This work is supported by NIDDK of the NIH under Award Number R01DK116899, USDA/ARS under Award Number 3092-51000-064-000D, and a pilot award from the Baylor College of Medicine Cardiovascular Research Institute. The flowcharts were produced using BioRender.

The animal procedures were approved by the Institutional Animal Care and Use Committee at Baylor College of Medicine. All procedures were performed on C57BL/6J male mice aged 3 weeks and 3 months old. Prior to the dissection, all mice were euthanized using the approved rodent carbon dioxide euthanasia procedure. See the Table of Materials for details related to all materials, reagents, and instruments used in this protocol.
1. Dissection of scBAT
<ol>
	<li>Place the mouse carcass on the workbench and clean the surgical scissors and superfine point forceps with 70% ethanol.</li>
	<li>Spray the mouse&#39;s ventral neck with 70% ethanol to wet the fur and minimize fur contamination.</li>
	<li>Make a bilateral incision, approximately 1.5 cm, along the clavicles.</li>
	<li>From the ends of the previous incision, cut longitudinally towards the ears, approximately 1 cm long. This will form a squared U-shaped incision around the neck (Figure 1A,B). 
	NOTE: scBAT lies in the intermediate layer of the neck. The superficial layer, composed of the skin, subcutaneous adipose tissue, and salivary glands, is exposed during this step. The intermediate layer, along with scBAT, contains the jugular veins and neck muscles. The deep layer of the neck, containing deep neck BAT and artery and jugular veins, is exposed by removing the skeletal muscle.</li>
	<li>Place the mouse under a dissecting microscope and bring the exposed neck into focus (Figure 1C). 
	NOTE: This added step greatly increases the precision of tissue collection, necessary given the small size of scBAT.</li>
	<li>Expose the salivary glands fully by lifting the incised skin sections away with forceps.</li>
	<li>Using surgical scissors and forceps, disconnect the tissue connecting the salivary glands to the tissue around the clavicles and to each other.</li>
	<li>Expose the scBAT depots by lifting the salivary glands. Look for the BAT along the external jugular vein and possibly connected to the underside of the salivary glands. Identify it by its orangish color, which stands out against the surrounding tissue.</li>
	<li>Hold the target adipose tissue with forceps and gently peel it away from the salivary glands.</li>
	<li>Once detached from the salivary glands, continue to disconnect the scBAT from the external jugular vein and the musculature of the neck until the depots on either side of the neck can be removed whole.</li>
	<li>Inspect each dissected scBAT sample under the dissecting microscope (Figure 1D,E), using forceps to remove any remaining connective tissue.</li>
	<li>Place each sample into a glass scintillation vial containing 10 mL of phosphate-buffered saline solution (PBS) and remove the mouse from under the microscope.</li>
</ol>
2. Processing and hematoxylin and eosin (H&#38;E) staining of scBAT (illustrated in Figure 2A)
<ol>
	<li>Replace the PBS (step 1.12) with 10 mL of cold 4% paraformaldehyde (PFA) and place the vial on a nutator, rocking at 4 &#176;C overnight to fix the scBAT. 
	NOTE: Perfusion fixation may be applied in postnatal, especially adult mice, when further processing for immunohistochemistry analysis is needed.</li>
	<li>The next day, remove the PFA solution from the vial with a sterile transfer pipette and replace it with 10-15 mL of PBS. Place the vial on a nutator and rock for 30 min at room temperature. Replace PBS with 0.85% saline solution and continue rocking for another 30 min at room temperature. 
	NOTE: The saline solution is 0.85% saline (NaCl) w/v in DEPC-treated water (RNase-free). PBS can be substituted for the saline solution in this and the following step.</li>
	<li>Remove the 0.85% saline with a transfer pipette and add 10 mL of 70% Ethanol/0.85% saline solution to the vial. Store the vial in a 4 &#176;C fridge overnight or until ready for paraffin embedding. 
	NOTE: PBS can be used if 0.85% saline is not available. scBAT should be processed as soon as possible for easier sectioning and better-preserved tissue morphology.</li>
	<li>Prior to paraffin embedding, dehydrate scBAT through a series of ethanol exchanges to remove water from the tissue.
	<ol>
		<li>To begin, remove 70% ethanol/0.85% saline from the vial with a transfer pipette and add 10-15 mL of 95% Dehydrant Alcohol, rocking the vial on a nutator at room temperature for 1 h. Repeat this step one time. 
		NOTE: Ethanol can be used in place of dehydrant alcohol solutions.</li>
		<li>Next, replace 95% Dehydrant Alcohol with 10-15 mL of 100% Dehydrant Alcohol and continue rocking on a nutator for 1 h. Refill with new 100% Dehydrant Alcohol and continue to rock for several hours or overnight, depending on the quantity of scBAT in the vial.</li>
	</ol>
	</li>
	<li>To clear scBAT for embedding, add 10 mL of toluene to the vial and continue rocking on a nutator until scBAT is transparent, approximately 6-8 h. 
	NOTE: The duration of time necessary to achieve satisfactory clearing is dependent on the size of the scBAT. It is recommended to begin clearing immediately in the morning so that infiltration and embedding can take place in the afternoon.</li>
	<li>To embed scBAT in paraffin wax, remove toluene and add 10 mL of melted infiltration paraffin wax to the vial. Place the vial in an oven at 65 &#176;C for 1 h. Repeat this step with new wax. 
	NOTE: Begin melting wax pellets in an oven overnight before embedding begins to ensure the wax is fully liquid.</li>
	<li>Replace infiltration paraffin wax with embedding paraffin wax and place the vial at the same temperature for 1 h. Repeat this step once. 
	NOTE: The infiltration stage can be interrupted and continued later. Remove the vial from the oven and store it at room temperature until ready to continue.</li>
	<li>Embed the tissue by first placing it in a tissue embedding mold, add melted embedding wax to the mold, and reorient the tissue under a stereomicroscope. Then, place an embedding cassette on top of the wax and continue to pour embedding wax over the top of it until it is full and the embedding cap is fastened to the wax block. Transfer the block to a 4 &#176;C fridge overnight to let the wax stiffen and shrink before removing the metal mold.</li>
	<li>Section the scBAT with a microtome to a thickness of 5-6 &#181;m18, three to four sections per microscope slide, and place in a warm paraffin section floatation bath at ~42 &#176;C to allow the tissue sections to smooth out.</li>
	<li>Transfer the sections to slides and place the slides upright against the floatation bath to allow water to drip off the slides.</li>
	<li>Transfer the slides to a stainless staining rack and place the rack onto a slide drying bench to dry overnight. 
	NOTE: The paraffin slides can be stored long-term at room temperature before further processing is achieved.</li>
	<li>Perform the H&#38;E staining19. To begin, place the slides in a staining rack, then place the rack in a staining jar with xylene for 40 s. Repeat this step once. 
	NOTE: If paraffin is still visible after the two stages, wait until it has completely dissolved before continuing.</li>
	<li>To rehydrate the tissue, place the slide rack in a staining jar filled with 100% Dehydrant Alcohol for two 20 s stages, followed by a 15 s stage in 95% Dehydrant Alcohol, and a final 15 s rinse in ddH2O.</li>
	<li>Place the slides in a staining dish filled with hematoxylin solution for 75 s to achieve nuclear staining, then rinse the slides in a staining dish with ddH2O for 45 s. 
	NOTE: Time can be adjusted depending on the desired stain color.</li>
	<li>Differentiate the staining by dipping slides in a staining dish filled with HCl-ethanol solution for 15 s, then transfer slides to another ddH2O rinse for 15 s. 
	NOTE: The HCl-ethanol solution is prepared according to a published method19.</li>
	<li>For cytoplasmic staining, place the slide in an Eosin Y counterstain solution for 15 s.</li>
	<li>Dehydrate the tissue by dipping the slides for 15 s each in three sequential 95% Dehydrant Alcohol solution stages, then two sequential 100% Dehydrant Alcohol baths-the first for 15 s and the second for 45 s-to finish dehydration.</li>
	<li>Finally, transfer the slides to a xylene bath for 45 s to reacclimate the tissue to organic solvents. After this step, the staining is completed; remove the tissue from the solution.</li>
	<li>Apply mounting medium to each slide and coverslip it inside a chemical fume hood. Dry overnight before imaging. Imaging results are shown in Figure 2B.</li>
</ol>
3. Gene expression analysis of scBAT
<ol>
	<li>Tissue Collection (grinding)
	<ol>
		<li>After dissecting scBAT, immediately put the tissue into a microcentrifuge tube, poke a hole in the top of the tube with a sterile needle, and snap freeze in liquid nitrogen. 
		NOTE: The major steps of the protocol outlined here are illustrated in Figure 3A. Poking a hole in the top of the tube before dropping it into liquid nitrogen prevents the tube from bursting due to the sudden pressure change.</li>
		<li>Fill a plastic beaker with liquid nitrogen and leave a pestle and thin spatula to soak. 
		NOTE: It is important to keep the temperature of all tools and tissue samples as cold as possible, close to the temperature of liquid nitrogen, during the entire procedure to prevent the tissue from thawing. Thawed adipose tissue is very adherent and makes the powdering more challenging. Only remove tools and samples from liquid nitrogen baths immediately before use.</li>
		<li>Take one snap-frozen tissue sample at a time and pour it from its microcentrifuge tube into the mortar.</li>
		<li>Add a small amount of liquid nitrogen to the mortar, then use the pestle to grind the frozen tissue until it is completely pulverized. 
		NOTE: If the tissue starts becoming soft or sticky at any point, it is thawing; pour more liquid nitrogen into the mortar.</li>
		<li>Use the thin spatula to carefully scrape and transfer the pulverized tissue back into the microcentrifuge tube. Pour liquid nitrogen into the mortar while scraping to gather leftover bits of tissue before transferring with a spatula. Repeat the transfer steps until all the tissue is removed from the mortar.</li>
		<li>Clean the mortar with a light-duty tissue wiper and 70% ethanol before dumping the next sample to grind. Store the powdered tissue in a -80 &#176;C freezer long-term.</li>
	</ol>
	</li>
	<li>Total RNA isolation
	<ol>
		<li>Preparation
		<ol>
			<li>Clean the workbench, pipettes, tip holders, and tube racks with both 70% ethanol and surface decontaminant to remove RNase.</li>
			<li>Run the centrifuge machine to reach 4 &#176;C.</li>
			<li>Warm the elution solution to 70 &#176;C.</li>
			<li>Dilute the DNase I by mixing 5 &#956;L of reconstituted DNase I with 75 &#956;L of DNase dilution solution per sample. Place the DNase I solution on ice until use.</li>
		</ol>
		</li>
		<li>Procedure
		<ol>
			<li>For each sample, label two microcentrifuge tubes, two column holding tubes (two capless graduated microcentrifuge tubes), and one binding mini column.</li>
			<li>Add 500 &#956;L of RNA isolation solution to each sample and sonicate using a pellet pestle motor for 30 s.</li>
			<li>Get a syringe for each sample and pipet up and down 10x to further lyse the tissue. Ensure that no solids are visible after syringing.</li>
			<li>Add 250 &#956;L of chloroform and vortex occasionally while waiting 5 min for the samples to incubate at room temperature.</li>
			<li>Centrifuge at 21,000 &#215; g for 20 min at 4 &#176;C.</li>
			<li>Transfer the top aqueous portion to a new microcentrifuge tube and add an equivalent amount of 70% ethanol (~500 &#956;L). 
			NOTE: The top aqueous portion should be clear, the bottom should be the red RNA isolation solution, and between the two layers should be some unwanted solids.</li>
			<li>Transfer 500 &#956;L of the new lysate into the binding column. Centrifuge at 18,000 &#215; g for 60 s and then discard the filtrate.</li>
			<li>Repeat the previous step with the remaining lysate to get all the RNA into the binding column.</li>
			<li>Add 700 &#956;L of low-stringency wash to the binding column, centrifuge for 30 s, and discard the filtrate.</li>
			<li>Add 80 &#956;L of diluted DNase I to each binding column. Incubate for 15 min at room temperature.</li>
			<li>Add 700 &#956;L of high stringency wash, centrifuge for 30 s, and discard the filtrate.</li>
			<li>Add 700 &#956;L of low stringency wash, centrifuge for 60 s, and discard the filtrate.</li>
			<li>Move the binding columns into the 2nd new capless column holding tube and centrifuge for 2 min to ensure all liquids are removed from the binding column.</li>
			<li>Move the binding columns to a new microcentrifuge tube and add 30 &#956;L of warmed elution solution. Incubate at room temperature for 1 min.</li>
			<li>Centrifuge for 2 min to collect the eluted RNA at the bottom of the microcentrifuge tube.</li>
			<li>Measure the total RNA concentration using a spectrophotometer. 
			NOTE: If total RNA purity is low, indicated by a 260/280 value below 2.0 or 260/230 value below 1.8, then after step 3.2.2.12., the samples can be washed once more with low stringency wash followed by being washed with 80% ethanol before continuing with step 3.2.2.13.</li>
			<li>Store the RNA in a -80 &#176;C freezer.</li>
		</ol>
		</li>
		<li>Reverse transcription (RT)
		<ol>
			<li>In a PCR tube strip, add 0.5-1 &#956;g of total RNA diluted in DEPC-treated water to a total of 8 &#956;L for each RNA sample to a different well. 
			NOTE: The amount of RNA used for reverse transcription can be scaled up or down according to the manufacturer&#39;s instructions.</li>
			<li>Add 1 &#956;L Oligo dT and 1 &#956;L of dNTPs to each sample in the PCR tube. Ensure that the total volume is 10 &#956;L per sample.</li>
			<li>Place the PCR tube strip in a thermocycler and set it to 65 &#176;C for 5 min followed by 4 &#176;C indefinitely.</li>
			<li>After 5 min at 65 &#176;C, take out the PCR tube strip and place the tube on ice for at least 2 min. After incubation on ice, add five reagents: 4 &#956;L of 5x First-Strand buffer, 2 &#956;L of 25 mM MgCl2, 2 &#956;L of 0.1 M DTT, 1 &#956;L of RNase inhibitor, and 1 &#956;L of reverse transcriptase to each sample. Ensure that the total volume is now 20 &#956;L per sample.</li>
			<li>Place the PCR tube strip back into the thermocycler and set the program to 50 &#176;C for 50 min, then 85 &#176;C for 5 min, then 4 &#176;C indefinitely.</li>
			<li>Once the program reaches 4 &#176;C, take out the strip and add 1 &#956;L of Ribonuclease H (RNase H). 
			NOTE: RNase H is used to remove any remaining RNA template in the RT reaction; by this step, the desired RNA should already be converted to cDNA.</li>
			<li>Place the strip back into the thermocycler and run 37 &#176;C for 20 min and then 4 &#176;C indefinitely.</li>
			<li>Reverse transcription is complete; measure cDNA concentration using a spectrophotometer.</li>
			<li>Dilute the cDNA to 250 ng/&#956;L; store the cDNA in either a -80 &#176;C or -20 &#176;C freezer.</li>
		</ol>
		</li>
		<li>Quantitative PCR (qPCR)
		<ol>
			<li>Make a spreadsheet to organize the position of every primer and sample on the 96-well qPCR plate. 
			NOTE: One of the primers needs to be a reference gene to normalize the expression of all other genes of interest, such as 36B4.</li>
			<li>Make a primer master mix for each &#34;primer + sample&#34; combination. To each qPCR reaction well, add 3 &#956;L of Molecular Biology Grade Water, 5 &#956;L of qPCR enzyme master mixture, 0.5 &#956;L of forward primer, and 0.5 &#956;L of reverse primer, which adds up to 9 &#956;L per reaction. Add 1 &#956;L of cDNA per reaction to make a total of 10 &#956;L per reaction well. 
			NOTE: The standard is to have three technical replicates for each &#34;primer + sample&#34; combination, so each master mix should be 4x of the above quantities.</li>
			<li>Add 1 &#956;L of cDNA for each replicate to each primer master mix. If each master mix is 4x, then pipet 4 &#956;L of each sample cDNA into their own labeled tube.</li>
			<li>Finally, pipet 10 &#956;L of each reaction mix into the 96-well qPCR plate in the positions determined by the spreadsheet.</li>
			<li>Seal the plate with a thick adhesive seal, and then centrifuge the 96-well plate at 450 &#215; g at 20 &#176;C for 2 min. 
			NOTE: It is critical that the plate is fully sealed to avoid samples evaporating during thermocycling. Use light-duty tissue wipers to press the seal down onto the plate, especially the edges.</li>
			<li>Run the plate in a real-time PCR instrument. Program the PCR reaction according to the manufacturer&#39;s instructions: 2 min at 50 &#176;C, followed by another 2 min at 95 &#176;C, and finally 40 cycles of 15 s at 95 &#176;C and 30 s at 60 &#176;C. The results of qPCR gene expression analysis are shown in Figure 3B.</li>
		</ol>
		</li>
	</ol>
	</li>
</ol>

Morphological and Molecular Characterization of the scBAT in Mice

<ol>
	<li>Boutari, C., Mantzoros, C. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+2022+update+on+the+epidemiology+of+obesity+and+a+call+to+action:+as+its+twin+COVID-19+pandemic+appears+to+be+receding,+the+obesity+and+dysmetabolism+pandemic+continues+to+rage+on.">A 2022 update on the epidemiology of obesity and a call to action: as its twin COVID-19 pandemic appears to be receding, the obesity and dysmetabolism pandemic continues to rage on.</a> Metabolism. 133, 155217 (2022).</li><li>Hales, C. M., Carroll, M. D., Fryar, C. D., Ogden, C. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Prevalence+of+obesity+and+severe+obesity+among+adults:+United+States,+2017-2018.">Prevalence of obesity and severe obesity among adults: United States, 2017-2018.</a> NCHS Data Brief. (360), 1-8 (2020).</li><li>Berry, D. C., Stenesen, D., Zeve, D., Graff, J. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+developmental+origins+of+adipose+tissue.">The developmental origins of adipose tissue.</a> Development. 140 (19), 3939-3949 (2013).</li><li>Wang, W., Seale, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Control+of+brown+and+beige+fat+development.">Control of brown and beige fat development.</a> Nat Rev Mol Cell Biol. 17 (11), 691-702 (2016).</li><li>Maliszewska, K., Kretowski, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Brown+adipose+tissue+and+its+role+in+insulin+and+glucose+homeostasis.">Brown adipose tissue and its role in insulin and glucose homeostasis.</a> Int J Mol Sci. 22 (4), 1530 (2021).</li><li>Cannon, B., Nedergaard, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Brown+adipose+tissue:+function+and+physiological+significance.">Brown adipose tissue: function and physiological significance.</a> Physiol Rev. 84 (1), 277-359 (2004).</li><li>Cypess, A. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+and+importance+of+brown+adipose+tissue+in+adult+humans.">Identification and importance of brown adipose tissue in adult humans.</a> N Engl J Med. 360 (15), 1509-1517 (2009).</li><li>van Marken Lichtenbelt, W. D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cold-activated+brown+adipose+tissue+in+healthy+men.">Cold-activated brown adipose tissue in healthy men.</a> N Engl J Med. 360 (15), 1500-1508 (2009).</li><li>Virtanen, K. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Functional+brown+adipose+tissue+in+healthy+adults.">Functional brown adipose tissue in healthy adults.</a> N Engl J Med. 360 (15), 1518-1525 (2009).</li><li>Cypess, A. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Anatomical+localization,+gene+expression+profiling+and+functional+characterization+of+adult+human+neck+brown+fat.">Anatomical localization, gene expression profiling and functional characterization of adult human neck brown fat.</a> Nat Med. 19 (5), 635-639 (2013).</li><li>Leitner, B. P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mapping+of+human+brown+adipose+tissue+in+lean+and+obese+young+men.">Mapping of human brown adipose tissue in lean and obese young men.</a> Proc Natl Acad Sci U S A. 114 (32), 8649-8654 (2017).</li><li>Mo, Q., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+and+characterization+of+a+supraclavicular+brown+adipose+tissue+in+mice.">Identification and characterization of a supraclavicular brown adipose tissue in mice.</a> JCI Insight. 2 (11), e93166 (2017).</li><li>Shi, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gene+Expression+Analysis+of+Environmental+Temperature+and+High-Fat+Diet-Induced+Changes+in+Mouse+Supraclavicular+Brown+Adipose+Tissue.">Gene Expression Analysis of Environmental Temperature and High-Fat Diet-Induced Changes in Mouse Supraclavicular Brown Adipose Tissue.</a> Cells. 10 (6), 1370 (2021).</li><li>Chang, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Loss+of+perivascular+adipose+tissue+on+peroxisome+proliferator-activated+receptor-gamma+deletion+in+smooth+muscle+cells+impairs+intravascular+thermoregulation+and+enhances+atherosclerosis.">Loss of perivascular adipose tissue on peroxisome proliferator-activated receptor-gamma deletion in smooth muscle cells impairs intravascular thermoregulation and enhances atherosclerosis.</a> Circulation. 126 (9), 1067-1078 (2012).</li><li>Ye, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Developmental+and+functional+characteristics+of+the+thoracic+aorta+perivascular+adipocyte.">Developmental and functional characteristics of the thoracic aorta perivascular adipocyte.</a> Cell Mol Life Sci. 76 (4), 777-789 (2019).</li><li>de Jong, J. M., Larsson, O., Cannon, B., Nedergaard, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+stringent+validation+of+mouse+adipose+tissue+identity+markers.">A stringent validation of mouse adipose tissue identity markers.</a> Am J Physiol Endocrinol Metab. 308 (12), E1085-E1105 (2015).</li><li>Fu, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neural+crest+cells+differentiate+into+brown+adipocytes+and+contribute+to+periaortic+arch+adipose+tissue+formation.">Neural crest cells differentiate into brown adipocytes and contribute to periaortic arch adipose tissue formation.</a> Arterioscler Thromb Vasc Biol. 39 (8), 1629-1644 (2019).</li><li>Tucker, D. K., Foley, J. F., Bouknight, S. A., Fenton, S. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sectioning+mammary+gland+whole+mounts+for+lesion+identification.">Sectioning mammary gland whole mounts for lesion identification.</a> J Vis Exp. (125), e55796 (2017).</li><li>Berry, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Imaging+of+adipose+tissue.">Imaging of adipose tissue.</a> Methods Enzymol. 537, 47-73 (2014).</li></ol>

The authors have no conflicts of interest to disclose.

In this protocol, we present in detail the procedures for dissecting and processing scBAT for H&#38;E and gene expression analyses. Because scBAT resides in the intermediate layer of the neck and lies along the large veins, the isolation of this depot requires precise technique. Specifically, to gain a clear view of the depot, we recommend placing the mouse under a dissecting microscope after the neck has been opened. Using a pair of superfine point forceps to peel scBAT off the salivary gland and surrounding veins, care...

The increasing prevalence of obesity in the U.S. and worldwide has ignited great interest in understanding its etiology and identifying potential treatments1,2. Adipose tissue plays a vital role in metabolism, and dysregulation of the adipose tissue can lead to the development of obesity. Generally, there are two types of adipose tissues, white and brown adipose tissue. While white adipose tissue (WAT) can store chemical energy and secrete endocrine factors, brown adipose tissue (BAT) can use chemical energy to generate heat and maintain body temperature in the cold3,4. Because of this unique ability, activation of BAT can also increase energy expenditure and improve insulin sensitivity5.
BAT exerts its function through non-shivering thermogenesis, a process mediated by uncoupling protein 1 (UCP1)6. Mammals, including mice and humans, possess varying amounts of BAT. The classical view of BAT is that these adipose tissues are more abundant in mice and infants than in adult humans. iBAT, located in the upper dorsal flank between the scapulae, is the most studied BAT depot in mice. By applying radioisotope imaging and biopsy tests, recent studies identified several BAT depots in adult humans. Some of them, including the depots found in the deep neck and supraclavicular region, had not previously been identified in mice or other model animals7,8,9,10,11. Among these BAT depots, the scBAT is the most frequently seen depot in adult humans. To better understand the origin and molecular contribution of these newly found BAT depots in humans, it is essential to identify equivalent depots in mice that allow genetic and molecular manipulations to trace and test the functional role of these depots. Thus, we and others identified a few previously unknown BAT depots in different anatomical locations in mice, including scBAT12,13, thoracic perivascular BAT14,15, perirenal BAT16, and periaortic BAT17. Mouse scBAT anatomically resembles human scBAT and morphologically resembles classical iBAT, expressing high levels of UCP112.
Unlike mouse iBAT, which can be readily dissected, scBAT is situated in the intermediate layer of the mouse neck, beneath the salivary glands and along the external jugular vein. Isolation of this depot for histological and molecular analyses can be challenging. Here, we describe in detail the procedure for dissecting scBAT from postnatal and adult mice and processing this depot for histology and gene expression analysis.

<table><tbody><tr><td>95% Dehydrant Alcohol (Flex 95)</td><td>Epredia</td><td>8201</td><td></td></tr><tr><td>100% Dehydrant Alcohol (Flex 100)</td><td>Epredia</td><td>8101</td><td></td></tr><tr><td>96-well PCR plate</td><td>Bio-Rad</td><td>MLL9601</td><td></td></tr><tr><td>Aurum Binding Mini Column</td><td>Bio-Rad</td><td>7326826</td><td></td></tr><tr><td>Aurum High Stringency Wash</td><td>Bio-Rad</td><td>7326803</td><td></td></tr><tr><td>Aurum Low Stringency Wash</td><td>Bio-Rad</td><td>7326804</td><td></td></tr><tr><td>Base Molds (for embedding)</td><td>Tissue-Tek</td><td>4122</td><td></td></tr><tr><td>BD PrecisionGlide Needle 21g x 1 1/2&quot;</td><td>Becton Dickinson</td><td>305167</td><td></td></tr><tr><td>C1000 Touch Thermal Cycler</td><td>Bio-Rad</td><td>1840148</td><td></td></tr><tr><td>Capless Microcentrifuge Tubes 2 mL</td><td>Fisherbrand</td><td>02-681-453</td><td></td></tr><tr><td>Centrifuge&amp;nbsp;</td><td>Eppendorf</td><td>5430R</td><td></td></tr><tr><td>CFX Opus 96 Real-Time PCR Instrument</td><td>Bio-Rad</td><td>12011319</td><td></td></tr><tr><td>Chloroform</td><td>Thermo Scientific Chemicals</td><td>383760010</td><td></td></tr><tr><td>Cytoseal 60 Low-viscosity mounting medium</td><td>Epredia</td><td>83104</td><td></td></tr><tr><td>DEPC-Treated Water</td><td>Ambion</td><td>AM 9906</td><td></td></tr><tr><td>Dissecting Microscope</td><td>Nikon</td><td>SMZ1500</td><td></td></tr><tr><td>DNase Dilution Solution</td><td>Bio-Rad</td><td>7326805</td><td></td></tr><tr><td>DNase I</td><td>Bio-Rad</td><td>7326828</td><td></td></tr><tr><td>dNTPs</td><td>Invitrogen</td><td>18427013</td><td></td></tr><tr><td>Elution solution</td><td>Bio-Rad</td><td>7326801</td><td></td></tr><tr><td>EM 400 embedding medium paraffin</td><td>Leica Biosystems</td><td>3801320</td><td></td></tr><tr><td>Eosin Y (0.5% w/v)</td><td>RICCA</td><td>2858-16</td><td></td></tr><tr><td>Formula R Infiltration medium paraffin</td><td>Leica Biosystems</td><td>3801470</td><td></td></tr><tr><td>Genemark Nutator Gyromixer 349</td><td>Bio Express</td><td>S-3200-2</td><td></td></tr><tr><td>Gill #3 Hematoxylin</td><td>Sigma-Aldrich</td><td>GHS332-1L</td><td></td></tr><tr><td>HCl (for HCL-Ethanol)</td><td>Fisher Chemical</td><td>A142212</td><td></td></tr><tr><td>IP VI Embedding Cassettes</td><td>Leica Biosystems</td><td>39LC-550-5-L</td><td></td></tr><tr><td>Koptec&#039;s Pure Ethanol - 200 Proof (for 70% Ethanol)</td><td>Decon Labs</td><td>V1001</td><td></td></tr><tr><td>MgCl&lt;sub&gt;2&lt;/sub&gt; (25 mM)</td><td>Thermo Fisher Scientific</td><td>R0971</td><td></td></tr><tr><td>Microcentrifuge Tubes 1.7 mL</td><td>Avantor</td><td>87003-294</td><td></td></tr><tr><td>Microseal &#039;B&#039; Seals (adhseive seals)</td><td>Bio-Rad</td><td>MSB1001</td><td></td></tr><tr><td>Microtome</td><td>Leica Biosystems</td><td>RM2245</td><td></td></tr><tr><td>Molecular Biology Grade Water</td><td>Corning</td><td>46-000-CM</td><td></td></tr><tr><td>Mortar Coors Tek</td><td>Thomas Scientific</td><td>60310</td><td></td></tr><tr><td>NaCl (for 0.85% saline)</td><td>Fisher Bioreagents</td><td>BP358-212</td><td></td></tr><tr><td>NanoDrop Spectrophotometer</td><td>NanoDrop Technologies</td><td>ND-1000 UV/Vis</td><td></td></tr><tr><td>Oligo dT</td><td>Invitrogen</td><td>18418020</td><td></td></tr><tr><td>Paraffin Section Flotation Bath</td><td>Boekel Scientific</td><td>14792V</td><td></td></tr><tr><td>Paraformaldehyde (PFA)</td><td>Sigma-Aldrich</td><td>P6148-500G</td><td></td></tr><tr><td>PCR Tube Strip</td><td>Avantor</td><td>76318-802</td><td></td></tr><tr><td>Pestle by Coors Tek</td><td>Thomas Scientific</td><td>60311</td><td></td></tr><tr><td>Pestle Pellet Motor</td><td>Kimble</td><td>749540-0000</td><td></td></tr><tr><td>Phosphate Buffer Saline (PBS)</td><td>Sigma-Aldrich</td><td>D8537-500ML</td><td></td></tr><tr><td>Precision Model 19 Vacuum Oven&amp;nbsp;</td><td>Thermo Fisher Scientific</td><td>CAT# 51221162</td><td></td></tr><tr><td>Primer: 36B4&amp;nbsp; (forward) 10 &amp;mu;M&lt;br/&gt; 5&#039; TGA AGT GCT CGA CAT CAC AGA GCA 3&amp;rsquo;</td><td></td><td></td><td>Chen lab Oligo database</td></tr><tr><td>Primer: 36B4 (reverse) 10 &amp;mu;M&lt;br/&gt; 5&#039; GCT TGT ACC CAT TGA TGA TGG AGT GT 3&amp;rsquo;</td><td></td><td></td><td>Chen lab Oligo database</td></tr><tr><td>Primer: Fabp4 (forward) 10 &amp;mu;M&lt;br/&gt; 5&amp;rsquo; ACA CCG AGA TTT CCT TCA AAC TG 3&amp;rsquo;</td><td></td><td></td><td>Chen lab Oligo database</td></tr><tr><td>Primer: Fabp4 (reverse) 10 &amp;mu;M&lt;br/&gt; 5&amp;rsquo; CCA TCT AGG GTT ATG ATG CTC TTC A 3&amp;rsquo;</td><td></td><td></td><td>Chen lab Oligo database</td></tr><tr><td>Primer: Glut 4 (forward primer) 10 &amp;mu;M&lt;br/&gt; 5&amp;rsquo; CTG ATT CTG CTG CCC TTC TGT CCT 3&amp;rsquo;</td><td></td><td></td><td>Chen lab Oligo database</td></tr><tr><td>Primer: Glut 4 (reverse) 10 &amp;mu;M&lt;br/&gt; 5&amp;rsquo; GAC ATT GGA CGC TCT CTC TCC AAC TT 3&amp;rsquo;</td><td></td><td></td><td>Chen lab Oligo database</td></tr><tr><td>Primer: PPARg (forward) 10 &amp;mu;M&lt;br/&gt; 5&amp;rsquo; AGG GCG ATC TTG ACA GGA AAG ACA 3&amp;rsquo;</td><td></td><td></td><td>Chen lab Oligo database</td></tr><tr><td>Primer: PPARg (reserve) 10 &amp;mu;M&lt;br/&gt; 5&amp;rsquo; AAA TTC GGA TGG CCA CCT CTT TGC 3&amp;rsquo;</td><td></td><td></td><td>Chen lab Oligo database</td></tr><tr><td>Primer: Ppargc1a (reverse) 10 &amp;mu;M&lt;br/&gt; 5&#039; ATG TTG CGA CTG CGG TTG TGT ATG 3&amp;rsquo;</td><td></td><td></td><td>Chen lab Oligo database</td></tr><tr><td>Primer: Ppargc1a(forward) 10 &amp;mu;M&lt;br/&gt; 5&#039; ACG TCC CTG CTC AGA GCT TCT CA 3&amp;rsquo;</td><td></td><td></td><td>Chen lab Oligo database</td></tr><tr><td>Primer: Ucp1 (forward) 10 &amp;mu;M&lt;br/&gt; 5&amp;rsquo; AGC CAC CAC AGA AAG CTT GTC AAC 3&amp;rsquo;</td><td></td><td></td><td>Chen lab Oligo database</td></tr><tr><td>Primer: Ucp1 (reverse) 10 &amp;mu;M&lt;br/&gt; 5&amp;rsquo; ACA GCT TGG TAC GCT TGG GTA CTG 3&amp;rsquo;</td><td></td><td></td><td>Chen lab Oligo database</td></tr><tr><td>RNA isolation solution (PureZol)</td><td>Bio-Rad</td><td>7326880</td><td></td></tr><tr><td>RNase Away (surface decontaminant)</td><td>Thermo Scientific</td><td>1437535</td><td></td></tr><tr><td>RNase H</td><td>NEB</td><td>M0297S</td><td></td></tr><tr><td>Rnase inhibitor (RNase Out)</td><td>Invitrogen</td><td>10777019</td><td></td></tr><tr><td>Scintillation Vial (glass)</td><td>Electron Microscopy Sciences</td><td>72632</td><td></td></tr><tr><td>Slide drying bench&amp;nbsp;</td><td>Electrothermal (Cole-Parmer)</td><td>MH6616</td><td></td></tr><tr><td>Stainless staining rack</td><td>Electron Microscopy Sciences</td><td>70312-54</td><td></td></tr><tr><td>Stereo microscope (for embedding)</td><td>Olympus</td><td>SZ51</td><td></td></tr><tr><td>Sugical scissors</td><td>McKesson</td><td>43-1-104</td><td></td></tr><tr><td>Superfine point Straight Dissecting Forceps</td><td>Avantor</td><td>82027-402</td><td></td></tr><tr><td>Superfrost Plus Microscope Slides</td><td>Fisher Scientific</td><td>12-550-15</td><td></td></tr><tr><td>Superscript III Reverse Transcriptase (Includes 5x First-Strand Buffer and 0.1M DTT)&amp;nbsp;</td><td>Invitrogen</td><td>18080044</td><td></td></tr><tr><td>SUR-VET syringe with needle 25 G x 5/8&quot;, 1 mL</td><td>Terumo</td><td>100281</td><td></td></tr><tr><td>SYBR Green (qPCR enzyme master mixture)</td><td>Applied Biosystems</td><td>A25778</td><td></td></tr><tr><td>Tissue-Tek Manual Slide Staining Set (jars)</td><td>Electron Microscopy Sciences</td><td>SKU: 62540-01</td><td></td></tr><tr><td>Toluene</td><td>Fisher Chemical</td><td>T324-1</td><td></td></tr><tr><td>Transfer pipette</td><td>Avantor</td><td>414004-005</td><td></td></tr><tr><td>Xylene</td><td>Fisher Chemical</td><td>X3P-1GAL</td><td></td></tr></tbody></table>

dissection, histological processing, and gene expression analysis of murine supraclavicular brown adipose tissue

Brown adipose tissue (BAT)-mediated thermogenesis plays an important role in the regulation of metabolism, and its morphology and function can be greatly impacted by environmental stimuli in mice and humans. Currently, murine interscapular BAT (iBAT), which is located between two scapulae in the upper dorsal flank of mice, is the main BAT depot used by research laboratories to study BAT function. Recently, a few previously unknown BAT depots were identified in mice, including one analogous to human supraclavicular brown adipose tissue. Unlike iBAT, murine supraclavicular brown adipose tissue (scBAT) is situated in the intermediate layer of the neck and thus cannot be accessed as readily.
To facilitate the study of newly identified mouse scBAT, presented herein is a protocol detailing the steps to dissect intact scBAT from postnatal and adult mice. Due to scBAT&#39;s small size relative to other adipose depots, procedures have been modified and optimized specifically for processing scBAT. Among these modifications is the use of a dissecting microscope during tissue collection to increase the precision and homogenization of frozen scBAT samples to raise the efficiency of subsequent qPCR analysis. With these optimizations, the identification of, morphological appearance of, and molecular characterization of the scBAT can be determined in mice.

Unlike iBAT, which is situated in the subcutaneous layer of the back between two scapulae, scBAT is situated in the intermediate layer of the neck, extending deep between layers of skeletal muscle and the salivary gland as it grows along the external jugular vein (Figure 1A). Dissecting scBAT is not as straightforward as iBAT. Here, we provide a detailed procedure including crucial steps for dissecting intact scBAT from postnatal and adult mice (<strong class...

Watch this Scientific Journal Video about Author Spotlight: Optimizing Supraclavicular Brown Adipose Tissue Extraction for Genetic Analysis at JoVE.com

Author Spotlight: Optimizing Supraclavicular Brown Adipose Tissue Extraction for Genetic Analysis

Here, we provide a practical procedure for dissecting and performing histological and gene expression analyses of murine supraclavicular brown adipose tissue.

Dissection, Histological Processing, and Gene Expression Analysis of Murine Supraclavicular Brown Adipose Tissue

Brown adipose tissue (BAT)-mediated thermogenesis plays an important role in the regulation of metabolism, and its morphology and function can be greatly ...

dissection-histological-processing-gene-expression-analysis-murine

Research

JoVE Journal

Biology

1.7K Views.  Baylor College of Medicine. Here, we provide a practical procedure for dissecting and performing histological and gene expression analyses of murine supraclavicular brown adipose tissue.

Video: Author Spotlight: Optimizing Supraclavicular Brown Adipose Tissue Extraction for Genetic Analysis

Bacterial Gene Expression Analysis Using Microarrays

Hi, my name is Ena and We routinely do gene expression profiling in the lab. And we use this technique to monitor differential regulated genes between meth and wild type. And today I have a wild type and meth RNA samples and we all do C first.We use a indirect labeling methods and the advantage of this technique is to prevent eye bias that can occur in direct labeling. And to do that we have RNA samples and we opt obtain three microgram of RNA in 13 microliter of to total volume. And we add 2.5 micro of random he in our parks.And we'll incubate sample at seven five degree to have to the nature of the RNA for eight minutes. And now we'll add the, we'll add reverse transcription cocktail that contains AM L-D-L-D-U-T-P continu mix, reverse transcriptase buffer and also ET TT Big it down And incubate the sample at 42 degree for four hours. So after four hours we just take the samples out.And now in the tube we have CDNA and RNA mix. And what we want to do is do hydrox RNA by adding sodium hydroxide and EDTA and final concentration for sodium hydroxide should be a hundred molar. And final concentration for e BT should be five molar.And now we will incubate samples at 65 degree water bath for 10 minutes. So the incubation is done and we'll utilize samples by adding pH seven heaps one water to the final concentration of 500 molar. At this point you can store the samples at minus 20 or you can continue with the cleanup.For cleanup of the CDNA, we use KaiGen PCR purification kit. However, since Bush buffer and ion buffer contains freeing, we don't, we prepare our own fate bush buffer and fate ion buffer and you'll add 300 liter of PPI and we'll pipe that pond down slowly to you will transfer the mixture into columns And you'll spin for one minute at the highest speed And you'll watch the, the buffer that we prepared. Phosphate wash buffer, you'll add 750 microliter and so, and you'll add another For one again.So we'll spin again just to make sure that we got all bed all. And we will transfer these tubes into empty offender tubes. And I'll add 30 markers of pho phosphate E buffer, which is four four molar of potassium phosphate at pH 8.5.And here you just need to make sure that you add everything into center of the column and you'll incubate at room temperature for one minute. So it'll spin for one minute again and I'll add another 30 micro zero buffer I incubate or bedroom. So I remove the column and we have total volume of 60 micros or CDA.Once we clean up the CDNA, you can, you can store it minus 20 degrees out and we can also dry it and then store it so we can dry the CDNA in feedback. So now in the tube we have dry CDA, which is am modified. And what we'll do is I'll suspend the dry sample in.I'll suspend the sample in 10 ture of 15 LAR bicarbonate at pH nine. And I'll just do this by ing up and down at this step, it's very important to Resus the cDNA. Well for buying corporation reaction to work, this reaction should take place in the dark room because fluorescent labels are die sensitive.However, the opting these from life sciences and they're, they came in individual packages. S five has purple cap and side three has orange cap and also S five appears Sion when it's getting suspended and Cary appears magenta. So what I will do in dark room is I'll transfer these samples into dye tubes, I'll re suspend the dye and transfer them back into the tube I have.And then I'll incubate in the dark for two hours after two hours incubation these stops reaction by adding 35 re of a hundred millimolar sodium acetate at pH 5.2. And after that we cleaned up with the similar cleanup procedure. However, this time we use Cajun provided wash buffer and elution buffer.You can describe off the places that you put the sample in and that should clean the instrument. So you can your sample or your blend right now I To, So this is my scifi labeled sample and here what we see is OD two 60, which shows the CDA content and OD six 50, which shows the D incorporation for scifi. And here is my side three label sample.Again, twist six concentration and five 50 measures site three incorporation. Since my D corporation work efficiently, I'll combine samples Now, Ms.Miss it briefly. And now we'll write a sample again using feedback.Okay, so for ization of the slide, we'll rehydrate by universally putting the slide on top of water and that will make spots larger. And then to protect that, we'll just snap dry on a hundred degrees Celsius and we'll then UV hybridize or UV cross link the spots into the slide and then we'll incubate in the pre high buffer that we have. So I place the slide face down, but it doesn't touch the water yet.And we'll wait like this for five minutes. I, So this box looks larger, they should be shinier than before you put, and you'll just snap dry by putting the slide on a hundred degrees and you'll observe for condensation. And we will cross link in with youi.So for hydration, I'll just dip the slide into pre-war water. And this should be really quick because the aim here that you want to get rid of all the spots or all the oligos on the spot that is not linked. And if you go slow in this process, you'll just get com tails on your spots.So just make sure that you're really doing it fast and make sure that you don't take Your flight out the water and do This Stuff For 30 seconds and just fut immediately at room temperature for five minutes and 700 air pm Get This, we fit this slide into the prewar pipe station buffer that we had And slowly pushing the slide into The jar and we'll incubate this at 42 degree for at least 45 minutes. So here we have our dried sample to be hybridized. So we'll first Resus suspend in water.At this step we just resus suspend by happening up and down and possible don't expose the sample too white, white. And then you'll add someone's sperm DNA 1.5 and the concentration is 10 milligram per mil. And you'll add 1.2 marketer of TRNA.Concentration is 12.5 milligram per, we add tRNA and som sperm DNA to block nonspecific hydro. And we add 5.35 marker zero three XSSC, which gives final concentration of three x. And finally we add 3.5 microliter of 1%SDS.Now we will boil the mixture for five minutes and we'll spin at the highest speed for five minutes and it'll be ready to have that. It's been an hour since we incubate our slide and right now I have water and isopropanol. So I'll agitate the slide in water first to get rid of SDS and then wash your dza propanol and directly put into the standard gauge.And in here, just be careful that you don't expose light too much to air to prevent drying. So I go directly from harm station buffer into the water And we wash the slide. Couple minutes, just make sure that the motion is only up and down, not sideways.And also make sure that the slide is not above water and we will transfer it into isopropanol immediately. And it just stay here for a couple minutes again. And could your page Please answer your page at room temperature for five minutes?700 R.Cool. So our slide is also ready to be hybridized and it's better if you keep it in a slide box to protect it from the bus. So for harvest station we'll use lift or slip.There are white strips on the cover slip and they'll provide some lift and they'll provide some space for our sample to go in between cover slip and the slide. And I clean it with ethanol And then wire put down And just make sure that there is no test particle. So first we'll take our template slide that we have print area marked, and on top of it we'll put the slide that we prepared and make sure they align perfectly.Make sure they align perfectly. And you need to make sure that the strips are on the side, that we are gonna face it down. So it's really hard to see, but make sure that you can see it.And the stripes should be on the sides of the slides. And we'll load our sample from the sides. I take small amounts of sample, so I take 15 microliter first and I start loading from the corner off the cover slip.And slowly I would pull it in and I just move along the edge to cover all the area. At this stage it's very important not to introduce any bubbles and I take another 15 migrator and apply it to side of the slides to prevent any drying. So our sample is ready and you'll incubate our slides and prioritization chambers, which has micro channels to hydrate the slide while it's hybridizing.And we'll add 10 marketer of three XSSC into six corners of the slide. There were six places on the, on the chamber, sorry, on each corner I, and on each side, Make sure that you transfer the slide really gently so that the cover slip doesn't slip away. And when you put the slide right side up, you'll see that it'll stack, it'll stick to the water that you put and put the cover And Make sure the screws are tight.We'll incubate the conversation chamber at 65 degree water bag, but we don't wanna put it directly at the bottom. So we just put some sort of plastic barrier to prevent excess heat transfer. And we place our ization chamber gently and to prevent any displacement, you can also put some sort of weight.And this incubation will go overnight, typically between 10 to 12 hours. So for washing of slice, we use one XSSC with 0.05 per cent SDS. This is gonna be for removing the cover slip.And this is gonna be for washing the first step. And we'll do two more steps only with 0.06%six XSC through all the SDS that we have. So we all screw the conversation and we take slides and put it face down into purse container.And we'll just shake it side to side and we'll see that cover slip will fall off gently. All right, and, And we'll just transfer into other wash buffer that contains XES. You aate for one minute.Move into going oh six XSSC. And just to make sure we got rid of all the FDS, we'll repeat it one more time. Centrifuge to dry was at room temperature for five minutes at 700 RP.You keep this slide in the slide box because it's light sensitive.So This is slide scanner and you'll put slide in here, little space right here, put the slide face down, labeled toward and, And in the second slide you'll just define the area that you wanna scan. And you'll just take this area in our slides. We have, we use 16 pins to print our slides.So each block is corresponding to one pin and our slides contain over 8, 000 spots. And we represent vi color genome twice because it's around 4, 000 genes. So we have two spots per each oligo that we use.And if these zoom in, you would see in this particular experiment, we compare transcription regulator mutants to wild type, and mutant would be labeled with scifi, which gives red color. And wild type was site three, which gives green color. So anything that is, that seems red, like these spots, indicates that abundance of the transcripts in the mutant was higher than the wild type.So they appear red or shades of red, and anything that would appear green indicates that abundance of the transcript was higher in the wild type compared to mutant. And any spot that appears yellow indicates that, that that transcript was equally present in both mutant and the wild type. So when they overlay, they would appear yellow like these buts.

Chromatin Immunoprecipitation of Murine Brown Adipose Tissue

Most cellular processes are regulated by transcriptional modulation of specific gene programs. Such modulation is achieved through the combined actions of a wide range of transcription factors (TFs) and cofactors mediating transcriptional activation or repression via changes in chromatin structure. Chromatin immunoprecipitation (ChIP) is a useful molecular biology approach for mapping histone modifications and profiling transcription factors/cofactors binding to DNA, thus providing a snapshot of the dynamic nuclear changes occurring during different biological processes.
To study transcriptional regulation in adipose tissue, samples derived from in vitro cell cultures of immortalized or primary cell lines are often favored in ChIP assays because of the abundance of starting material and reduced biological variability. However, these models represent a limited snapshot of the actual chromatin state in living organisms. Thus, there is a critical need for optimized protocols to perform ChIP on adipose tissue samples derived from animal models.
Here we describe a protocol for efficient ChIP-seq of both histone modifications and non-histone proteins in brown adipose tissue (BAT) isolated from a mouse. The protocol is optimized for investigating genome-wide localization of proteins of interest and epigenetic markers in the BAT, which is a morphologically and physiologically distinct tissue amongst fat depots.

Here we describe a protocol for efficient chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) of brown adipose tissue (BAT) isolated from a mouse. This protocol is suitable for both mapping histone modifications and investigating genome-wide localization of non-histone proteins of interest in vivo.

Most cellular processes are regulated by transcriptional modulation of specific gene programs. Such modulation is achieved through the combined actions of ...

Genetics

Isolation and Processing of Murine White Adipocytes for Transcriptome and Epigenome Analyses

Obesity is a complex disease influenced by genetics, epigenetics, the environment, and their interactions. Mature adipocytes represent the major cell type in white adipose tissue. Understanding how adipocytes function and respond to (epi)genetic and environmental signals is essential for identifying the cause(s) of obesity. RNA and chromatin have previously been isolated from adipocytes using enzymatic digestion. In addition, protocols have been developed for nuclear isolation, where purification is achieved by fluorescence-activated cell sorting (FACS) of adipocyte-specific transgenic reporters. One of the greatest challenges to achieving high yield and quality during such protocols is the substantial amount of lipid contained in adipose tissue. The present protocol describes an optimized procedure for isolating mature adipocytes that leverages heptane to separate lipids from the targets of interest (RNA/chromatin). The resulting RNA has high integrity and generates high-quality RNA-seq results. Likewise, the procedure improves nuclei yield rate and generates reproducible ChIP-seq results across samples. Therefore, the current study provides a reliable and universal murine adipocyte isolation protocol suitable for whole-genome transcriptome and epigenome studies.

The present protocol summarizes a universal method for isolating, purifying, and upstream processing of murine white adipocytes optimized for downstream total RNA sequencing, Nuclei Extraction by SONication (NEXSON), and ChIP-seq.

Obesity is a complex disease influenced by genetics, epigenetics, the environment, and their interactions. Mature adipocytes represent the major cell type ...

Localization, Identification, and Excision of Murine Adipose Depots

Obesity has increased dramatically in the last few decades and affects over one third of the adult US population. The economic effect of obesity in 2005 reached a staggering sum of $190.2 billion in direct medical costs alone. Obesity is a major risk factor for a wide host of diseases. Historically, little was known regarding adipose and its major and essential functions in the body. Brown and white adipose are the two main types of adipose but current literature has identified a new type of fat called brite or beige adipose. Research has shown that adipose depots have specific metabolic profiles and certain depots allow for a propensity for obesity and other related disorders. The goal of this protocol is to provide researchers the capacity to identify and excise adipose depots that will allow for the analysis of different factorial effects on adipose; as well as the beneficial or detrimental role adipose plays in disease and overall health. Isolation and excision of adipose depots allows investigators to look at gross morphological changes as well as histological changes. The adipose isolated can also be used for molecular studies to evaluate transcriptional and translational change or for in vitro experimentation to discover targets of interest and mechanisms of action. This technique is superior to other published techniques due to the design allowing for isolation of multiple depots with simplicity and minimal contamination.

Due to the drastic and negative connection between obesity and other comorbidities, research on the role adipose plays in disease and overall health is warranted. We present a protocol for the isolation and excision of adipose depots allowing for the study of adipose using in situ and in vitro methods.

Obesity has increased dramatically in the last few decades and affects over one third of the adult US population. The economic effect of obesity in 2005 ...

Medicine

Isolating Brown Adipocytes from Murine Interscapular Brown Adipose Tissue for Gene and Protein Expression Analysis

Brown adipose tissue (BAT) is responsible for non-shivering thermogenesis in mammals, and brown adipocytes (BAs) are the functional units of BAT. BAs contain both multilocular lipid droplets and abundant mitochondria, and they express uncoupling protein 1 (UCP1). BAs are categorized into two sub-types based on their origin: embryo derived classical BAs (cBAs) and white adipocytes derived BAs. Due to their relatively low density, BAs cannot be isolated from BAT with traditional centrifugation method. In this study, a new method was developed to isolate BAs from mice for gene and protein expression analysis. In this protocol, interscapular BAT from adult mice was digested with Collagenase and Dispase solution, and the dissociated BAs were enriched with 6% iodixanol solution. Isolated BAs were then lysed with Trizol&#160;reagent for simultaneous isolation of RNA, DNA, and protein. After RNA isolation, the organic phase of the lysate was used for protein extraction. Our data showed that 6% iodixanol solution efficiently enriched BAs without interfering with follow-up gene and protein expression studies. Platelet-derived growth factor (PDGF) is a growth factor that regulates the growth and proliferation of mesenchymal cells. Compared to the brown adipose tissue, isolated BAs had significantly higher expression of Pdgfa. In summary, this new method provides a platform for studying the biology of brown adipocytes at a single cell-type level.

This study describes a new method of isolating murine brown adipocytes for gene and protein expression analysis.

Brown adipose tissue (BAT) is responsible for non-shivering thermogenesis in mammals, and brown adipocytes (BAs) are the functional units of BAT. BAs ...

Immunology and Infection

Identification and Dissection of Diverse Mouse Adipose Depots

Adipose tissues are complex organs with a wide array of functions, including storage and mobilization of energy in response to local and global needs, uncoupling of metabolism to generate heat, and secretion of adipokines to regulate whole-body homeostasis and immune responses. Emerging research is identifying important regional differences in the developmental, molecular, and functional profiles of adipocytes located in discrete depots throughout the body. Different properties of the depots are medically relevant since metabolic diseases often demonstrate depot-specific effects. This protocol will provide investigators with a detailed anatomic atlas and dissection guide for the reproducible and accurate identification and excision of diverse mouse adipose tissues. Standardized dissection of discrete adipose depots will allow detailed comparisons of their molecular and metabolic characteristics and contributions to local and systemic pathologic states under various nutritional and environmental conditions.

Adipocytes exist in discrete depots and have diverse roles within their unique microenvironments. As regional differences in adipocyte character and function are uncovered, standardized identification and isolation of depots is crucial for advancement of the field. Herein, we present a detailed protocol for the excision of various mouse adipose depots.

Adipose tissues are complex organs with a wide array of functions, including storage and mobilization of energy in response to local and global needs, ...

Isolation and Differentiation of Primary White and Brown Preadipocytes from Newborn Mice

The understanding of the mechanisms underlying adipocyte differentiation and function has greatly benefited from the use of immortalized white preadipocyte cell lines. These cultured cell lines, however, have limitations. They do not fully capture the diverse functional spectrum of the heterogenous adipocyte populations that are now known to exist within white adipose depots. To provide a more physiologically relevant model to study the complexity of white adipose tissue, a protocol has been developed and optimized to enable simultaneous isolation of primary white and brown adipocyte progenitors from newborn mice, their rapid expansion in culture, and their differentiation in vitro into mature, fully functional adipocytes. The primary advantage of isolating primary cells from newborn, rather than adult mice, is that the adipose depots are actively developing and are, therefore, a rich source of proliferating preadipocytes. Primary preadipocytes isolated using this protocol differentiate rapidly upon reaching confluence and become fully mature in 4-5 days, a temporal window that accurately reflects the appearance of developed fat pads in newborn mice. Primary cultures prepared using this strategy can be expanded and studied with high reproducibility, making them suitable for genetic and phenotypic screens and enabling the study of the cell-autonomous adipocyte phenotypes of genetic mouse models. This protocol offers a simple, rapid, and inexpensive approach to study the complexity of adipose tissue in vitro.

This report describes a protocol for the simultaneous isolation of primary brown and white preadipocytes from newborn mice. Isolated cells can be grown in culture and induced to differentiate into fully mature white and brown adipocytes. The method enables genetic, molecular, and functional characterization of primary fat cells in culture.

The understanding of the mechanisms underlying adipocyte differentiation and function has greatly benefited from the use of immortalized white ...

Visualization and Quantification of Brown and Beige Adipose Tissues in Mice using [18F]FDG Micro-PET/MR Imaging

Brown and beige adipocytes are now recognized as potential therapeutic targets for obesity and metabolic syndromes. Non-invasive molecular imaging methods are essential to provide critical insights into these thermogenic adipose depots. Here, the protocol presents a PET/MR imaging-based method to evaluate the activity of brown and beige adipocytes in mouse interscapular brown adipose tissue (iBAT) and inguinal subcutaneous white adipose tissue (iWAT). Visualization and quantification of the thermogenic adipose depots were achieved using [18F]FDG, the non-metabolizable glucose analog, as the radiotracer, when combined with the precise anatomical information provided by MR imaging. The PET/MR imaging was conducted 7 days after cold acclimation and quantitation of [18F]FDG signal in different adipose depots was conducted to assess the relative mobilization of thermogenic adipose tissues. Removal of iBAT substantially increased cold-evoked [18F]FDG uptake in iWAT of the mice.

Visualization and Quantification of Brown and Beige Adipose Tissues in Mice using [18F]FDG Micro-PET/MR Imaging

Functional imaging and quantitation of thermogenic adipose depots in mice using a micro-PET/MR imaging-based approach.

Brown and beige adipocytes are now recognized as potential therapeutic targets for obesity and metabolic syndromes. Non-invasive molecular imaging methods ...

Differentiation and Imaging of Brown Adipocytes from the Stromal Vascular Fraction of Interscapular Adipose Tissue from Newborn Mice

Brown adipose tissue (BAT) is only present in mammals and has a thermogenic function. Brown adipocytes are characterized by a multilocular cytoplasm with multiple lipid droplets, a central nucleus, a high mitochondrial content, and the expression of uncoupling protein 1 (UCP1). BAT has been proposed as a potential therapeutic target for obesity and its associated metabolic disorders due to its ability to dissipate metabolic energy as heat. To investigate BAT function and regulation, brown adipocyte culturing is indispensable. The present protocol optimizes tissue processing and cell differentiation for culturing brown adipocytes from newborn mice. Additionally, procedures for the imaging of differentiated adipocytes with both confocal immunofluorescence and transmission electron microscopy are shown. In the brown adipocytes differentiated with the techniques described herein, the major defining features of classical BAT are preserved, including high UCP1 levels, increased mitochondrial mass, and very close physical contact between the lipid droplets and mitochondria, making this method a valuable tool for BAT studies.

Preadipocytes are isolated from the stromal vascular fraction of interscapular brown adipose tissue from newborn mice and differentiated into cells that accumulate lipid droplets, express molecular markers, and show the mitochondrial morphology of mature brown adipocytes. These cells are further analyzed by immunofluorescence and transmission electron microscopy.

Brown adipose tissue (BAT) is only present in mammals and has a thermogenic function. Brown adipocytes are characterized by a multilocular cytoplasm with ...

White and Brown Adipose Depot Collection from Mouse Pup: A Surgical Procedure to Harvest the White Adipose Tissue and Brown Adipose Tissue from Mouse Pup

Source: Galmozzi, A. et al. <a href="https://www.jove.com/v/62005">Isolation and Differentiation of Primary White and Brown Preadipocytes from Newborn Mice.</a> J. Vis. Exp. (2021)
In this video, we demonstrate the surgical procedure to isolate the subcutaneous white adipose tissue and interscapular brown adipose tissue from a newborn mouse.

Source: Galmozzi, A. et al. Isolation and Differentiation of Primary White and Brown Preadipocytes from Newborn Mice. J. Vis. Exp. (2021)
In this video, ...