37&#160;oC.</li>
		<li>Run a small aliquot on an agarose gel to check that the plasmid is fully linearized.</li>
	</ol>
	</li>
	<li>Purify the linearized plasmid using phenol-chloroform.
	<ol>
		<li>Add 1/10 volume of 3 M sodium acetate, one volume of 10 mM Tris HCl (pH 8.0) - equilibrated phenol and one volume of chloroform/isoamyl alcohol (IAA) (24:1).</li>
		<li>Centrifuge at 16,000 x g for 1 min at RT (20 - 25 &#176;C, RT) and extract upper aqueous phase.</li>
		<li>Add one volume of chloroform/IAA, centrifuge at 16,000 x g for 1 min and extract upper aqueous phase.</li>
		<li>Repeat step 1.4.3.</li>
		<li>Add 2 volumes of ethanol and leave at -20oC for 1 hr or O/N.</li>
		<li>Centrifuge at 16,000 x g at 4 &#176;C for 10 min. Discard the supernatant.</li>
		<li>Wash the pellet with 70% cold ethanol and re-suspend at approximatively 1 &#181;g cDNA per 2.5 &#181;l in TE (10 mM Tris-HCl, 1 mM EDTA pH 7.5).</li>
	</ol>
	</li>
	<li>Synthesize the two probes, one labelled with Digoxigenin (DIG) and the other with fluorescein isothiocyanate (FITC ).
	<ol>
		<li>Select the appropriate RNA polymerase to make the anti-sense probe (complementary to the target mRNA). For this example, use T7 RNA polymerase to make Aspa probe.</li>
		<li>Prepare in vitro transcription reaction: add 1 &#181;g of the linearized DNA, 4.0 &#181;l 5 x transcription buffer, 6.0 &#181;l of 100 mM DTT, 2.0 &#181;l of 10x DIG or FITC RNA labelling mix containing dNTPs, 1 &#181;l RNase inhibitor, and 20 - 40 units of RNA polymerase; make the final volume up to 20 &#181;l with DEPC-treated water.</li>
		<li>Incubate at 37&#160;oC for 1.5 hr.</li>
	</ol>
	</li>
	<li>Run1 &#181;l of the transcription reaction on a 1.0% agarose gel to check that the reaction has worked. The gel should show the linear template and a bright band of the probe.</li>
	<li>Make the volume up to 100 &#181;l with hybridization buffer and store 10 &#181;l aliquots at -80 &#176;C.</li>
</ol>
2. Perfusion, Fixation and Tissue Collection
<ol>
	<li>CAUTION: When handling paraformaldehyde (PFA), both solid and aqueous, wear PPE and use a safety cabinet. Prepare formaldehyde solution by dissolving 4% (w/v) PFA into 1x phosphate buffered saline (PBS) solution using heat (55 &#176;C). Filter the formaldehyde solution with filter paper.</li>
	<li>Prepare sucrose solution by dissolving 20% (w/v) sucrose in distilled water and add 0.1% (v/v) DEPC solution. Leave O/N at RT with a loose lid and then autoclave.</li>
	<li>Terminally anaesthetize a mouse by intra-peritoneal injection of pentobarbitone (50 mg/kg). Assess the depth of anaesthesia by toe pinch and the absence of withdrawal reflex indicates deep anaesthesia.</li>
	<li>Once the mouse is under deep anaesthesia, make an incision beneath the rib cage and cut through the rib cage on both sides, lift it to expose the heart.</li>
	<li>Insert a 25-G needle into the left ventricle of the heart. Make a small incision in the right atrium of the heart.</li>
	<li>Perfuse the animal with 20 ml PBS and then 40 ml formaldehyde solution. For P30 and older mice, use a perfusion rate of 12 ml/ min but for younger animals use a lower rate (7 - 10 ml/min).</li>
	<li>Dissect the brain.
	<ol>
		<li>Sever the mouse head with surgical scissors by making a cut posterior from the ears. Make a caudal midline incision in the skin and work rostrally to remove the skin from skull.</li>
		<li>Starting from the caudal part, cut through the top of the skull along midline and between the eyes with Iris scissors. Remove the parietal and frontal bone plates by tilting one side of a bone plate each time and snapping it off with tweezers.</li>
		<li>Gently tilt the brain upward from the anterior part with tweezers and cut the optic nerves and other cranial nerves. Gently lift the brain out of the skull.</li>
	</ol>
	</li>
	<li>Place the brain into a mouse coronal brain matrix. Slice the brain into 3 approximately 4 mm pieces with a feather razor blade.</li>
	<li>Transfer the slices into 4% PFA solution and incubate O/N at 4 &#176;C.</li>
	<li>Transfer brain slices to DEPC-treated 20% sucrose solution and incubate O/N at 4 &#176;C</li>
	<li>Place each brain slice into a dry cryomould, surround with optimum cutting temperature (OCT) medium and freeze on dry ice. Store at -80 &#176;C.</li>
</ol>
3. Cryosectioning
<ol>
	<li>Cut 15 &#181;m sections of frozen tissue in a cryostat and collect the sections onto microscope slides. If required, wet the sections with DEPC-treated PBS and flatten them with a fine paintbrush.</li>
	<li>Leave the slides to dry for approximately 1 hr to ensure that the tissue adheres to the slide.</li>
</ol>
4. Hybridization
<ol>
	<li>Prepare 65 &#176;C wash buffer: 150 mM NaCl, 15 mM Na3C3H5O(COO)3 (= 1x saline sodium citrate), 50% (v/v) formamide and 0.1% (v/v) Tween-20.</li>
	<li>Prepare MABT buffer: 100 mM maleic acid, 150 mM NaCl, 0.1% (v/v) Tween-20, pH 7.5.</li>
	<li>Dilute the two probes (DIG-labelled and FITC-labelled) 1/1,000 in hybridization buffer pre-warmed to 65 &#176;C and mix well.</li>
	<li>Apply around 300 &#181;l of hybridization mixture onto each slide, coverslipwith oven-baked (200&#160;oC) coverslips and incubate O/N at 65 &#176;C in a humidified chamber.</li>
	<li>Transfer the slides into a Coplin jar containing pre-warmed wash buffer. Wash the slides for 30 min twice at 65 &#176;C with wash buffer.</li>
	<li>Wash the slides for 10 min three times with MABT at RT.</li>
</ol>
5. Visualization of the FITC Probe
<ol>
	<li>Prepare ISH blocking buffer: MABT with 2% blocking reagent and 10% heat-inactivated sheep serum.</li>
	<li>Optional: use a hydrophobic pen to draw circles around the tissue sections on the slide to reduce the volume of antibody solutions required.</li>
	<li>Incubate the slides for 1 hr at RT with ISH blocking buffer in a humidified chamber.</li>
	<li>Incubate the slides O/N at 4 &#176;C with a horseradish peroxidase (POD)- conjugated anti-FITC antibody diluted 1/500 (v/v) in ISH blocking buffer.</li>
	<li>Place the slides into a Coplin jar containing PBS with 0.1% (v/v) Tween-20 (PBST). Wash 3 times for 10 min in PBST and replace with fresh PBST each time.</li>
	<li>Immediately before use, prepare the fluorescent tyramide by diluting 100 times into the Amplification diluent. For this example, use FITC-tyramide.</li>
	<li>Add this to the slides and leave for 10 min at RT.</li>
	<li>Place the slides into a Coplin jar and wash 3 times in PBST for 10 min.</li>
</ol>
6. Visualization of the DIG Probe
<ol>
	<li>Prepare 0.1 M Tris- HCl pH 8.2.</li>
	<li>Incubate the slides with ISH blocking buffer for 1 hr at RT.</li>
	<li>Incubate the slides O/N&#160;at 4 &#176;C with an alkaline phosphatase (AP) -conjugated anti-DIG antibody diluted 1/1,500 (v/v) in ISH blocking buffer.</li>
	<li>Wash with MABT for 10 min three times.</li>
	<li>Wash twice with 0.1 M Tris-HCl pH 8.2 for 5 min at RT.</li>
	<li>Immediately before use, prepare Fast Red solution by dissolving the tablets in 0.1 M Tris pH 8.2. Filter the solution through a 0.22 &#181;M filter.</li>
	<li>Incubate the slides at 37 &#176;C with Fast Red solution in a humidified chamber. As the time for optimal development varies, check the slides regularly with a fluorescent microscope to monitor the formation of precipitate. For this example, stop the reaction after 2 - 3 hr.</li>
	<li>Wash with PBST for 10 min three times.</li>
</ol>
7. Immunohistochemistry
<ol>
	<li>Prepare IHC blocking buffer: 10% (v/v) serum (of a different species to primary antibody host) in PBST.</li>
	<li>Incubate slides with IHC blocking buffer for 1 hr at RT in a humidified chamber.</li>
	<li>Prepare primary antibody: dilute the primary antibody at an appropriate dilution in PBST with 5% serum (of a different species to primary antibody host). For this example, use a rabbit anti-Olig2 antibody at 1/400 (v/v) dilution.</li>
	<li>Incubate in the primary antibody solution at 4 &#176;C O/N.</li>
	<li>Wash with PBST for 10 min three times.</li>
	<li>Prepare secondary antibody: dilute a fluorophore-conjugated secondary antibody at an appropriate dilution in PBST with 5% (v/v) serum (of a different species to primary antibody host) and 0.1% (v/v) Hoechst 33258. For this example, use a donkey anti-rabbit Alexa647 secondary antibody at 1/1,000 (v/v) dilution.</li>
	<li>Incubate in the secondary antibody solution at RT for 1 hr.</li>
	<li>Wash with PBST for 10 min three times.</li>
</ol>
8. Mounting
<ol>
	<li>Partially dry the slides at RT, and mount with a fluorescence mounting medium. Leave the slides to dry and then image in a confocal microscope under 10X, 20X and 63X objectives using 4 different channels with the following excitation wavelengths: 570 nm for Fast Red, 488 nm for FITC, 647 nm for Olig2 immunolabelling and 350 nm for Hoechst.</li>
</ol>

<ol>
	<li>Lobsiger, C. 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=Glial+cells+as+intrinsic+components+of+non-cell-autonomous+neurodegenerative+disease.">Glial cells as intrinsic components of non-cell-autonomous neurodegenerative disease.</a> Nat Neurosci. 10 (11), 1355-1360 (2007).</li><li>Baslow, M. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=N-acetylaspartate+in+the+vertebrate+brain:+metabolism+and+function.">N-acetylaspartate in the vertebrate brain: metabolism and function.</a> Neurochem Res. 28 (6), 941-953 (2003).</li><li>Hoshino, H., Kubota, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Canavan+disease:+clinical+features+and+recent+advances+in+research.">Canavan disease: clinical features and recent advances in research.</a> Pediatr Int. 56 (4), 477-483 (2014).</li><li>Kaul, R., Gao, G. P., Balamurugan, K., Matalon, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cloning+of+the+human+aspartoacylase+cDNA+and+a+common+missense+mutation+in+Canavan+disease.">Cloning of the human aspartoacylase cDNA and a common missense mutation in Canavan disease.</a> Nat Genet. 5 (2), 118-123 (1993).</li><li>Divry, P., Mathieu, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Aspartoacylase+deficiency+and+N-acetylaspartic+aciduria+in+patients+with+Canavan+disease.">Aspartoacylase deficiency and N-acetylaspartic aciduria in patients with Canavan disease.</a> Am J Med Genet. 32 (4), 550-551 (1989).</li><li>Bartalini, G., 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=Biochemical+diagnosis+of+Canavan+disease.">Biochemical diagnosis of Canavan disease.</a> Childs Nerv Syst. 8 (8), 468-470 (1992).</li><li>Moffett, J. R., Ross, B., Arun, P., Madhavarao, C. N., Namboodiri, A. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=N-Acetylaspartate+in+the+CNS:+from+neurodiagnostics+to+neurobiology.">N-Acetylaspartate in the CNS: from neurodiagnostics to neurobiology.</a> Prog Neurobiol. 81 (2), 89-131 (2007).</li><li>D'Adamo, A. F., Smith, J. C., Woiler, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+occurrence+of+N-acetylaspartate+amidohydrolase+(aminoacylase+II)+in+the+developing+rat.">The occurrence of N-acetylaspartate amidohydrolase (aminoacylase II) in the developing rat.</a> J Neurochem. 20 (4), 1275-1278 (1973).</li><li>Bhakoo, K. K., Craig, T. J., Styles, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Developmental+and+regional+distribution+of+aspartoacylase+in+rat+brain+tissue.">Developmental and regional distribution of aspartoacylase in rat brain tissue.</a> J Neurochem. 79 (1), 211-220 (2001).</li><li>Sommer, A., Sass, J. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Expression+of+aspartoacylase+(ASPA)+and+Canavan.">Expression of aspartoacylase (ASPA) and Canavan.</a> Gene. 505 (2), 206-210 (2012).</li><li>Klugmann, 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=Identification+and+distribution+of+aspartoacylase+in+the+postnatal+rat+brain.">Identification and distribution of aspartoacylase in the postnatal rat brain.</a> Neuroreport. 14 (14), 1837-1840 (2003).</li><li>Madhavarao, C. N., 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=Immunohistochemical+localization+of+aspartoacylase+in+the+rat+central+nervous+system.">Immunohistochemical localization of aspartoacylase in the rat central nervous system.</a> J Comp Neurol. 472 (3), 318-329 (2004).</li><li>Hershfield, J. 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=Aspartoacylase+is+a+regulated+nuclear-cytoplasmic+enzyme.">Aspartoacylase is a regulated nuclear-cytoplasmic enzyme.</a> Faseb J. 20 (12), 2139-2141 (2006).</li><li>Moffett, J. 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=Extensive+aspartoacylase+expression+in+the+rat+central+nervous+system.">Extensive aspartoacylase expression in the rat central nervous system.</a> Glia. 59 (10), 1414-1434 (2011).</li><li>Kirmani, B. F., Jacobowitz, D. M., Kallarakal, A. T., Namboodiri, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Aspartoacylase+is+restricted+primarily+to+myelin+synthesizing+cells+in+the+CNS:+therapeutic+implications+for+Canavan+disease.">Aspartoacylase is restricted primarily to myelin synthesizing cells in the CNS: therapeutic implications for Canavan disease.</a> Brain Res Mol Brain Res. 107 (2), 176-182 (2002).</li><li>Kirmani, B. F., Jacobowitz, D. M., Namboodiri, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Developmental+increase+of+aspartoacylase+in+oligodendrocytes+parallels+CNS+myelination.">Developmental increase of aspartoacylase in oligodendrocytes parallels CNS myelination.</a> Brain Res Dev Brain Res. 140 (1), 105-115 (2003).</li><li>Zhang, Y., 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=An+RNA-sequencing+transcriptome+and+splicing+database+of+glia,+neurons,+and+vascular+cells+of+the+cerebral+cortex.">An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex.</a> J Neurosci. 34 (36), 11929-11947 (2014).</li></ol>

The authors declare that they have no competing financial interests.

This protocol provides a step-by-step procedure for a double RNA in situ hybridization followed by immunostaining. We have used this protocol to confirm that Aspa is expressed in mature oligodendrocytes in several brain areas.
This multi-step procedure has many potential pitfalls that can affect sensitivity and should be avoided. First, all the solutions and storage buffers for the transcription reaction need to be RNase-free. Second, the choice of cDNA templates is important...

Glial cells, which are the most abundant cells in the central nervous system (CNS), comprise oligodendrocytes (the myelinating cells of CNS), oligodendrocytes precursors (OPs, also known as &#34;NG2 cells&#34;), astrocytes and microglia. There is growing interest in the functions of glial cells and their potential roles in neurological diseases1. For example, Canavan disease (CD) is a hereditary neurodegenerative disorder starting early in infancy with spongiform leukodystrophy and a progressive loss of neurons, leading to death usually before 10 years of age2,3. Mutations in the Aspartoacyclase (ASPA) gene that lead to drastically reduced ASPA activity4 in CD have been identified. ASPA is an enzyme catalysing the deacetylation of N-acetylaspartate (NAA), a molecule highly concentrated in the brain, generating acetate and aspartate 5-7. Many CD patients show higher levels of NAA due to lack of ASPA activity. Some studies speculate that NAA-derived acetate could be a major source of fatty acids/lipids in the brain during development and CD may result from decreased myelin synthesis during development caused by the failure of NAA to be broken down3,5,6.
ASPA is predominantly found in the kidney, liver and white matter of the brain, and given the important role of ASPA in CD, the cellular expression of this enzyme in the brain has been studied by several labs. By looking at ASPA enzymatic activity in the brain, earlier studies found that the increase in ASPA activity during brain development parallels the time course of myelination 8-10. At the cellular level, assays for enzymatic activity as well as in situ hybridization (ISH) and immunohistochemistry (IHC) analyses suggest that ASPA is mainly expressed in oligodendrocytes in the brain but not in neurons or astrocytes11-16. A few studies found that ASPA might also be expressed in microglia in the CNS12,14. So far data on ASPA expression in OPs are limited. According to a recent study where transcriptomes of different cell types in the mouse cerebral cortex including neurons, astrocytes, OPs, newly formed oligodendrocytes, myelinating oligodendrocytes, microglia, endothelial cells, and pericytes were analysed by RNA sequencing17, ASPA is exclusively expressed in oligodendrocytes, in particular in myelinating oligodendrocytes (http://web.stanford.edu/group/barres_lab/brain_rnaseq.html).&#160; Despite these studies on ASPA expression pattern in the brain, a number of uncertainties remain.
Different techniques can be used to study gene expression patterns. IHC is a commonly used method for detecting the functional product (i.e., protein) of a gene expression in tissue sections. Despite its great utility, this technique has limitations as its application and specificity are subject to the availability and specificity of the antibody needed. By comparison, ISH has the advantage of being able to reveal the expression of any gene at the mRNA level. However, it can be technically challenging to use several probes at the same time in order to localize a gene expression to specific cell types. In this article, we describe a protocol combining double fluorescence RNA in situ hybridization with fluorescence immunolabelling of a protein. We have used this set of techniques to examine the expression pattern of Aspa in mouse brain. This method allows the precise study of gene expression using confocal microscopy.

<table><tbody><tr><td>QIAprep Miniprep</td><td>Qiagen</td><td>27104</td><td></td></tr><tr><td>Deionized formamide</td><td>Sigma</td><td>F9037</td><td>for ISH blocking buffer</td></tr><tr><td>Sodium chloride</td><td>Sigma</td><td>S3014</td><td></td></tr><tr><td>Trizma Base</td><td>Sigma</td><td>T1503</td><td></td></tr><tr><td>Hydrochloric acid</td><td>VWR International</td><td>20252.290</td><td></td></tr><tr><td>Sodium phosphate monobasic anhydrous</td><td>Sigma</td><td>S8282</td><td></td></tr><tr><td>Sodium phosphate dibasic dihydrate</td><td>Sigma</td><td>30435</td><td></td></tr><tr><td>Yeast tRNA</td><td>Roche</td><td>10109495001</td><td></td></tr><tr><td>50x Denhardt&#039;s solution</td><td>Life Technologies</td><td>750018</td><td></td></tr><tr><td>Dextran sulfate</td><td>Sigma</td><td>D8906</td><td></td></tr><tr><td>Aspa cDNA clone</td><td>Source Bioscience</td><td>IRAVp968C0654D</td><td></td></tr><tr><td>SalI</td><td>New England Biolabs</td><td>R0138</td><td></td></tr><tr><td>Sodium acetate</td><td>Sigma</td><td>S2889</td><td></td></tr><tr><td>Equilibrated phenol</td><td>Sigma</td><td>P4557</td><td></td></tr><tr><td>Chloroform</td><td>Sigma-Aldrich</td><td>C2432</td><td></td></tr><tr><td>Isoamyl alcohol</td><td>Aldrich</td><td>496200</td><td></td></tr><tr><td>Ethanol</td><td>VWR International</td><td>20821.321</td><td></td></tr><tr><td>T7 RNA polymerase</td><td>Promega</td><td>P4074</td><td></td></tr><tr><td>Transcription buffer</td><td>Promega</td><td>P118B</td><td></td></tr><tr><td>100 mM DTT</td><td>Promega</td><td>P117B</td><td></td></tr><tr><td>UTP-DIG NTP mix</td><td>Roche</td><td>11277073910</td><td></td></tr><tr><td>Rnasin</td><td>Promega</td><td>N251B</td><td></td></tr><tr><td>Paraformaldehyde</td><td>Sigma</td><td>P6148</td><td></td></tr><tr><td>Filter paper</td><td>Fisher scientific</td><td>005479470</td><td></td></tr><tr><td>Sucrose</td><td>Sigma</td><td>59378</td><td></td></tr><tr><td>Diethyl pyrocarbonate</td><td>Sigma</td><td>D5758</td><td></td></tr><tr><td>Pentobarbitone</td><td>Animalcare Ltd</td><td>BN43054</td><td></td></tr><tr><td>Dissecting scissors</td><td>World Precision Instruments</td><td>15922</td><td></td></tr><tr><td>25 gauge needle</td><td>Terumo</td><td>300600</td><td></td></tr><tr><td>Peristaltic pump</td><td>Cole-Parmer Instrument Co. Ltd</td><td>WZ-07522-30</td><td></td></tr><tr><td>Iris scissors</td><td>Weiss</td><td>103227</td><td></td></tr><tr><td>No.2 tweezers</td><td>World Precision Instruments</td><td>500230</td><td></td></tr><tr><td>Coronal Brain Matrix</td><td>World Precision Instruments</td><td>RBMS-200C</td><td></td></tr><tr><td>Razor blade</td><td>Personna Medical</td><td>PERS60-0138</td><td></td></tr><tr><td>OCT medium</td><td>Tissue tek</td><td>4583</td><td></td></tr><tr><td>Cryostat/microtome</td><td>Bright</td><td></td><td></td></tr><tr><td>Superfrost plus slides</td><td>Thermo Scientific</td><td>J1800AMNZ</td><td></td></tr><tr><td>Sodium citrate</td><td>Sigma</td><td>S4641</td><td>for 65 &amp;deg;C wash buffer</td></tr><tr><td>Formamide</td><td>Sigma-Aldrich</td><td>F7503</td><td></td></tr><tr><td>Tween-20</td><td>Sigma-Aldrich</td><td>P1379</td><td></td></tr><tr><td>Coverslips</td><td>VWR International</td><td>631-0146</td><td></td></tr><tr><td>Coplin Jar</td><td>Smith Scientific Ltd</td><td>2959</td><td></td></tr><tr><td>Blocking reagent</td><td>Roche</td><td>11096176001</td><td></td></tr><tr><td>Heat-inactivated sheep serum</td><td>Sigma</td><td>S2263</td><td></td></tr><tr><td>Hydrophobic pen</td><td>Cosmo Bio</td><td>DAI-PAP-S</td><td>1:500</td></tr><tr><td>&amp;alpha;-FITC POD-conjugated antibody</td><td>Roche</td><td>11426346910</td><td></td></tr><tr><td>TSA&amp;trade; Plus Fluorescein System</td><td>Perkin Elmer</td><td>NEL741001KT</td><td>1:1,500</td></tr><tr><td>&amp;alpha;-DIG AP-conjugated</td><td>Roche</td><td>11093274910</td><td></td></tr><tr><td>Fast red tablets</td><td>Roche</td><td>11496549001</td><td></td></tr><tr><td>.22 &amp;micro;M filter</td><td>Millex</td><td>SLGP033RS</td><td></td></tr><tr><td>&amp;alpha;-Olig2 Rabbit antbody</td><td>Millipore</td><td>AB9610</td><td></td></tr><tr><td>Alexa Fluor&amp;reg; 647-conjugated &amp;alpha;-rabbit antibody</td><td>Life technologies</td><td>A-31573</td><td>1:1,000</td></tr><tr><td>bisBenzimide H 33258</td><td>sigma</td><td>B2883</td><td></td></tr><tr><td>Mounting medium</td><td>Dako</td><td>S3023</td><td></td></tr><tr><td>Leica SP2 confocal microscope</td><td>Leica</td><td></td><td></td></tr></tbody></table>

combining double fluorescence in situ hybridization with immunolabelling for detection of the expression of three genes in mouse brain sections

Detection of gene expression in different types of brain cells e.g., neurons, astrocytes, oligodendrocytes, oligodendrocyte precursors and microglia, can be hampered by the lack of specific primary or secondary antibodies for immunostaining. Here we describe a protocol to detect the expression of three different genes in the same brain section using double fluorescence in situ hybridization with two gene-specific probes followed by immunostaining with an antibody of high specificity directed against the protein encoded by a third gene. The Aspartoacyclase (ASPA) gene, mutations of which can lead to a rare human white matter disease - Canavan disease - is thought to be expressed in oligodendrocytes and microglia but not in astrocytes and neurons. However, the precise expression pattern of ASPA in the brain has yet to be established. This protocol has allowed us to determine that ASPA is expressed in a subset of mature oligodendrocytes and it can be generally applied to a wide range of gene expression pattern studies.

This article describes a method for a double fluorescence ISH followed by immunolabelling in mouse brain sections. A brief description of this protocol is shown in Figure 1.&#160;The first step was to synthesize probes specific to Aspa and Mbp (myelin basic protein). To check that the probes had been synthesized, a small aliquot of each reaction was run on an agarose gel. The faint linear template and a large amount of the RNA probe can be seen (...

Watch this Scientific Journal Video about Combining Double Fluorescence In Situ Hybridization with Immunolabelling for Detection of the Expression of Three Genes in Mouse Brain Sections at JoVE.com

Combining Double Fluorescence In Situ Hybridization with Immunolabelling for Detection of the Expression of Three Genes in Mouse Brain Sections

Localizing gene expression to specific cell types can be challenging due to the lack of specific antibodies. Here we describe a protocol for simultaneous triple detection of gene expression by combining double fluorescence RNA in situ hybridization with immunostaining.

Combining Double Fluorescence In Situ Hybridization with Immunolabelling for Detection of the Expression of Three Genes in Mouse Brain Sections

Detection of gene expression in different types of brain cells e.g., neurons, astrocytes, oligodendrocytes, oligodendrocyte precursors and microglia, can ...

combining-double-fluorescence-situ-hybridization-with-immunolabelling

Research

JoVE Journal

Neuroscience

14.0K Views.  University College London. Localizing gene expression to specific cell types can be challenging due to the lack of specific antibodies. Here we describe a protocol for simultaneous triple detection of gene expression by combining double fluorescence RNA in situ hybridization with immunostaining.

Video: Combining Double Fluorescence In Situ Hybridization with Immunolabelling for Detection of the Expression of Three Genes in Mouse Brain Sections

Double Fluorescence in situ Hybridization in Fresh Brain Sections

Here we describe a modified version of a double fluorescence in situ hybridization (dFISH) method optimized for detecting two mRNAs of interest in fresh frozen brain sections. Our group has successfully used this approach to study gene co-regulation. More specifically, we have used this dFISH method to explore the anatomical organization, neurochemical properties, and the impact of sensory experience in central sensory circuits, at single cell resolution. This protocol has been validated in brain tissue from mice, rats and songbirds but is expected to be easily adaptable to other vertebrate species, as well as to an array of non-neural tissues. In this film we provide a detailed demonstration of the main steps of this procedure.

Double Fluorescence in situ Hybridization in Fresh Brain Sections

This protocol involves a non-radioactive in-situ hybridization procedure that enables the simultaneous identification of two transcript species, at a single cell resolution, in thin sections of the vertebrate brain.

Here we describe a modified version of a double fluorescence in situ hybridization (dFISH) method optimized for detecting two mRNAs of interest in fresh ...

Combining Lipophilic dye, in situ Hybridization, Immunohistochemistry, and Histology

Going beyond single gene function to cut deeper into gene regulatory networks requires multiple mutations combined in a single animal. Such analysis of two or more genes needs to be complemented with in situ hybridization of other genes, or immunohistochemistry of their proteins, both in whole mounted developing organs or sections for detailed resolution of the cellular and tissue expression alterations. Combining multiple gene alterations requires the use of cre or flipase to conditionally delete genes and avoid embryonic lethality. Required breeding schemes dramatically enhance effort and cost proportional to the number of genes mutated, with an outcome of very few animals with the full repertoire of genetic modifications desired. Amortizing the vast amount of effort and time to obtain these few precious specimens that are carrying multiple mutations necessitates tissue optimization. Moreover, investigating a single animal with multiple techniques makes it easier to correlate gene deletion defects with expression profiles. We have developed a technique to obtain a more thorough analysis of a given animal; with the ability to analyze several different histologically recognizable structures as well as gene and protein expression all from the same specimen in both whole mounted organs and sections. Although mice have been utilized to demonstrate the effectiveness of this technique it can be applied to a wide array of animals. To do this we combine lipophilic dye tracing, whole mount in situ hybridization, immunohistochemistry, and histology to extract the maximal possible amount of data.

Combining Lipophilic dye, in situ Hybridization, Immunohistochemistry, and Histology

A combination of different techniques to maximize data collection from mouse tissue is presented.

Going beyond single gene function to cut deeper into gene regulatory networks requires multiple mutations combined in a single animal.  Such analysis of ...

Multi-target Chromogenic Whole-mount In Situ Hybridization for Comparing Gene Expression Domains in Drosophila Embryos

To analyze gene regulatory networks active during embryonic development and organogenesis it is essential to precisely define how the different genes are expressed in spatial relation to each other in situ. Multi-target chromogenic whole-mount in situ hybridization (MC-WISH) greatly facilitates the instant comparison of gene expression patterns, as it allows distinctive visualization of different mRNA species in contrasting colors in the same sample specimen. This provides the possibility to relate gene expression domains topographically to each other with high accuracy and to define unique and overlapping expression sites. In the presented protocol, we describe a MC-WISH procedure for comparing mRNA expression patterns of different genes in Drosophila embryos. Up to three RNA probes, each specific for another gene and labeled by a different hapten, are simultaneously hybridized to the embryo samples and subsequently detected by alkaline phosphatase-based colorimetric immunohistochemistry. The described procedure is detailed here for Drosophila, but works equally well with zebrafish embryos.

Multi-target Chromogenic Whole-mount In Situ Hybridization for Comparing Gene Expression Domains in Drosophila Embryos

We describe a multi-target chromogenic whole-mount in situ hybridization (MC-WISH) procedure in intact Drosophila embryos allowing simultaneous and specific detection of three different mRNA distribution patterns by contrasting color precipitates.

To analyze gene regulatory networks active during embryonic development and organogenesis it is essential to precisely define how the different genes are ...

Developmental Biology

Quantitative Analysis of Alternative Pre-mRNA Splicing in Mouse Brain Sections Using RNA In Situ Hybridization Assay

Alternative splicing (AS) occurs in more than 90% of human genes. The expression pattern of an alternatively spliced exon is often regulated in a cell type-specific fashion. AS expression patterns are typically analyzed by RT-PCR and RNA-seq using RNA samples isolated from a population of cells. In situ examination of AS expression patterns for a particular biological structure can be carried out by RNA in situ hybridization (ISH) using exon-specific probes. However, this particular use of ISH has been limited because alternative exons are generally too short to design exon-specific probes. In this report, the use of BaseScope, a recently developed technology that employs short antisense oligonucleotides in RNA ISH, is described to analyze AS expression patterns in mouse brain sections. Exon 23a of neurofibromatosis type 1 (Nf1) is used as an example to illustrate that short exon-exon junction probes exhibit robust hybridization signals with high specificity in RNA ISH analysis on mouse brain sections. More importantly, signals detected with exon inclusion- and skipping-specific probes can be used to reliably calculate the percent spliced in values of Nf1 exon 23a expression in different anatomical areas of a mouse brain. The experimental protocol and calculation method for AS analysis are presented. The results indicate that BaseScope provides a powerful new tool to assess AS expression patterns in situ.

Quantitative Analysis of Alternative Pre-mRNA Splicing in Mouse Brain Sections Using RNA In Situ Hybridization Assay

An in situ hybridization (ISH) protocol that uses short antisense oligonucleotides to detect alternative pre-mRNA splicing patterns in mouse brain sections is described.

Alternative splicing (AS) occurs in more than 90% of human genes. The expression pattern of an alternatively spliced exon is often regulated in a cell ...

Genetics

Detection of Axonally Localized mRNAs in Brain Sections Using High-Resolution In Situ Hybridization

mRNAs are frequently localized to vertebrate axons and their local translation is required for axon pathfinding or branching during development and for maintenance, repair or neurodegeneration in postdevelopmental periods. High throughput analyses have recently revealed that axons have a more dynamic and complex transcriptome than previously expected. These analysis, however have been mostly done in cultured neurons where axons can be isolated from the somato-dendritic compartments. It is virtually impossible to achieve such isolation in whole tissues in vivo. Thus, in order to verify the recruitment of mRNAs and their functional relevance in a whole animal, transcriptome analyses should ideally be combined with techniques that allow the visualization of mRNAs in situ. Recently, novel ISH technologies that detect RNAs at a single-molecule level have been developed. This is especially important when analyzing the subcellular localization of mRNA, since localized RNAs are typically found at low levels. Here we describe two protocols for the detection of axonally-localized mRNAs using a novel ultrasensitive RNA ISH technology. We have combined RNAscope ISH with axonal counterstain using fluorescence immunohistochemistry or histological dyes to verify the recruitment of Atf4 mRNA to axons in vivo in the mature mouse and human brains.

Detection of Axonally Localized mRNAs in Brain Sections Using High-Resolution In Situ Hybridization

RNA in situ hybridization (ISH) enables the visualization of RNAs in cells and tissues. Here we show how combination of RNAscope ISH with immunohistochemistry or histological dyes can be successfully used to detect mRNAs localized to axons in sections of mouse and human brains.

mRNAs are frequently localized to vertebrate axons and their local translation is required for axon pathfinding or branching during development and for ...

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 ...

The Detection of 5-Hydroxymethylcytosine in Neural Stem Cells and Brains of Mice

Multiple&#160;DNA modifications have been identified in the mammalian genome. Of that, 5-methylcytosine and 5-hydroxymethylcytosine-mediated epigenetic mechanisms have been intensively studied. 5-hydroxymethylcytosine displays dynamic features during embryonic and postnatal development of the brain, plays a regulatory function in gene expression, and is involved in multiple neurological disorders. Here, we describe the detailed methods including immunofluorescence staining and&#160;DNA dot-blot to detect 5-hydroxymethylcytosine in cultured cells and brain tissues of mouse.

Here, we present a protocol to detect 5-hydroxymethylcytosine in cells and brain tissues, utilizing immunofluorescence staining and DNA dot-blot methods.

Multiple&#160;DNA modifications have been identified in the mammalian genome. Of that, 5-methylcytosine and 5-hydroxymethylcytosine-mediated epigenetic ...

Combining Multiplex Fluorescence In Situ Hybridization with Fluorescent Immunohistochemistry on Fresh Frozen or Fixed Mouse Brain Sections

Fluorescent in situ hybridization (FISH) is a molecular technique that identifies the presence and spatial distribution of specific RNA transcripts within cells. Neurochemical phenotyping of functionally identified neurons usually requires concurrent labelling with multiple antibodies (targeting protein) using immunohistochemistry (IHC) and optimization of in situ hybridization (targeting RNA), in tandem. A &#34;neurochemical signature&#34; to characterize particular neurons may be achieved however complicating factors include the need to verify FISH and IHC targets before combining the methods, and the limited number of RNAs and proteins that may be targeted simultaneously within the same tissue section.
Here we describe a protocol, using both fresh frozen and fixed mouse brain preparations, which detects multiple mRNAs and proteins in the same brain section using RNAscope FISH followed by fluorescence immunostaining, respectively. We use the combined method to describe the expression pattern of low abundance mRNAs (e.g., galanin receptor 1) and high abundance mRNAs (e.g., glycine transporter 2), in immunohistochemically identified brainstem nuclei.
Key considerations for protein labelling downstream of the FISH assay extend beyond tissue preparation and optimization of FISH probe labelling. For example, we found that antibody binding and labelling specificity can be detrimentally affected by the protease step within the FISH probe assay. Proteases catalyze hydrolytic cleavage of peptide bonds, facilitating FISH probe entry into cells, however they may also digest the protein targeted by the subsequent IHC assay, producing off target binding. The subcellular location of the targeted protein is another factor contributing to IHC success following FISH probe assay. We observed IHC specificity to be retained when the targeted protein is membrane bound, whereas IHC targeting cytoplasmic protein required extensive troubleshooting. Finally, we found handling of slide-mounted fixed frozen tissue more challenging than fresh frozen tissue, however IHC quality was overall better with fixed frozen tissue, when combined with RNAscope.

Combining Multiplex Fluorescence In Situ Hybridization with Fluorescent Immunohistochemistry on Fresh Frozen or Fixed Mouse Brain Sections

This protocol describes a method for combining fluorescence in situ hybridization (FISH) and fluorescence immunohistochemistry (IHC) in both fresh frozen and fixed mouse brain sections, with the goal of achieving multilabel FISH and fluorescence IHC signal. IHC targeted cytoplasmic and membrane attached proteins.

Fluorescent in situ hybridization (FISH) is a molecular technique that identifies the presence and spatial distribution of specific RNA transcripts within ...

Multiplex Detection of Gene Expression in the Intact Drosophila Brain Using Expansion-Assisted Iterative Fluorescence In Situ Hybridization

Understanding gene expression is essential for deciphering cellular functions. However, methods for analyzing the expression of numerous genes in situ within a given tissue remain limited. The EASI-FISH protocol described here has been adapted to detect the expression of dozens of genes in the intact adult Drosophila central nervous system (CNS) using commercially available reagents. This protocol includes a new gel formulation that enhances gel robustness, enabling multiple rounds of hybridization and allowing the embedding of multiple brains per gel. This improvement increases throughput, facilitates optimal comparison of experimental conditions, and reduces reagent costs. Additionally, by employing the GAL4-UAS system for co-detection of green fluorescent protein (GFP), gene expression can be visualized in specific neuronal or glial cell types. Notably, the high resolution achieved through expansion microscopy, combined with the sensitivity of the method, allows for the detection of single RNA transcripts. This approach effectively integrates high image quality with high throughput, making it a powerful tool for studying gene expression throughout the intact fly brain.

Expansion-Assisted Iterative Fluorescence In Situ Hybridization (EASI-FISH) is a robust technique that combines expansion microscopy with fluorescence in situ hybridization (FISH) to detect the expression of multiple genes in thick tissue. This protocol outlines recent advancements in the method and its adaptation for labeling the intact Drosophila central nervous system..

Understanding gene expression is essential for deciphering cellular functions. However, methods for analyzing the expression of numerous genes in situ ...

 Performing Double Fluorescence In Situ Hybridization to Detect Gene Expression in Mouse Brain Sections

<a href='https://app.jove.com/v/53976/combining-double-fluorescence-situ-hybridization-with-immunolabelling'>Source: Jolly, S., et.al. Combining Double Fluorescence In Situ Hybridization with Immunolabelling for Detection of the Expression of Three Genes in Mouse Brain Sections. J. Vis. Exp. (2016).</a>This video demonstrates the use of double fluorescence in situ hybridization to visualize the expression of two RNA targets in mouse brain sections. The protocol involves sequential detection of RNA using probes labeled with fluorescein isothiocyanate and digoxigenin, followed by enzymatic signal amplification to enhance sensitivity. The resulting fluorescence enables co-localization analysis of the target RNAs within the tissue.

Source: Jolly, S., et.al. Combining Double Fluorescence In Situ Hybridization with Immunolabelling for Detection of the Expression of Three Genes in Mouse ...

Combining Double Fluorescence In Situ Hybridization with Immunolabelling for Detection of the Expression of Three Genes in Mouse Brain Sections

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