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><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>QIAGEN</td><td>73404</td><td></td></tr><tr><td>QIAshredder</td><td>QIAGEN</td><td>79654</td><td></td></tr><tr><td>High Capacity cDNA Reverse Transcription kit</td><td>Invitrogen</td><td>AB-4368814</td><td></td></tr><tr><td>TE Buffer</td><td>Invitrogen</td><td>1355656</td><td></td></tr><tr><td>Behavior Chamber (MDF; 50 x 45 cm)</td><td></td><td></td><td>Self assembled</td></tr><tr><td>Inner Perspex box (30 x 30 cm)</td><td></td><td></td><td>Self assembled</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>Vibratome</td><td>Campden Inst.</td><td>7000SMZ-2</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 microspoon 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 96.96 gene 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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11.6K 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

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Upon activation, cells rapidly change their functional programs and, thereby, their gene expression profile. Massive changes in gene expression occur, for example, during cellular differentiation, morphogenesis, and functional stimulation (such as activation of immune cells), or after exposure to drugs and other factors from the local environment. Depending on the stimulus and cell type, these changes occur rapidly and at any possible level of gene regulation. Displaying all molecular processes of a responding cell to a certain type of stimulus/drug is one of the hardest tasks in molecular biology. Here, we describe a protocol that enables the simultaneous analysis of multiple layers of gene regulation. We compare, in particular, transcription factor binding (Chromatin-immunoprecipitation-sequencing (ChIP-seq)), de novo transcription (4-thiouridine-sequencing (4sU-seq)), mRNA processing, and turnover as well as translation (ribosome profiling). By combining these methods, it is possible to display a detailed and genome-wide course of action.
Sequencing newly transcribed RNA is especially recommended when analyzing rapidly adapting or changing systems, since this depicts the transcriptional activity of all genes during the time of 4sU exposure (irrespective of whether they are up- or downregulated). The combinatorial use of total RNA-seq and ribosome profiling additionally allows the calculation of RNA turnover and translation rates. Bioinformatic analysis of high-throughput sequencing results allows for many means for analysis and interpretation of the data. The generated data also enables tracking co-transcriptional and alternative splicing, just to mention a few possible outcomes.
The combined approach described here can be applied for different model organisms or cell types, including primary cells. Furthermore, we provide detailed protocols for each method used, including quality controls, and discuss potential problems and pitfalls.

This protocol describes the combinatorial use of ChIP-seq, 4sU-seq, total RNA-seq, and ribosome profiling for cell lines and primary cells. It enables tracking changes in transcription-factor binding, de novo transcription, RNA processing, turnover and translation over time, and displaying the overall course of events in activated and/or rapidly changing cells.

Upon activation, cells rapidly change their functional programs and, thereby, their gene expression profile. Massive changes in gene expression occur, for ...

Genetics

Transcriptome Analysis of Single Cells

Many gene expression analysis techniques rely on material isolated from heterogeneous populations of cells from tissue homogenates or cells in culture.1,2,3 In the case of the brain, regions such as the hippocampus contain a complex arrangement of different cell types, each with distinct mRNA profiles. The ability to harvest single cells allows for a more in depth investigation into the molecular differences between and within cell populations. We describe a simple and rapid method for harvesting cells for further processing. Pipettes often used in electrophysiology are utilized to isolate (using aspiration) a cell of interest and conveniently deposit it into an Eppendorf tube for further processing with any number of molecular biology techniques. Our protocol can be modified for the harvest of dendrites from cell culture or even individual cells from acute slices.
We also describe the aRNA amplification method as a major downstream application of single cell isolations. This method was developed previously by our lab as an alternative to other gene expression analysis techniques such as reverse-transcription or real-time polymerase chain reaction (PCR).4,5,6,7,8 This technique provides for linear amplification of the polyadenylated RNA beginning with only femtograms of material and resulting in microgram amounts of antisense RNA. The linearly amplified material provides a more accurate estimation than PCR exponential amplification of the relative abundance of components of the transcriptome of the isolated cell. The basic procedure consists of two rounds of amplification. Briefly, a T7 RNA polymerase promoter site is incorporated into double stranded cDNA created from the mRNA transcripts. An overnight in vitro transcription (IVT) reaction is then performed in which T7 RNA polymerase produces many antisense transcripts from the double stranded cDNA. The second round repeats this process but with some technical differences since the starting material is antisense RNA. It is standard to repeat the second round, resulting in three rounds of amplification. Often, the third round in vitro transcription reaction is performed using biotinylated nucleoside triphosphates so that the antisense RNA produced can be hybridized and detected on a microarray.7,8

In this article we describe a simple method for the harvesting of single cells from rat primary neuronal cultures and subsequent transcriptome analysis using aRNA amplification. This approach is generalizable to any cell type.

Many gene expression analysis techniques rely on material isolated from heterogeneous populations of cells from tissue homogenates or cells in ...

Neuroscience

A Chromatin Assay for Human Brain Tissue

Chronic neuropsychiatric illnesses such as schizophrenia, bipolar disease and autism are thought to result from a combination of genetic and environmental factors that might result in epigenetic alterations of gene expression and other molecular pathology. Traditionally, however, expression studies in postmortem brain were confined to quantification of mRNA or protein. The limitations encountered in postmortem brain research   such as variabilities in autolysis time and tissue integrities   are also likely to impact any studies of higher order chromatin structures. However, the nucleosomal organization of genomic DNA   including DNA:core histone binding - appears to be largely preserved in representative samples provided by various brain banks. Therefore, it is possible to study the methylation pattern and other covalent modifications of the core histones at defined genomic loci in postmortem brain. Here, we present a simplified native chromatin immunoprecipitation (NChIP) protocol for frozen (never-fixed) human brain specimens. Starting with micrococcal nuclease digestion of brain homogenates, NChIP followed by qPCR can be completed within three days. The methodology presented here should be useful to elucidate epigenetic mechanisms of gene expression in normal and diseased human brain.

Until recently, expression studies on human brain were limited to quantification of RNA or protein. With the chromatin immunoprecipitation techniques described in this paper, it will be possible to map histone methylation and other epigenetic regulators of gene expression in postmortem brain.

Chronic neuropsychiatric illnesses such as schizophrenia, bipolar disease and autism are thought to result from a combination of genetic and environmental ...

Biology

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

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

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

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

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

Optimized Analysis of DNA Methylation and Gene Expression from Small, Anatomically-defined Areas of the Brain

Exposure to diet, drugs and early life adversity during sensitive windows of life 1,2 can lead to lasting changes in gene expression that contribute to the display of physiological and behavioural phenotypes. Such environmental programming is likely to increase the susceptibility to metabolic, cardiovascular and mental diseases 3,4.
DNA methylation and histone modifications are considered key processes in the mediation of the gene-environment dialogue and appear also to underlay environmental programming 5. In mammals, DNA methylation typically comprises the covalent addition of a methyl group at the 5-position of cytosine within the context of CpG dinucleotides.
CpG methylation occurs in a highly tissue- and cell-specific manner making it a challenge to study discrete, small regions of the brain where cellular heterogeneity is high and tissue quantity limited. Moreover, because gene expression and methylation are closely linked events, increased value can be gained by comparing both parameters in the same sample.
Here, a step-by-step protocol (Figure 1) for the investigation of epigenetic programming in the brain is presented using the 'maternal separation' paradigm of early life adversity for illustrative purposes. The protocol describes the preparation of micropunches from differentially-aged mouse brains from which DNA and RNA can be simultaneously isolated, thus allowing DNA methylation and gene expression analyses in the same sample.

A streamlined workflow to study DNA methylation and gene expression changes upon early-life stress is shown. Starting from maternal separation of newborn mice and isolation of discrete brain tissues, we represent a protocol to simultaneously isolate DNA and RNA from brain tissue punches for subsequent bisulfite sequencing and RT-PCR analysis.

Exposure to diet, drugs and early life adversity during sensitive windows of life 1,2 can lead to lasting changes in gene expression that contribute to ...

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

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

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

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

Pipeline for Analyzing Behavioral Responses to External Cues in MRI Environments

Profiling Maternal Behavior Responses During Whole-Brain Imaging

Recent advancements in whole-brain imaging tools have enabled neuroscientists to investigate how coordinated brain activity processes external cues, influencing internal state changes and eliciting behavioral responses. For example, functional magnetic resonance imaging (fMRI) is a noninvasive technique that allows for the measurement of whole-brain activity in awake, behaving mice using the blood oxygenation-level-dependent (BOLD) response. However, to fully understand BOLD responses evoked by external stimuli, it is crucial that experimenters also assess behavioral responses during scans. The MRI environment poses challenges to this goal, rendering commonly employed methods of behavioral monitoring incompatible. These challenges include (1) a restricted field of view and (2) the limited availability of equipment without ferromagnetic components. Presented here is a behavioral video analysis pipeline that overcomes these limitations by extracting valuable information from videos acquired within these environmental constraints, enabling the evaluation of behavior during the acquisition of whole-brain neural data. Employing methods such as optical flow estimation and dimensionality reduction, robust differences can be detected in behavioral responses to stimuli presented during fMRI scans. For example, representative results suggest that mouse pup vocalizations, but not pure tones, evoke significantly different behavioral responses in maternal versus virgin female mice. Moving forward, this behavioral analysis pipeline, initially tailored to overcome challenges in fMRI experiments, can be extended to various neural recording methods, providing versatile behavioral monitoring in constrained environments. The coordinated evaluation of behavioral and neural responses will offer a more comprehensive understanding of how the perception of stimuli leads to the coordination of complex behavioral outputs.

Presented here is a video analysis pipeline that overcomes challenges in behavioral monitoring within MRI environments, allowing for the detection of uninstructed behavioral responses to external cues. This analysis will facilitate a more comprehensive understanding of evoked internal state changes and brain-wide activity.

Recent advancements in whole-brain imaging tools have enabled neuroscientists to investigate how coordinated brain activity processes external cues, ...

High Resolution Quantitative Synaptic Proteome Profiling of Mouse Brain Regions After Auditory Discrimination Learning

The molecular synaptic mechanisms underlying auditory learning and memory remain largely unknown. Here, the workflow of a proteomic study on auditory discrimination learning in mice is described. In this learning paradigm, mice are trained in a shuttle box Go/NoGo-task to discriminate between rising and falling frequency-modulated tones in order to avoid a mild electric foot-shock. The protocol involves the enrichment of synaptosomes from four brain areas, namely the auditory cortex, frontal cortex, hippocampus, and striatum, at different stages of training. Synaptic protein expression patterns obtained from trained mice are compared to na&#239;ve controls using a proteomic approach. To achieve sufficient analytical depth, samples are fractionated in three different ways prior to mass spectrometry, namely 1D SDS-PAGE/in-gel digestion, in-solution digestion and phospho-peptide enrichment. 
High-resolution proteomic analysis on a mass spectrometer and label-free quantification are used to examine synaptic protein profiles in phospho-peptide-depleted and phospho-peptide-enriched fractions of synaptosomal protein samples. A commercial software package is utilized to reveal proteins and phospho-peptides with significantly regulated relative synaptic abundance levels (trained/na&#239;ve controls). Common and differential regulation modes for the synaptic proteome in the investigated brain regions of mice after training were observed. Subsequently, meta-analyses utilizing several databases are employed to identify underlying cellular functions and biological pathways.

The identification of molecules and pathways controlling synaptic plasticity and memory is still a major challenge in neuroscience. Here, a workflow is described addressing the relative quantification of synaptic proteins supposedly involved in the molecular reorganization of synapses during learning and memory consolidation in an auditory learning paradigm.

The molecular synaptic mechanisms underlying auditory learning and memory remain largely unknown. Here, the workflow of a proteomic study on auditory ...

Preparing Adult Drosophila melanogaster for Whole Brain Imaging during Behavior and Stimuli Responses

We present a method developed specifically to image the whole Drosophila brain during ongoing behavior such as walking. Head fixation and dissection are optimized to minimize their impact on behavior. This is first achieved by using a holder that minimizes movement hindrances. The back of the fly&#8217;s head is glued to this holder at an angle that allows optical access to the whole brain while retaining the fly&#8217;s ability to walk, groom, smell, taste and see. The back of the head is dissected to remove tissues in the optical path and muscles responsible for head movement artefacts. The fly brain can subsequently be imaged to record brain activity, for instance using calcium or voltage indicators, during specific behaviors such as walking or grooming, and in response to different stimuli. Once the challenging dissection, which requires considerable practice, has been mastered, this technique allows to record rich data sets relating whole brain activity to behavior and stimulus responses.

Preparing Adult Drosophila melanogaster for Whole Brain Imaging during Behavior and Stimuli Responses

We present a method specifically tailored to image the whole brain of adult Drosophila during behavior and in response to stimuli. The head is positioned to allow optical access to the whole brain, while the fly can move its legs and the antennae, the tip of the proboscis, and the eyes can receive sensory stimuli.

We present a method developed specifically to image the whole Drosophila brain during ongoing behavior such as walking. Head fixation and dissection are ...

Investigating Drivers of Antireward in Addiction Behavior with Anatomically Specific Single-Cell Gene Expression Methods

Increasing rates of addiction behavior have motivated mental health researchers and clinicians alike to understand antireward and recovery. This shift away from reward and commencement necessitates novel perspectives, paradigms, and hypotheses along with an expansion of the methods applied to investigate addiction. Here, we provide an example: A systems biology approach to investigate antireward that combines laser capture microdissection (LCM) and high-throughput microfluidic reverse transcription quantitative polymerase chain reactions (RT-qPCR). Gene expression network dynamics were measured and a key driver of neurovisceral dysregulation in alcohol and opioid withdrawal, neuroinflammation, was identified. This combination of technologies provides anatomic and phenotypic specificity at single-cell resolution with high-throughput sensitivity and specific gene expression measures yielding both hypothesis-generating datasets and mechanistic possibilities that generate opportunities for novel insights and treatments.

The combination of laser capture microdissection and microfluidic RT-qPCR provides anatomic and biotechnical specificity in measuring the transcriptome in single neurons and glia. Applying creative methods with a system's biology approach to psychiatric disease may lead to breakthroughs in understanding and treatment such as the neuroinflammation antireward hypothesis in addiction.

Increasing rates of addiction behavior have motivated mental health researchers and clinicians alike to understand antireward and recovery. This shift ...

Comprehensive Analysis of Transcription Dynamics from Brain Samples Following Behavioral Experience

Summary

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Chapters in this video

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Transcriptome Analysis of Single Cells

A Chromatin Assay for Human Brain Tissue

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

Optimized Analysis of DNA Methylation and Gene Expression from Small, Anatomically-defined Areas of the Brain

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

Profiling Maternal Behavior Responses During Whole-Brain Imaging

High Resolution Quantitative Synaptic Proteome Profiling of Mouse Brain Regions After Auditory Discrimination Learning

Preparing Adult Drosophila melanogaster for Whole Brain Imaging during Behavior and Stimuli Responses

Investigating Drivers of Antireward in Addiction Behavior with Anatomically Specific Single-Cell Gene Expression Methods