This work has been funded by the Israel Science Foundation Grant (ISF # 393/12), Israel Centers of Research Excellence Grant (I-CORE 1796/12), German-Israel Foundation Grant (GIF # 2299-2291.1/2011) and the Marie Curie Career Integration Grant (FP7-PEOPLE-2013-CIG #618201). Initial steps in the project were funded by an AXA postdoctoral fellowship to AC. We acknowledge the generous startup funds provided by the Edmond and Lily Safra Center for Brain Sciences.
Critical reading by members of the Citri lab is greatly appreciated.

NOTE: The protocol follows the animal care guidelines of The Hebrew University of Jerusalem.
1. Preparation of ACSF Solution
<ol>
	<li>Prepare ACSF solution as described in Table 1. Make 1 L in ddH2O (&#62;18 M&#937; purity), bringing osmolarity to ~300 mOsm/L with appropriate addition of water or NaCl.</li>
</ol>
2. Equipment and Room Set Up
The equipment for monitoring of cocaine-induced locomotor behavior consists of behavior chambers (50 x 45 cm) wired with an inner light source, fan and camera (or infrared sensors), and fitted with an inner perspex box (30 x 30 cm) in which the mice are allowed to move freely while their locomotion is monitored. The behavioral testing should be performed between 1 hr after lights on to 1 hr before lights off, on a regular light/dark cycle. Animals should be trained consistently at the same time each day.
<ol>
	<li>Connect camera or infrared system to an appropriate system for monitoring and recording the locomotor behavior of the mice.</li>
	<li>Clean the chambers after each trial with disinfectant provided by mouse facility and/or odor removing reagent, in order to prevent olfactory cue bias and to ensure proper disinfection.</li>
</ol>
IMPORTANT: While handling the mice be quiet, calm and careful.
3. Animal Preparation
<ol>
	<li>House 5 C57BL6 male mice (6-12 weeks old; ~25-35 g of weight) per cage, in a room with a 12 hr light/dark cycle and free access to food and water, according to standards and requirements of local Animal Care Committee guidance and protocols. Before initiating the experiment, weigh the mice and log the data. Cocaine is later administered according to the weight of the mice.</li>
	<li>Transfer all the cages containing mice into the behavioral room 30 min before starting the first trial.</li>
	<li>Habituate all of the mice used in the experiment to experimenter handling, injections and monitoring in the behavior setup. This is achieved by 3 consecutive daily intraperitoneal injections of 250 &#956;l saline as described below.</li>
	<li>Administer an intraperitoneal injection of 250 &#956;l saline. Immediately following the injection, place the mouse in a behavior chamber to monitor locomotor activity for 15 min. Repeat this action for 3 consecutive days, at the same hour each day.</li>
	<li>On the fourth day, divide the mice into two groups. Prepare a stock solution of cocaine at 2 mg/ml in saline. Administer a single injection of cocaine solution (final 20 mg/kg) to the experimental group according to the weight of the mouse (e.g. for a 25 g mouse &#8211; inject 250 &#956;l, whereas a 30 g mouse will receive 300 &#956;l). Administer saline to the control group. Immediately following the injection, place the mouse for 20 min in a behavior chamber for monitoring of locomotor activity (typically, the first 15 min are monitored).</li>
	<li>After the cocaine injection, sacrifice the mice at different time points (0, 1, 2, 4, 8 and 24 hr following injection). Importantly, make sure that reference mice (0 time point) will not receive any injection on this day. Due to its significance, it is imperative to include replicates of the reference group.</li>
</ol>
4. Dissection of the Nucleus Accumbens
<ol>
	<li>Anesthetize the mice with isoflurane at the appropriate time after the cocaine/saline injection. The isoflurane must be directly vented out of the room. Therefore, the procedure should be performed in a chemical fume hood.</li>
	<li>Monitor the depth of anesthesia by testing the rear foot reflex. Pinch the paw to elicit a withdrawal response by the animal. An animal that shows a reflex is not at a surgical level of anesthesia and not in a state to euthanize.</li>
	<li>Extraction of the brain:
	<ol>
		<li>Euthanize the mouse by decapitation.</li>
		<li>Remove the skin above the center of the skull and cut the skull with sharp scissors.</li>
		<li>Insert the scissors at the point where the spinal cord enters the brain (foramen magnum) and make two lateral cuts.</li>
		<li>From the same point, make a long sagittal cut along the sagittal suture. Upon reaching the olfactory bulb, clip to the left and to the right.</li>
		<li>With a forceps, remove the skull carefully, grasping each half of the skull firmly and pulling to the side, taking care not to press onto or damage the brain.</li>
		<li>Remove the brain while severing the cranial nerves by using an inverted micro spoon spatula.</li>
	</ol>
	</li>
	<li>Place the brain in an ice-cold ACSF solution for 1-2 min to chill and harden.</li>
	<li>Remove brain from the ACSF, wick excess fluid with a paper towel, create a coronal cut between the cerebellum and the rest of the brain and glue the brain, with the rostral part facing up, onto the vibratome stage.</li>
	<li>Cutting the NAc:
	<ol>
		<li>Maintain ACSF solutions at ice-cold temperatures in the slicing chamber of the vibratome. Section at 200 &#956;m until the nucleus accumbens (NAc) is clearly identified according to the Paxinos and Franklin Mouse Brain Atlas (approximately 1.8 mm anterior to Bregma; pay attention to the shape of the corpus callosum, the location and shape of the anterior commissure and the ventricles, as well as the overall morphology of the brain section). At this point, create two 400 &#956;m sections, from which the NAc will be dissected.</li>
		<li>Under a stereoscope, use a fine blade to dissect the NAc area out from the slices. The definition of the NAc is according to the Paxinos and Franklin mouse brain atlas, and could conveniently be dissected in appropriate sections by four quick passes of the blade on the tissue. (Figure 2).</li>
		<li>Place NAc sections immediately in 900 &#956;l Trizol lysis reagent in a microcentrifuge tube and store at -80 &#176;C until RNA extraction.</li>
	</ol>
	</li>
</ol>
5. RNA Extraction and cDNA Reverse Transcription
<ol>
	<li>Thaw the tubes containing nucleus accumbens sections in trizol lysis reagent at room temperature and homogenize the lysate with a 1 ml syringe connected to 25 G needle until the tissue is completely homogenized (at least 15-20 times). The first few rounds are difficult, and require pushing the tissue against the wall of the tube in order to break it to small pieces that could enter the tip of the needle.</li>
	<li>To ensure homogenization, pipet the lysate into a QIAshredder mini spin column and centrifuge at 12,000 x g for 1 min.</li>
	<li>Pipet the lysate into new microcentrifuge tube and extract the RNA according to the manufacturer&#8217;s instructions. Store the RNA at -80 &#176;C until use.</li>
	<li>Measure the RNA concentration, analyze integrity and quality using a Bioanalyzer or equivalent equipment. Use 100-500 ng RNA for each round of cDNA preparation with random hexamer primers.</li>
</ol>
6. Primer Design and Primer Testing
<ol>
	<li>Choosing good primers: For an optimal primer pair for qPCR of mRNA transcripts, follow these requirements (Figure 3):
	<ol>
		<li>Design primers containing no longer than 17-28 bases. Avoid nucleotide repeats as they promote mispriming.</li>
		<li>Design primers with melting temperature (Tm) between 56-68&#176;C (optimally 60-64&#176;C). The Tm within the primer pair should be within 1 &#176;C of each other.</li>
		<li>Be aware that the product size should ideally be between 80 and 150bp.</li>
		<li>Ensure that at least one of the primers covers an exon-exon junction, or the amplicon contains a large intron (intron-spanning), to avoid amplification of genomic DNA contaminants.</li>
		<li>Use a reliable software based on Primer3 (for examples see Table 2) in order to improve primer design.</li>
	</ol>
	</li>
	<li>Testing the primers: In order to ensure the specificity and efficiency of the primers, a control qPCR reaction should be performed:
	<ol>
		<li>Use a positive sample (containing cDNA template for all relevant primer pairs) and titrate the cDNA (e.g. eight three-fold dilutions from an initial concentration of ~10 ng) in duplicate parallel reactions. Include a no-template control, which controls for contamination within the solutions used for the reaction.</li>
		<li>Calculate primer efficiency by using the formula: (10(&#8722;1/slope)-1) &#215; 100, such that the curve of the optimal slope is &#8722; 3.333 (i.e. 10(&#8722; 1/3.333) = 2) (Figure 4).</li>
		<li>Determine the specificity of the amplification. Specific amplification is demonstrated by a single prominent peak common to all the melting curves of the amplified products, whereas off-target amplification would appear as an obvious deviation from the single large peak.</li>
	</ol>
	</li>
</ol>
7. qPCR Analysis
<ol>
	<li>Pre-amplification:
	<ol>
		<li>Comprehensive qPCR analysis is based on parallel querying of limiting quantities of RNA with a large number of primer pairs. Therefore, a step of pre-amplification is essential. In this step, the cDNA undergoes 14-18 cycles of pre-amplification with a mixture of all the primers that will be utilized for querying the sample in the future (up to 800 primer pairs).</li>
		<li>Dilute all primers in TE (low EDTA) to 50 &#956;M for Specific Target Amplification (STA).</li>
		<li>Pool together 1 &#956;l aliquots of all of the 50 &#956;M primer sets to be included in the STA reaction, up to 800 assays.</li>
		<li>Prepare pre-mix and samples for STA as described in Table 3. Allow for error by preparing mix for 110% of the number of samples that need to be amplified. </li>
		<li>Aliquot 3.75 &#956;l STA pre-mix for each sample. Add 1.25 &#956;l of cDNA to each.</li>
		<li>Vortex to mix the reactions and centrifuge for 10 sec.</li>
		<li>Place the STA reactions in a thermal cycler and cycle as indicated at Table 4.</li>
	</ol>
	</li>
	<li>Exonuclease I (ExoI) treatment:
	<ol>
		<li>Dilute the Exo I as indicated in Table 5.</li>
		<li>Add 2 &#956;l of diluted ExoI (4 U/&#956;l) to each 5 &#956;l STA reaction, vortex, spin down (&#62;6,000 x g) and place in a thermal cycler at 37 &#176;C for 30 min and then at 80 &#176;C for 15 min.</li>
		<li>Dilute the final products to an appropriate concentration for testing. Use TE Buffer (add 43 &#956;l TE buffer to the 7 &#956;l TSA sample).</li>
		<li>Store the diluted STA products at -20 &#176;C or use immediately.</li>
	</ol>
	</li>
	<li>Primer and sample setup for qPCR:
	<ol>
		<li>Prepare samples as shown in Table 6. Prepare mix according to the chip chosen for the experiment, and add samples as appropriate.</li>
		<li>Agitate the Sample Mix solutions for a minimum of 20 sec, and centrifuge (&#62;6,000 x g) for at least 30 sec. Prepared reactions can be stored for short durations at 4 &#176;C until the chip is ready for loading.</li>
		<li>Prepare the assays as described in Table 7.</li>
		<li>Agitate the Assay Mix for a minimum of 20 sec and centrifuge (&#62;6,000 x g) for at least 30 sec to spin down all components. 
		IMPORTANT: Vortex thoroughly and centrifuge all sample and assay solutions before pipetting into the chip inlets. Failure to do so may result in a decrease in data quality. 
		NOTE: The final concentration of each primer is 5 &#956;M in the inlet and 500 nM in the final reaction.</li>
	</ol></li>
	<li>Priming and Loading the Dynamic Array IFC (integrated fluidic circuit) chip. The IFC chip has inlets for samples and assays, as well as specified inlets (accumulators) for control line fluid (mineral oil) used to pressurize the microfluidic chambers (Figure 4A).
	<ol>
		<li>Inject control line fluid into each accumulator on the chip.</li>
		<li>Remove and discard the blue protective film from the bottom of the chip.</li>
		<li>Place the chip into the appropriate IFC controller (controller MX for the 48.48 Dynamic Array IFC or the IFC controller HX for the 96.96 Dynamic Array IFC), then run the Prime (113x) script for the 48.48 Dynamic Array IFC or the Prime (136x) script for the 96.96 Dynamic Array IFC in order to prime the chip.</li>
		<li>When the script has finished, remove the primed chip from the IFC controller.</li>
		<li>Pipette 5 &#956;l of each Assay Mix and 5 &#956;l of each Sample Mix into their inlets.</li>
		<li>Return the chip to the IFC controller.</li>
		<li>Using the IFC controller software, run the Load Mix (113x) script for the 48.48 Dynamic Array IFC) or Load Mix (136x) script for the 96.96 Dynamic Array IFC to load the samples and assays into the chip. When the Load Mix script has finished, remove the loaded chip from the IFC controller.</li>
		<li>Load the chip on the thermal cycler, create a new chip run (according to manufacturer guidelines), including melting curve analysis. Using the thermal cycler software, ensure that the reaction chambers are recognized properly, and allow the reaction to run to completion.</li>
	</ol>
	</li>
</ol>
8. Data Analysis
<ol>
	<li>Quality assurance: In order to ensure data quality, verify the quality of the primers by addressing dilution curves (as described above). Monitor the specificity of amplification by viewing the melting curves of amplicons, the peaks of which should optimally be tightly aligned29.</li>
	<li>Visualization: For visualization of large quantities of data obtained by high-throughput qPCR, use software generated heatmaps, in which expression is color-coded by intensity. In addition, display the transcriptional dynamics of single genes as lined scatter plots.</li>
	<li>Publication: In publishing the gene expression results, it is advised to follow the MIQE Guidelines for publication of quantitative Real-Time PCR experiments, detailing the minimum information that must be reported for a qPCR experiment to ensure its relevance, accuracy, correct interpretation, and reproducibility.</li>
</ol>

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We have nothing to disclose.

Successful characterization of gene expression from brain tissue following behavioral paradigms depends upon: 1) Careful handling of mice during the behavioral paradigm; 2) Quick and precise dissection of tissue of interest; 3) RNA-safe measures to ensure the integrity of RNA; and 4) Careful planning of primers and experimental layout as well as precision and attention to detail in preparation for the qPCR analysis.
The aim of the procedure described is to characterize dynamics of transcriptio...

The brain&#8217;s dynamic organization enables cognitive and behavioral flexibility. Experiences are encoded through modifications of the structure and strength of connections between neurons in the brain3. This &#8220;experience-dependent plasticity&#8221; is the result of induction of specific patterns of gene expression that provides the necessary proteins for modification of synaptic structure and strength4. The identification of gene regulatory networks mediating the formation of long-term memories is a central tenet of molecular neuroscience, with the expectation that identification of the dominant elements of transcriptional programs will provide insight into the fundamental principles regulating memory formation, as well as targets for treatment of neurodegenerative and neuropsychiatric disorders. Transcriptional programs unfold in temporally-defined waves, each of which encode genes of different character, which are important for different stages in the implementation of the outcome of the signalling event1,2. It is therefore important to address transcriptional dynamics on a detailed temporal timescale, so as to identify the full complement of genes induced, and gain insight into their potential function according to the dynamics of their induction.
Drug addiction is a robust form of experience-dependent plasticity caused by the long-lasting effects of drugs of abuse on neural circuits in the brain5,6. Initial, acute exposure to drugs may lead to the development of addiction and the transition to chronic use. Contextual information is a crucial element in the development of addiction. Drug-associated environmental cues are assigned significant importance in the minds of drug abusers. Contextual information reminding a drug abuser of past drug experience can induce relapse to drug craving even following long periods of abstinence from drug exposure7,8. Hence the great clinical challenge in addiction - the propensity of addicts to relapse even long after withdrawal symptoms have subsided9.
Behavioral sensitization to cocaine is a simple model of cocaine experience useful in the study of mechanisms of drug addiction. In this widely-studied model for the long-lasting sensitization induced by chronic exposure to drugs of abuse, rodents are first habituated to saline injections (intraperitoneal; IP) in a novel environment (an open field chamber in which their locomotor activity is monitored); then, they receive daily injections of cocaine in the open field chambers while their activity is monitored10 (Figure 1). This behavioral paradigm typically results in a robust sensitization of locomotor behavior (8-12 fold above baseline activity)11, which is maintained for a period of months following cessation of cocaine injections, demonstrating the formation of a pervasive memory trace of drug experience.
The neural circuitry of reward, naturally involved in reinforcing behaviors essential for the success of a species (e.g. feeding, sex), is exploited by drugs of abuse to reinforce drug-associated behaviors12,13. The molecular and cellular mechanisms by which the experience of drugs of abuse is enhanced appear to be similar to the mechanisms underlying the formation of declarative or semantic memories in other brain structures14. Therefore, the robustness of the behavioral sensitization model makes it an attractive model system to study mechanisms of experience-dependent plasticity.
The nucleus accumbens (NAc) is a central integrator of the brain&#8217;s reward circuitry, and has been extensively associated with the development of addiction5,6. The formation of addiction depends on transcription of novel proteins in the nucleus accumbens, and robust induction of clearly structured transcription programs is observed in the NAc following cocaine experience15-19. The acute transcriptional response to cocaine exposure is likely to function at multiple levels in order to adapt to the strong induction stimulus and to direct the production of new proteins that are responsible for the structural and electrophysiological changes induced by exposure to the drug 6,19-22. 
In order to promote the study of molecular mechanisms of experience-dependent plasticity in the brain, a protocol is described for the comprehensive analysis of transcription dynamics in brain tissue samples following behavioral manipulation. The protocol is illustrated in the context of the behavioral experience studied in the Citri lab &#8211; behavioral sensitization to cocaine, utilizing microfluidic dynamic arrays for transcriptional analysis. The protocol described is obviously not limited to studying the nucleus accumbens in the context of behavioral sensitization, but could be applied to a large number of behavioral paradigms and brain regions. In fact, this protocol could be applied to body tissues outside the brain, and a variety of experiences or manipulations of the organism studied.
The protocol is roughly divided into four steps. In the first step, the animal is subjected to the behavioral paradigm; in the second step the tissue is microdissected; in the third step &#8211; mRNA is purified, reverse-transcribed and probed, and in the final step the data is analyzed.
In the context of studying transcriptional dynamics, the precise timing and definition of the experience are probably the most important experimental parameters to control. For this reason, our behavioral model of choice is that of behavioral sensitization to cocaine, a system which enables high level of experimenter control over the parameters of the experience. Additional behavioral paradigms that enable precise timing and address different models of experience-dependent plasticity or memory formation are available. These models include fear conditioning23, acute environmental enrichment24,25, novel object exploration26 and visual experience following dark rearing27. Still, behavioral sensitization to cocaine is a consistently robust behavioral manipulation, creating a highly pervasive memory trace which lasts for months following cocaine experience28.
The brain is sectioned, followed by manual microdissection of the nucleus accumbens. It has been our experience that manual microdissection from rapidly prepared brain slices provides the most reliable and rapid method of extracting the tissue relevant to the behavioral paradigm, and with experience, the boundaries of the tissue become evident and readily recognized. Alternatively, fine slices could be prepared, followed by laser-capture microdissection. Although this method enables highly defined delineation of the region of interest, it is slow (thus risking loss of labile mRNA), tedious and requires costly dedicated equipment (a microscope fitted with a laser-capture setup). The protocol defined herein could also be adapted to single-cell transcriptional analysis, by manual aspiration of cytoplasm of visually identified cells using patch pipettes29. It is important to note that the protocol described provides a population average, while it is highly likely that in most cases, only a subpopulation of the cells within the tissue are actually involved in responding to the experience. It is of interest to profile transcription in a selective manner from within specific cell populations responding to the experience, but discussion of these approaches is beyond the current scope.
For mRNA purification, reverse-transcription and qPCR querying, the tissue is disrupted by passing it through fine needles, followed by the utilization of commercially available kits (for more information, see Table 8). The choice is informed by experience with these methodologies, which ensure reliable extraction of high quality RNA and robust results from downstream applications.
While the protocol is described for high-throughput qPCR utilizing dynamic arrays, samples can be probed for gene expression using end-point PCR, low-throughput qPCR, gene expression microarrays or deep sequencing. The preference for high-throughput qPCR utilizing dynamic arrays is due to the fact that mRNA obtained from brain nuclei following behavioral paradigms is often of limiting quantities. Dynamic arrays provide a platform that enables efficient comprehensive analysis of transcripts from a large number of parallel samples in a single experiment. After the initial acquisition of the microfluidic system (commonly an institutional purchase), experiments are relatively inexpensive to run. Following this analysis, further querying of the samples could be performed using more costly platforms to search for novel transcripts (by microarrays or RNAseq) with the dynamic arrays providing a comprehensive reference for quality assurance. Finally, for data analysis, standard approaches are utilized. Specific pointers regarding issues that may arise will be discussed in the text of the protocol.
This protocol is most appropriate for investigators interested in a thorough investigation of their system of interest, studying multiple conditions and replicates. The protocol is also most suitable for investigators who have already honed in (through microarray or RNAseq experiments) on a subset of 50-500 genes of interest, which they are interested in querying repeatedly.

<table border="0" cellpadding="0" cellspacing="0" width="453">
	<tbody>
		<tr>
			<td>Virusol</td>
			<td>Oriek Medical</td>
			<td>J29D</td>
			<td></td>
		</tr>
		<tr>
			<td>Isoflurane, USP 100%</td>
			<td>MINRAD INC</td>
			<td>NDC 60307-110-25</td>
			<td></td>
		</tr>
		<tr>
			<td>RNeasy plus Universal Mini Kit</td>
			<td>QIAGENE</td>
			<td>73404</td>
			<td></td>
		</tr>
		<tr>
			<td>QIAshredder</td>
			<td>QIAGENE</td>
			<td>79654</td>
			<td></td>
		</tr>
		<tr>
			<td>High Capacity cDNA Reverse Transcription kit</td>
			<td>Invitrogene</td>
			<td>AB-4368814</td>
			<td></td>
		</tr>
		<tr>
			<td>TE Buffer</td>
			<td>Invitrogene</td>
			<td>1355656</td>
			<td></td>
		</tr>
		<tr>
			<td>Behaviour Chamber (MDF; 50X45cm)</td>
			<td>Self assembled</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Inner Perspex box (30X30cm)</td>
			<td>Self assembled</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>camera and video recorder</td>
			<td>Campden Inst</td>
			<td>CMD-80051</td>
			<td></td>
		</tr>
		<tr>
			<td>Media Recorder software</td>
			<td>Noldus</td>
			<td>NDS-NMR3-00M</td>
			<td></td>
		</tr>
		<tr>
			<td>Iris Scissors</td>
			<td>FST</td>
			<td>FST-14062-09</td>
			<td></td>
		</tr>
		<tr>
			<td>Sagital Brain slicer with a 0.5mm section</td>
			<td>Brain Tree Scientific</td>
			<td>BS-AL-505S</td>
			<td></td>
		</tr>
		<tr>
			<td>Bioanalyzer</td>
			<td>Agilent Technologies</td>
			<td>The Agilent 2100 Bioanalyzer</td>
			<td></td>
		</tr>
		<tr>
			<td>Thermal cycler</td>
			<td>Bio-Rad</td>
			<td>1852048</td>
			<td></td>
		</tr>
		<tr>
			<td>Inverted microspun spatula</td>
			<td>Bochem Instrument GmbH</td>
			<td>3213</td>
			<td></td>
		</tr>
		<tr>
			<td>Biomark HD Reader</td>
			<td>Fluidigm</td>
			<td>BMHD-BMKHD</td>
			<td></td>
		</tr>
		<tr>
			<td>Dynamic array Chip for 96.96gene expression</td>
			<td>Fluidigm</td>
			<td>BMK-M-96.96</td>
			<td></td>
		</tr>
	</tbody>
</table>

comprehensive analysis of transcription dynamics from brain samples following behavioral experience

The encoding of experiences in the brain and the consolidation of long-term memories depend on gene transcription. Identifying the function of specific genes in encoding experience is one of the main objectives of molecular neuroscience. Furthermore, the functional association of defined genes with specific behaviors has implications for understanding the basis of neuropsychiatric disorders. Induction of robust transcription programs has been observed in the brains of mice following various behavioral manipulations. While some genetic elements are utilized recurrently following different behavioral manipulations and in different brain nuclei, transcriptional programs are overall unique to the inducing stimuli and the structure in which they are studied1,2.
In this publication, a protocol is described for robust and comprehensive transcriptional profiling from brain nuclei of mice in response to behavioral manipulation. The protocol is demonstrated in the context of analysis of gene expression dynamics in the nucleus accumbens following acute cocaine experience. Subsequent to a defined in vivo experience, the target neural tissue is dissected; followed by RNA purification, reverse transcription and utilization of microfluidic arrays for comprehensive qPCR analysis of multiple target genes. This protocol is geared towards comprehensive analysis (addressing 50-500 genes) of limiting quantities of starting material, such as small brain samples or even single cells.
The protocol is most advantageous for parallel analysis of multiple samples (e.g. single cells, dynamic analysis following pharmaceutical, viral or behavioral perturbations). However, the protocol could also serve for the characterization and quality assurance of samples prior to whole-genome studies by microarrays or RNAseq, as well as validation of data obtained from whole-genome studies.

The quality of the results obtained by applying this protocol crucially depends upon a number of parameters. Proper experimental planning will result in minimal disturbance to the experimental mice, such that the experience tested (in this example, that of exposure to cocaine) will be the most dominant experience in their recent history, and therefore will result in a robust and specific transcriptional program. Figure 1 describes the experimental plan for behavioral sensitization to cocaine, defining th...

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Comprehensive Analysis of Transcription Dynamics from Brain Samples Following Behavioral Experience

This manuscript describes a protocol that applies comprehensive profiling for analysis of transcriptional programs induced in specific brain nuclei of rodents following behavioral paradigms. Herein, this approach is illustrated in the context of profiling genes induced in the nucleus accumbens (NAc) of mice following acute cocaine exposure, utilizing microfluidic qPCR arrays.

The encoding of experiences in the brain and the consolidation of long-term memories depend on gene transcription. Identifying the function of specific ...

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11.5K Views.  The Hebrew University of Jerusalem. This manuscript describes a protocol that applies comprehensive profiling for analysis of transcriptional programs induced in specific brain nuclei of rodents following behavioral paradigms. Herein, this approach is illustrated in the context of profiling genes induced in the nucleus accumbens (NAc) of mice following acute cocaine exposure, utilizing microfluidic qPCR arrays. 

Video: Comprehensive Analysis of Transcription Dynamics from Brain Samples Following Behavioral Experience

Stereotactic Injection of MicroRNA-expressing Lentiviruses to the Mouse Hippocampus CA1 Region and Assessment of the Behavioral Outcome

MicroRNAs (miRNAs) are small regulatory single-stranded RNA molecules around 22 nucleotides long that may each target numerous mRNA transcripts and dim an entire gene expression pathway by inducing destruction and/or inhibiting translation of these targets. Several miRNAs play key roles in maintaining neuronal structure and function and in higher-level brain functions, and methods are sought for manipulating their levels for exploring these functions. Here, we present a direct in vivo method for examining the cognitive consequences of enforced miRNAs excess in mice by stereotactic injection of miRNA-encoding virus particles. Specifically, the current protocol involves injection into the hippocampal CA1 region, which contributes to mammalian memory consolidation, learning, and stress responses, and offers a convenient injection site. The coordinates are measured according to the mouse bregma and virus perfusion is digitally controlled and kept very slow. After injection, the surgery wound is sealed and the animals recover. Lentiviruses encoding silencers of the corresponding mRNA targets serve to implicate the specific miRNA/target interaction responsible for the observed effect, with na&iuml;ve mice, mice injected with saline and mice injected with "empty" lentivirus vectors as controls. One month post-injection, the animals are examined in the Morris Water Maze (MWM) for assessing their navigation learning and memory abilities. The MWM is a round tank filled with colored water with a small platform submerged 1 cm below the water surface. Steady visual cues around the tank allow for spatial navigation (sound and the earth's magnetic field may also assist the animals in navigating). Video camera monitoring enables measuring the route of swim and the time to find and amount the platform. The mouse is first taught that mounting the hidden platform offers an escape from the enforced swimming; it is then tested for using this escape and finally, the platform is removed and probe tests examine if the mouse remembers its previous location. Repeated tests over several consecutive days highlight improved performance of tested mice at shorter latencies to find and mount the platform, and as more direct routes to reach the platform or its location. Failure to show such improvement represents impaired learning and memory and/or anxiety, which may then be tested specifically (e.g. in the elevated plus maze). This approach enables validation of specific miRNAs and target transcripts in the studied cognitive and/or stress-related processes.

MicroRNAs have significant roles in brain structure and function. Here we describe a method to enforce hippocampal miRNA over-expression using stereotactic injection of an engineered miRNA-expressing lentivirus. This approach can serve as a relatively rapid way to assess the in vivo effects of over-expressed miRNAs in specific brain regions.

MicroRNAs (miRNAs) are small regulatory single-stranded RNA molecules around 22 nucleotides long that may each target numerous mRNA transcripts and dim an ...

Compensatory Limb Use and Behavioral Assessment of Motor Skill Learning Following Sensorimotor Cortex Injury in a Mouse Model of Ischemic Stroke

Mouse models have become increasingly popular in the field of behavioral neuroscience, and specifically in studies of experimental stroke. As models advance, it is important to develop sensitive behavioral measures specific to the mouse. The present protocol describes a skilled motor task for use in mouse models of stroke. The Pasta Matrix Reaching Task functions as a versatile and sensitive behavioral assay that permits experimenters to collect accurate outcome data and manipulate limb use to mimic human clinical phenomena including compensatory strategies (i.e., learned non-use) and focused rehabilitative training. When combined with neuroanatomical tools, this task also permits researchers to explore the mechanisms that support behavioral recovery of function (or lack thereof) following stroke. The task is both simple and affordable to set up and conduct, offering a variety of training and testing options for numerous research questions concerning functional outcome following injury. Though the task has been applied to mouse models of stroke, it may also be beneficial in studies of functional outcome in other upper extremity injury models.

Mouse models have become increasingly popular in studies of behavioral neuroscience. As models advance, it is important to develop sensitive behavioral measures specific to the mouse. This protocol describes the Pasta Matrix Reaching Task, which is a skilled motor task for use in mouse models of stroke.

Mouse models have become increasingly popular in the field of behavioral neuroscience, and specifically in studies of experimental stroke. As models ...

Transcranial Magnetic Stimulation for Investigating Causal Brain-behavioral Relationships and their Time Course

Transcranial magnetic stimulation (TMS) is a safe, non-invasive brain stimulation technique that uses a strong electromagnet in order to temporarily disrupt information processing in a brain region, generating a short-lived &#8220;virtual lesion.&#8221; Stimulation that interferes with task performance indicates that the affected brain region is necessary to perform the task normally. In other words, unlike neuroimaging methods such as functional magnetic resonance imaging (fMRI) that indicate correlations between brain and behavior, TMS can be used to demonstrate causal brain-behavior relations. Furthermore, by varying the duration and onset of the virtual lesion, TMS can also reveal the time course of normal processing. As a result, TMS has become an important tool in cognitive neuroscience. Advantages of the technique over lesion-deficit studies include better spatial-temporal precision of the disruption effect, the ability to use participants as their own control subjects, and the accessibility of participants. Limitations include concurrent auditory and somatosensory stimulation that may influence task performance, limited access to structures more than a few centimeters from the surface of the scalp, and the relatively large space of free parameters that need to be optimized in order for the experiment to work. Experimental designs that give careful consideration to appropriate control conditions help to address these concerns. This article illustrates these issues with TMS results that investigate the spatial and temporal contributions of the left supramarginal gyrus (SMG) to reading.

Transcranial magnetic stimulation (TMS) is a technique for non-invasively disrupting neural information processing and measuring its effect on behavior. When TMS interferes with a task, it indicates that the stimulated brain region is necessary for normal task performance, allowing one to systematically relate brain regions to cognitive functions.

Transcranial magnetic stimulation (TMS) is a safe, non-invasive brain stimulation technique that uses a strong electromagnet in order to temporarily ...

Combined Shuttle-Box Training with Electrophysiological Cortex Recording and Stimulation as a Tool to Study Perception and Learning

Shuttle-box avoidance learning is a well-established method in behavioral neuroscience and experimental setups were traditionally custom-made; the necessary equipment is now available by several commercial companies. This protocol provides a detailed description of a two-way shuttle-box avoidance learning paradigm in rodents (here Mongolian gerbils; Meriones unguiculatus) in combination with site-specific electrical intracortical microstimulation (ICMS) and simultaneous chronical electrophysiological in vivo recordings. The detailed protocol is applicable to study multiple aspects of learning behavior and perception in different rodent species.
Site-specific ICMS of auditory cortical circuits as conditioned stimuli here is used as a tool to test the perceptual relevance of specific afferent, efferent and intracortical connections. Distinct activation patterns can be evoked by using different stimulation electrode arrays for local, layer-dependent ICMS or distant ICMS sites. Utilizing behavioral signal detection analysis it can be determined which stimulation strategy is most effective for eliciting a behaviorally detectable and salient signal. Further, parallel multichannel-recordings using different electrode designs (surface electrodes, depth electrodes, etc.) allow for investigating neuronal observables over the time course of such learning processes. It will be discussed how changes of the behavioral design can increase the cognitive complexity (e.g. detection, discrimination, reversal learning).

Shuttle-box avoidance learning is well-established in behavioral neuroscience. This protocol describes how shuttle-box learning in rodents can be combined with site-specific electrical intracortical microstimulation (ICMS) and simultaneous chronical in vivo recordings as a tool to study multiple aspects of learning and perception.

Shuttle-box avoidance learning is a well-established method in behavioral neuroscience and experimental setups were traditionally custom-made; the ...

Rodent Brain Microinjection to Study Molecular Substrates of Motivated Behavior

Brain microinjection can aid elucidation of the molecular substrates of complex behaviors, such as motivation. For this purpose rodents can serve as appropriate models, partly because the response to behaviorally relevant stimuli and the circuitry parsing stimulus-action outcomes is astonishingly similar between humans and rodents. In studying molecular substrates of complex behaviors, the microinjection of reagents that modify, augment, or silence specific systems is an invaluable technique. However, it is crucial that the microinjection site is precisely targeted in order to aid interpretation of the results. We present a method for the manufacture of surgical implements and microinjection needles that enables accurate microinjection and unlimited customizability with minimal cost. Importantly, this technique can be successfully completed in awake rodents if conducted in conjunction with other JoVE articles that covered requisite surgical procedures. Additionally, there are many behavioral paradigms that are well suited for measuring motivation. The progressive ratio is a commonly used method that quantifies the efficacy of a reinforcer to maintain responding despite an (often exponentially) increasing work requirement. This assay is sensitive to reinforcer magnitude and pharmacological manipulations, which allows reinforcing efficacy and/ or motivation to be determined. We also present a straightforward approach to program operant software to accommodate a progressive ratio reinforcement schedule.

Rodents are an appropriate model to investigate the molecular substrates of behavior and complex psychiatric disorders. Brain microinjection in awake rodents can be used to elucidate disease substrates. An efficient and customizable brain microinjection method as well as the execution of an operant paradigm that quantifies motivation is presented.

Brain microinjection can aid elucidation of the molecular substrates of complex behaviors, such as motivation. For this purpose rodents can serve as ...

Vagus Nerve Stimulation as a Tool to Induce Plasticity in Pathways Relevant for Extinction Learning

Extinction describes the process of attenuating behavioral responses to neutral stimuli when they no longer provide the reinforcement that has been maintaining the behavior. There is close correspondence between fear and human anxiety, and therefore studies of extinction learning might provide insight into the biological nature of anxiety-related disorders such as post-traumatic stress disorder, and they might help to develop strategies to treat them. Preclinical research aims to aid extinction learning and to induce targeted plasticity in extinction circuits to consolidate the newly formed memory. Vagus nerve stimulation (VNS) is a powerful approach that provides tight temporal and circuit-specific release of neurotransmitters, resulting in modulation of neuronal networks engaged in an ongoing task. VNS enhances memory consolidation in both rats and humans, and pairing VNS with exposure to conditioned cues enhances the consolidation of extinction learning in rats. Here, we provide a detailed protocol for the preparation of custom-made parts and the surgical procedures required for VNS in rats. Using this protocol we show how VNS can facilitate the extinction of conditioned fear responses in an auditory fear conditioning task. In addition, we provide evidence that VNS modulates synaptic plasticity in the pathway between the infralimbic (IL) medial prefrontal cortex and the basolateral complex of the amygdala (BLA), which is involved in the expression and modulation of extinction memory.

Vagus nerve stimulation (VNS) has emerged as a tool to induce targeted synaptic plasticity in the forebrain to modify a range of behaviors. This protocol describes how to implement VNS to facilitate the consolidation of fear extinction memory.

Extinction describes the process of attenuating behavioral responses to neutral stimuli when they no longer provide the reinforcement that has been ...

Assessing Working Memory in Children: The Comprehensive Assessment Battery for Children &#8211; Working Memory (CABC-WM)

The Comprehensive Assessment Battery for Children - Working Memory (CABC-WM) is a computer-based battery designed to assess different components of working memory in young school-age children. Working memory deficits have been identified in children with language-based learning disabilities, including dyslexia1,2 and language impairment3,4, but it is not clear whether these children exhibit deficits in subcomponents of working memory, such as visuospatial or phonological working memory. The CABC-WM is administered on a desktop computer with a touchscreen interface and was specifically developed to be engaging and motivating for children. Although the long-term goal of the CABC-WM is to provide individualized working memory profiles in children, the present study focuses on the initial success and utility of the CABC-WM for measuring central executive, visuospatial, phonological loop, and binding constructs in children with typical development. Immediate next steps are to administer the CABC-WM to children with specific language impairment, dyslexia, and comorbid specific language impairment and dyslexia.

Assessing Working Memory in Children: The Comprehensive Assessment Battery for Children &amp;#8211; Working Memory (CABC-WM)

Working memory predicts a significant amount of variance for a variety of cognitive tasks, including speaking, reading, and writing. However, few tools are available to assess working memory in children. We present an innovative, computer-based battery that comprehensively assesses different components of working memory in school-age children.

The Comprehensive Assessment Battery for Children - Working Memory (CABC-WM) is a computer-based battery designed to assess different components of ...

Detecting Behavioral Deficits in Rats After Traumatic Brain Injury

With the increasing incidence of traumatic brain injury (TBI) in both civilian and military populations, TBI is now considered a chronic disease; however, few studies have investigated the long-term effects of injury in rodent models of TBI. Shown here are behavioral measures that are well-established in TBI research for times early after injury, such as two weeks, until two months. Some of these methods have previously been used at later times after injury, up to one year, but by very few laboratories. The methods demonstrated here are a short neurological assessment to test reflexes, a Beam-Balance to test balance, a Beam-Walk to test balance and motor coordination, and a working memory version of the Morris water maze that can be sensitive to deficits in reference memory. Male rats were handled and pre-trained to neurological, balance, and motor coordination tests prior to receiving parasagittal fluid percussion injury (FPI) or sham injury. Rats can be tested on the short neurological assessment (neuroscore), the beam-balance, and the Beam-Walk multiple times, while testing on the water maze can only be done once. This difference is because rats can remember the task, thus confounding the results if repeated testing is attempted in the same animal. When testing from one to three days after injury, significant differences are detected in all three non-cognitive tasks. However, differences in the Beam-Walk task were not detectable at later time points (after 3 months). Deficits were detected at 3 months in the Beam-Balance and at 6 months in the neuroscore. Deficits in working memory were detected out to 12 months after injury, and a deficit in a reference memory first appeared at 12 months. Thus, standard behavioral tests can be useful measures of persistent behavioral deficits after FPI.

The goal of the behavioral tests presented here is to detect functional deficits in rats after traumatic brain injury. Four specific tests are presented that detect deficits in behaviors to reflect the damage to specific brain areas at times extending to one year after injury.

With the increasing incidence of traumatic brain injury (TBI) in both civilian and military populations, TBI is now considered a chronic disease; however, ...

An Automated T-maze Based Apparatus and Protocol for Analyzing Delay- and Effort-based Decision Making in  Free Moving Rodents

Many neurological and psychiatric patients demonstrate difficulties and/or deficits in decision making. Rodent models are helpful to produce a deeper understanding of the neurobiological causes underlying the decision-making problems. A cost-benefit based T-maze task is used for measuring decision making in which rodents choose between a high reward arm (HRA) and a low reward arm (LRA). There are two paradigms of the T-maze decision-making task, one in which the cost is a time delay and the other in which it is physical effort. Both paradigms require a tedious and labor-intensive management of experimental animals, multiple doors, pellet reward, and arm choice recordings. In the current work, we invented an apparatus based on traditional T-maze with full automation for pellet delivery, door management and choice recordings. This automated setup can be used for the evaluation of both delay- and effort-based decision making in rodents. With the protocol described here, our lab investigated the decision-making phenotypes of multiple genetically modified mice. In the representative data, we showed that the mice with ablated medial habenular showed aversions of both delay and effort and tended to choose the immediate and effortless reward. This protocol helps to decrease the variability caused by experimenter intervention and to enhance experiment efficiency. In addition, chronic silicon probe or microelectrode recording, fiber-optic imaging and/or manipulation of neural activity can be easily applied during the decision-making task using the setup described here.

This article introduces an automated T-maze apparatus that we invented, and a protocol based on this apparatus for analyzing delay-based decision making and effort-based decision making in free moving rodents.

Many neurological and psychiatric patients demonstrate difficulties and/or deficits in decision making. Rodent models are helpful to produce a deeper ...

Automated, Long-term Behavioral Assay for Cognitive Functions in Multiple Genetic Models of Alzheimer's Disease, Using IntelliCage

Multiple factors&#8212;such as aging and genes&#8212;are frequently associated with cognitive decline. Genetically modified mouse models of cognitive decline, such as Alzheimer&#39;s disease (AD), have become a promising tool to elucidate the underlying mechanisms and promote the therapeutic advances. An important step is the validation and characterization of expected behavioral abnormality in the models, in the case of AD, cognitive decline. The long-term behavioral investigations of laboratory animals to study the effect of aging demand substantial efforts from researchers. The IntelliCage system is a high-throughput and cost-effective test battery for mice that eliminates the need for daily human handling. Here, we describe how the system is utilized in the long-term phenotyping of a genetic Alzheimer&#39;s disease model, specifically focusing on the cognitive functions. The experiment employs repeated battery of tests that assess spatial learning and executive functions. This cost-effective age-dependent phenotyping allows us to identify the transient and/or permanent effects of genes on various cognitive aspects.

Automated, Long-term Behavioral Assay for Cognitive Functions in Multiple Genetic Models of Alzheimer&#039;s Disease, Using IntelliCage

This paper describes a protocol for cognitive assessments for genetic models of the Alzheimer&#39;s disease using the IntelliCage system, which is a high throughput automated behavioral monitoring system with operant conditioning.

Multiple factors&#8212;such as aging and genes&#8212;are frequently associated with cognitive decline. Genetically modified mouse models of cognitive ...