Diese Arbeit wurde von Diabetes Kanada unterstützt.

<ol>
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L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Localization,+identification,+and+excision+of+murine+adipose+depots.">Localization, identification, and excision of murine adipose depots.</a> J Vis Exp. (94), (2014).</li><li>Hemmrich, K., Denecke, B., Paul, N. E., Hoffmeister, D., Pallua, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA+Isolation+from+Adipose+Tissue:+An+Optimized+Procedure+for+High+RNA+Yield+and+Integrity.">RNA Isolation from Adipose Tissue: An Optimized Procedure for High RNA Yield and Integrity.</a> Laboratory Medicine. 41 (2), 104-106 (2010).</li><li>Cirera, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Highly+efficient+method+for+isolation+of+total+RNA+from+adipose+tissue.">Highly efficient method for isolation of total RNA from adipose tissue.</a> BMC Res Notes. 6, 472 (2013).</li><li>Tan, S. C., Yiap, B. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA,+RNA,+and+protein+extraction:+the+past+and+the+present.">DNA, RNA, and protein extraction: the past and the present.</a> J Biomed Biotechnol. 2009, 574398 (2009).</li><li>Sellin Jeffries, M. K., Kiss, A. J., Smith, A. W., Oris, J. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+comparison+of+commercially-available+automated+and+manual+extraction+kits+for+the+isolation+of+total+RNA+from+small+tissue+samples.">A comparison of commercially-available automated and manual extraction kits for the isolation of total RNA from small tissue samples.</a> BMC Biotechnol. 14, 94 (2014).</li><li>Tan, 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=Impact+of+the+prorenin/renin+receptor+on+the+development+of+obesity+and+associated+cardiometabolic+risk+factors.">Impact of the prorenin/renin receptor on the development of obesity and associated cardiometabolic risk factors.</a> Obesity (Silver. Spring). 22 (10), 2201-2209 (2014).</li><li>Taylor, S., Wakem, M., Dijkman, G., Alsarraj, M., Nguyen, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+practical+approach+to+RT-qPCR-Publishing+data+that+conform+to+the+MIQE+guidelines.">A practical approach to RT-qPCR-Publishing data that conform to the MIQE guidelines.</a> Methods. 50 (4), 1-5 (2010).</li><li>Aranda, P. S., LaJoie, D. M., Jorcyk, 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=Bleach+gel:+a+simple+agarose+gel+for+analyzing+RNA+quality.">Bleach gel: a simple agarose gel for analyzing RNA quality.</a> Electrophoresis. 33 (2), 366-369 (2012).</li><li>Mercure, C., Prescott, G., Lacombe, M. J., Silversides, D. W., Reudelhuber, T. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chronic+increases+in+circulating+prorenin+are+not+associated+with+renal+or+cardiac+pathologies.">Chronic increases in circulating prorenin are not associated with renal or cardiac pathologies.</a> Hypertension. 53 (6), 1062-1069 (2009).</li><li>Dusaulcy, 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=Adipose-specific+disruption+of+autotaxin+enhances+nutritional+fattening+and+reduces+plasma+lysophosphatidic+acid.">Adipose-specific disruption of autotaxin enhances nutritional fattening and reduces plasma lysophosphatidic acid.</a> J. Lipid Res. 52 (6), 1247-1255 (2011).</li><li>Nakamura, K., Fuster, J. J., Walsh, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Adipokines:+a+link+between+obesity+and+cardiovascular+disease.">Adipokines: a link between obesity and cardiovascular disease.</a> J Cardiol. 63 (4), 250-259 (2014).</li><li>Taylor, S. C., Mrkusich, E. 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+state+of+RT-quantitative+PCR:+firsthand+observations+of+implementation+of+minimum+information+for+the+publication+of+quantitative+real-time+PCR+experiments+(MIQE).">The state of RT-quantitative PCR: firsthand observations of implementation of minimum information for the publication of quantitative real-time PCR experiments (MIQE).</a> J Mol Microbiol Biotechnol. 24 (1), 46-52 (2014).</li><li>Hummon, A. B., Lim, S. R., Difilippantonio, M. J., Ried, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+and+solubilization+of+proteins+after+TRIzol+extraction+of+RNA+and+DNA+from+patient+material+following+prolonged+storage.">Isolation and solubilization of proteins after TRIzol extraction of RNA and DNA from patient material following prolonged storage.</a> Biotechniques. 42 (4), 467-470 (2007).</li></ol>

Die Autoren haben nichts preisgeben.

Fettleibige Mäusen ergab folgenden HF-Diät ernähren, Körper und weißen Fettgewebe Gewichte im Vergleich zu Mäusen eine N-Diät gefüttert zugenommen haben. RNA mit Phenol Lösung ergab Proben mit guter Reinheit extrahiert. Leptin ist ein Adipokine produziert in erster Linie von Fettgewebe und positiv korrelieren mit fat mass16bekannt. Wie erwartet erhöht Leptin mRNA Ausdruck bei fettleibigen Mäusen in Tateinheit mit ihrer Fettmasse.
Diese Methode hat mehrere wic...

Adipositas ist eine weltweite Epidemie Komplikationen wie Typ 2 Diabetes1führen kann. Diät-induzierten fettleibig und gentechnisch veränderten Tiermodelle sind häufig in Übergewicht und die damit verbundenen Komplikationen für die Forschung verwendet. Traditionell weißen Fettgewebe ist bekannt als ein Ablagefach für überschüssige Energie und besteht hauptsächlich aus Lipiden während braunes Fettgewebe Energie in Wärme2,3 wandelt. Fettgewebe ist dynamisch erweitern und verkleinern abhängig von vielen Faktoren wie Ernährung und körperliche Aktivität. Um Faktoren auf diese Veränderungen zu bestimmen, sind daher ausreichend Fettgewebe Erhebung und Verarbeitung erforderlich4.
Unter weißen Fettgewebe ist es allgemein anerkannt, dass viszeralen und subkutanen Fettdepots unterschiedliche Eigenschaften wie die anatomische Lokalisierung haben und Funktion2,5. Folglich muss zur Vermeidung von widersprüchlichen Ergebnissen oder große Variabilität Aufmerksamkeit getroffen werden, um Kreuzkontaminationen zwischen diesen verschiedenen Fettdepots beim Fettpolster zu sammeln.
Darüber hinaus gibt es drei große Herausforderungen, wenn Sie RNS oder Protein aus Mäusen weißen Fettgewebe zu isolieren. Erstens ist die Fettpolster bei fettleibigen Mäusen sammeln nicht leichte Aufgabe wie die Grenze trennt verschiedene weiße Fettdepots nicht immer klar, im Gegensatz zu anderen Organen wie Niere und Herz6. Zweitens wegen der hohen Fettgehalt des Fettgewebes, während RNS oder Protein isoliert, eine Schicht von Lipiden obenauf schwimmt und verhindert den direkten Zugriff auf die Probe. Drittens: im Gegensatz zu braunen Fettgewebe oder anderen Geweben, weißen Fettgewebe hat erheblich niedrigeren Gehalt an RNA und Protein und dies ist von großer Bedeutung bei der Verwendung von junger Mäusen, Mäuse eine normale (N) Diät gefüttert und Mäuse, die voraussichtlich haben geringe Dicke Massen (d.h. KO Modelle, Behandlung mit Medikamenten, Übung, Training, etc..) 7 , 8.
Daher ist es wichtig, auswählen der geeigneten Methode, die RNA aus Fettgewebe zu isolieren. Alternative Methoden zur Phenol/Chloroform Extraktion sind kommerzielle Kits. Sie basieren in der Regel auf eine anfängliche Phenol Extraktionsschritt, gefolgt von RNA-Reinigung auf eine Spalte9. Diese Kits sind in der Regel teurer und Proben von geringeren Ertrag zu geben, während die RNA-Qualität Variable möglicherweise jedoch sind weniger zeitaufwändig. Einer der größten Vorteile der Phenol-Lösung/Chloroform Extraktion hier beschriebene ist jedoch die Möglichkeit der Isolierung von RNA, DNA und Proteine aus einer einzigen Probe10. Da Mäuse Fettpolster meist klein sind und kleine Menge von RNA und Proteinen (insbesondere schlanke Maus-Modellen geben), maximieren Sie diese Protokolle die Daten, die man aus einer kleinen Probe abbekommt.
Das Ziel dieses Papiers ist es, im Detail beschreiben eine Methode, um adäquate Probenentnahme aus drei Mäuse weißen Fettgewebe Depots sowie Menge und Qualität der RNA Isolierung zu gewährleisten. RNA durch Anschluss an dieses Protokoll erhalten kann verwendet werden, um Echtzeit-PCR-Tests durchzuführen. Dieses Protokoll dient nicht zur RNA-Isolierung aus kultivierten primäre Adipozyten.

<table><tbody><tr><td>1 mL seringes</td><td></td><td></td><td></td></tr><tr><td>1X TE solution (10 mM Tris-HCl and 1 mM EDTA&amp;bull;Na&lt;sub&gt;2&lt;/sub&gt;. pH 8.0)</td><td></td><td></td><td></td></tr><tr><td>22 G needles</td><td></td><td></td><td></td></tr><tr><td>26 G needles</td><td></td><td></td><td></td></tr><tr><td>75% Ethanol</td><td></td><td></td><td></td></tr><tr><td>Block heater (dry bath)</td><td></td><td></td><td></td></tr><tr><td>Chloroform</td><td>Sigma</td><td>C2432-500mL</td><td></td></tr><tr><td>dATP&amp;nbsp;&amp;nbsp;&amp;nbsp;</td><td>Thermo scientific</td><td>R0141</td><td></td></tr><tr><td>dCTP&amp;nbsp;&amp;nbsp;</td><td>Thermo scientific</td><td>R0151</td><td></td></tr><tr><td>dGTP&amp;nbsp;&amp;nbsp;</td><td>Thermo scientific</td><td>R0161</td><td></td></tr><tr><td>DNase I (1 U/&amp;micro;l)&amp;nbsp;</td><td>Thermo scientific</td><td>EN0521</td><td></td></tr><tr><td>dTTP&amp;nbsp;</td><td>Thermo scientific</td><td>R0171</td><td></td></tr><tr><td>Faststart Universal SYBR green Master (Rox)</td><td>Roche</td><td>4913922001</td><td></td></tr><tr><td>Faststart universal SYBR green master (Rox) fluorescent dye&amp;nbsp;</td><td>Roche</td><td>4913914001</td><td></td></tr><tr><td>Filtered tips</td><td></td><td></td><td></td></tr><tr><td>Forceps&amp;nbsp;</td><td>Instrumentarium</td><td>HB275</td><td></td></tr><tr><td>Gauze</td><td></td><td></td><td></td></tr><tr><td>Hammer</td><td></td><td></td><td></td></tr><tr><td>High fat rodent diet</td><td>Bio-Serv, Frenchtown, NJ</td><td>F3282</td><td></td></tr><tr><td>Isopropanol&amp;nbsp;</td><td>Laboratoire MAT</td><td>IH-0101</td><td></td></tr><tr><td>Leptin forward PCR primer (5&amp;rsquo;-GGGCTTCACCCCATTCTGA-3&amp;rsquo;) 10 uM</td><td></td><td></td><td></td></tr><tr><td>Leptin reverse PCR primer (5&amp;rsquo;-GGCTATCTGCAGCACATTTTG-3&amp;rsquo;) 10 uM</td><td></td><td></td><td></td></tr><tr><td>Liquid nitrogen</td><td></td><td></td><td></td></tr><tr><td>Maxima Reverse Transcriptase (enzyme and 5x buffer)</td><td>Thermo scientific</td><td>EP0742</td><td></td></tr><tr><td>Nanopure water (referred as ultrapure water)</td><td></td><td></td><td></td></tr><tr><td>Nitrile examination gloves</td><td></td><td></td><td></td></tr><tr><td>Nitrile gloves</td><td></td><td></td><td></td></tr><tr><td>Normal rodent diet</td><td>Harlan Laboratories, Madison, WI</td><td>Harlan 2018</td><td></td></tr><tr><td>P1000 pipetman</td><td></td><td></td><td></td></tr><tr><td>P2 pipetman</td><td></td><td></td><td></td></tr><tr><td>P20 pipetman</td><td></td><td></td><td></td></tr><tr><td>P200 pipetman</td><td></td><td></td><td></td></tr><tr><td>Phenol solution (TRIzol)&amp;nbsp;</td><td>Ambion Life Technologies</td><td>15598018</td><td></td></tr><tr><td>Pre-identified aluminium foil</td><td></td><td></td><td></td></tr><tr><td>Quartz spectrophotometer cuvette</td><td></td><td></td><td></td></tr><tr><td>Rack for PCR tube strips</td><td></td><td></td><td></td></tr><tr><td>Racks for RT-PCR tube strips</td><td></td><td></td><td></td></tr><tr><td>Random hexamers&amp;nbsp;</td><td>Invitrogen</td><td>58875</td><td></td></tr><tr><td>Real-time PCR Rotor Gene system&amp;nbsp;</td><td>Corbett research</td><td>RG-3000 Rotor-Gene thermal cycler</td><td></td></tr><tr><td>Refrigerated bench-top centrifuge</td><td></td><td></td><td></td></tr><tr><td>RiboLock RNase Inhibitor&amp;nbsp;</td><td>Thermo scientific</td><td>EO0381</td><td></td></tr><tr><td>RNase-free 1.5 mL eppendorf tubes</td><td></td><td></td><td></td></tr><tr><td>RNase-free 1.5 mL screw cap tubes</td><td></td><td></td><td></td></tr><tr><td>RNase-free PCR tube strips (0.2 mL) and caps</td><td></td><td></td><td></td></tr><tr><td>RNase-free water&amp;nbsp;</td><td>Hyclone</td><td>SH30538.02</td><td></td></tr><tr><td>RT-PCR machine</td><td>Qiagen</td><td>Rotor-Gene Corbett 3000</td><td></td></tr><tr><td>RT-PCR tube strips (0.1 mL) and caps</td><td></td><td></td><td></td></tr><tr><td>S16 forward PCR primer (5&amp;rsquo;-ATCTCAAAGGCCCTGGTAGC-3&amp;rsquo;) 10 uM</td><td></td><td></td><td></td></tr><tr><td>S16 reverse PCR primer (5&amp;rsquo; ACAAAGGTAAACCCCGATCG-3&amp;rsquo;) 10 uM</td><td></td><td></td><td></td></tr><tr><td>Spectrophotometer</td><td>Biochrom</td><td>Ultrospec 3100 pro</td><td></td></tr><tr><td>Stainless steel mortar and pestle</td><td></td><td></td><td></td></tr><tr><td>Surgical pads</td><td>Home made a foam board wrapped in a disposable absorbent underpad</td><td></td><td></td></tr><tr><td>Surgical scissors&amp;nbsp;</td><td>Intrumentarium</td><td>130.450.11</td><td></td></tr><tr><td>Thermal cycler</td><td></td><td></td><td></td></tr><tr><td>Thermal cycler&amp;nbsp;</td><td>Biometra</td><td>Thermocycler</td><td></td></tr><tr><td>Vortex mixer</td><td></td><td></td><td></td></tr><tr><td>Weighing spatula</td><td></td><td></td><td></td></tr></tbody></table>

mouse adipose tissue collection and processing for rna analysis

Im Vergleich zu anderen Geweben, hat weißen Fettgewebe einen deutlich weniger RNA und Protein Inhalt für downstream-Anwendungen wie Real-Time PCR und Western-Blot, da es meist Lipide enthält. RNA Isolation aus Fettgewebe Proben ist auch herausfordernd, da zusätzliche Schritte erforderlich sind, um diese Lipide zu vermeiden. Hier präsentieren wir Ihnen ein Verfahren um drei anatomisch unterschiedlichen weißen Fettgewebe von Mäusen, verarbeiten diese Proben und durchführen von RNA Isolierung zu sammeln. Wir beschreiben weiter die Synthese der cDNA und gen-Ausdruck-Experimente mittels Real-Time PCR. Das hiermit beschriebene Protokoll ermöglicht die Reduzierung der Kontamination von Haar und Blut auf Fettpolster sowie Cross-Kontamination zwischen verschiedenen Fettpolster bei der Entnahme von Gewebe des Tieres. Es wurde auch optimiert, um angemessene Quantität und Qualität der extrahierten RNA zu gewährleisten. Dieses Protokoll kann weit angewendet werden, um jede Maus-Modell wo Fettgewebe Proben für routinemäßige Experimente wie Real-Time PCR erforderlich sind, aber ist nicht zur Isolation von primären Adipozyten Zellkultur.

Nach der Autopsie Prozedur wurden drei weißen Fettgewebe gesammelt und aus den zwei Gruppen von Mäusen (N und HF Diät gefüttert Mäuse) gewichtet. Wie erwartet, stieg Mäuse auf der HF-Diät endgültige Körpergewicht und Gewichtszunahme im Vergleich zu Wurfgeschwistern N Diät (Tabelle 1). Diese Beobachtungen wurden begleitet von mehr als eine 2-fache Erhöhung des Gewichts der SCF, PGF und PRF bei fettleibigen Mäusen im Vergleich zu den N-Diät.
<p class="jove_...

Watch this Scientific Journal Video about Mouse Adipose Tissue Collection and Processing for RNA Analysis at JoVE.com

Mouse Adipose Tissue Collection and Processing for RNA Analysis

Maus Fettgewebe Erhebung und Verarbeitung für die RNA-Analyse

Dieses Papier soll eine schrittweise Anleitung zu sammeln verschiedene weißen Fettgewebe von Mäusen, die Fett Proben zu verarbeiten und RNA extrahieren zu präsentieren.

Compared to other tissues, white adipose tissue has a considerably less RNA and protein content for downstream applications such as real-time PCR and ...

mouse-adipose-tissue-collection-and-processing-for-rna-analysis

Research

JoVE Journal

Biochemistry

48.2K Aufrufe.  Université de Montréal. Dieses Papier soll eine schrittweise Anleitung zu sammeln verschiedene weißen Fettgewebe von Mäusen, die Fett Proben zu verarbeiten und RNA extrahieren zu präsentieren.

Serie: Mouse Adipose Tissue Collection and Processing for RNA Analysis

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.

Non-Laser Capture Microscopy Ansatz für die Mikrodissektion von Discrete-Maus Hirnregionen für Gesamt-RNA Isolierung und 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 ...

Forschung

Neurowissenschaften

Isolation of Adipose Tissue Nuclei for Single-Cell Genomic Applications

Brown and beige fat are specialized adipose tissues that dissipate energy for thermogenesis by UCP1 (Uncoupling Protein-1)-dependent and independent pathways. Until recently, thermogenic adipocytes were considered a homogeneous population. However, recent studies have indicated that there are multiple subtypes or subpopulations that are distinct in developmental origin, substrate use, and transcriptome. Despite advances in single-cell genomics, unbiased decomposition of adipose tissues into cellular subtypes has been challenging because of the fragile nature of lipid-filled adipocytes. The protocol presented was developed to circumvent these obstacles by effective isolation of single nuclei from adipose tissue for downstream applications, including RNA sequencing. Cellular heterogeneity can then be analyzed by RNA sequencing and bioinformatic analyses.

This publication describes a protocol for the isolation of nuclei from mature adipocytes, purification by fluorescence-activated sorting, and single-cell level transcriptomics.

Isolierung von Adipose-Gewebekernen für einzellige Genomanwendungen

Brown and beige fat are specialized adipose tissues that dissipate energy for thermogenesis by UCP1 (Uncoupling Protein-1)-dependent and independent ...

Genetik

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 ...

Production of RNA for Transcriptomic Analysis from Mouse Spinal Cord Motor Neuron Cell Bodies by Laser Capture Microdissection

Preparation of high-quality RNA from cells of interest is critical to precise and meaningful analysis of transcriptional differences among cell types or between the same cell type in health and disease or following pharmacologic treatments.&#160;In the spinal cord, such preparation from motor neurons, the target of interest in many neurologic and neurodegenerative diseases, is complicated by the fact that motor neurons represent &#60;10% of the total cell population.&#160;Laser capture microdissection (LMD) has been developed to address this problem.&#160;Here, we describe a protocol to quickly recover, freeze, and section mouse spinal cord to avoid RNA damage by endogenous and exogenous RNases, followed by staining with Azure B in 70% ethanol to identify the motor neurons while keeping endogenous RNase inhibited.&#160;LMD is then used to capture the stained neurons directly into guanidine thiocyanate lysis buffer, maintaining RNA integrity.&#160;Standard techniques are used to recover the total RNA and measure its integrity.&#160;This material can then be used for downstream analysis of the transcripts by RNA-seq and qRT-PCR.

High-quality total RNA has been prepared from cell bodies of mouse spinal cord motor neurons by laser capture microdissection after staining spinal cord sections with Azure B in 70% ethanol.&#160;Sufficient RNA (~40-60 ng) is recovered from 3,000-4,000 motor neurons to allow downstream RNA analysis by RNA-seq and qRT-PCR.

Produktion von RNA für die Transkriptomische Analyse von Maus Spinal Cord Motor Neuron Cell Bodies durch Laser Capture Microdissection

Preparation of high-quality RNA from cells of interest is critical to precise and meaningful analysis of transcriptional differences among cell types or ...

A Cryo-pulverization Protocol for Processing Mouse Paws to Evaluate Molecular Pathways of Tissue Inflammation in a Collagen Induced Arthritis Model

Profiling molecular changes in local tissues is crucial to understand the mechanism(s) of action of therapeutic candidates in vivo. In the field of arthritis research, many studies are focused on inflamed joints that are composed of a complex mixture of bone, cartilage, muscle, stromal cells and immune cells. Here, we established a reliable and robust mechanical method to disrupt inflamed mouse paws into homogeneous pulverized samples in a cryogenically controlled environment. Protein and RNA lysates were processed to enable proteomic and transcriptional endpoints and molecular characterization of relevant disease pathways in local tissue.

A cryogenic pulverization method to process murine paws using a liquid nitrogen freezer mill was developed to improve the yield and quality of RNA or protein extracted from the tissues and enable the analysis of molecular profiles associated with inflammatory responses.

Ein Kryo-Pulverisierungsprotokoll zur Verarbeitung von Mauspfoten zur Bewertung molekularer Wege von Gewebeentzündungen in einem Kollagen-induzierten Arthritis-Modell

Profiling molecular changes in local tissues is crucial to understand the mechanism(s) of action of therapeutic candidates in vivo. In the field of ...

Immunologie und Infektion

Collection of Frozen Rodent Brain Regions for Downstream Analyses

As our understanding of neurobiology has progressed, molecular analyses are often performed on small brain areas such as the medial prefrontal cortex (mPFC) or nucleus accumbens. The challenge in this work is to dissect the correct area while preserving the microenvironment to be examined. In this paper, we describe a simple, low-cost method using resources readily available in most labs. This method preserves nucleic acid and proteins by keeping the tissue frozen throughout the process. Brains are cut into 0.5&#8211;1.0 mm sections using a brain matrix and arranged on a frozen glass plate. Landmarks within each section are compared to a reference, such as the Allen Mouse Brain Atlas, and regions are dissected using a cold scalpel or biopsy punch. Tissue is then stored at -80 &#176;C until use. Through this process rat and mouse mPFC, nucleus accumbens, dorsal and ventral hippocampus and other regions have been successfully analyzed using qRT-PCR and Western assays. This method is limited to brain regions that can be identified by clear landmarks.

This procedure describes the collection of discrete frozen brain regions to obtain high-quality protein and RNA using inexpensive and commonly available tools.

Sammlung von gefrorenen Nagetier-Hirnregionen für Downstream-Analysen

As our understanding of neurobiology has progressed, molecular analyses are often performed on small brain areas such as the medial prefrontal cortex ...

RNA Isolation from Mouse Pancreas: A Ribonuclease-rich Tissue

Isolation of high-quality RNA from ribonuclease-rich tissue such as mouse pancreas presents a challenge. As a primary function of the pancreas is to aid in digestion, mouse pancreas may contain as much a 75 mg of ribonuclease. We report modifications of standard phenol/guanidine thiocyanate lysis reagent protocols to isolate RNA from mouse pancreas. Guanidine thiocyanate is a strong protein denaturant and will effectively disrupt the activity of ribonuclease under most conditions. However, critical modifications to standard protocols are necessary to successfully isolate RNA from ribonuclease-rich tissues. Key steps include a high lysis reagent to tissue ratio, removal of undigested tissue prior to phase separation and inclusion of a ribonuclease inhibitor to the RNA solution. Using these and other modifications, we routinely isolate RNA with RNA Integrity Number (RIN) greater than 7. The isolated RNA is of suitable quality for routine gene expression analysis. Adaptation of this protocol to isolate RNA from ribonuclease rich tissues besides the pancreas should be readily achievable.

We report a procedure to isolate RNA with high integrity from the ribonuclease rich mouse pancreas.

RNA-Isolierung aus Maus Pankreas: Eine Ribonuklease-reichen Gewebe

Isolation of high-quality RNA from ribonuclease-rich tissue such as mouse pancreas presents a challenge.  As a primary function of the pancreas is to aid ...

Biologie

Isolation of Viable Adipocytes and Stromal Vascular Fraction from Human Visceral Adipose Tissue Suitable for RNA Analysis and Macrophage Phenotyping

Visceral adipose tissue (VAT) is an active metabolic organ composed mainly of mature adipocytes and stromal vascular fraction (SVF) cells, which release different bioactive molecules that control metabolic, hormonal, and immune processes; currently, it is unclear how these processes are regulated within the adipose tissue. Therefore, the development of methods evaluating the contribution of each cell population to the pathophysiology of adipose tissue is crucial. This protocol describes the isolation steps and provides the necessary troubleshooting guidelines for efficient isolation of viable mature adipocytes and SVF from human VAT biopsies in a single process, using a collagenase enzymatic digestion technique. Moreover, the protocol is also optimized to identify macrophage subsets and perform mature adipocyte RNA isolation for gene expression studies, which allows performing studies dissecting the interaction between these cell populations. Briefly, VAT biopsies are washed, minced mechanically, and digested to generate a single-cell suspension. After centrifugation, mature adipocytes are isolated by flotation from the SVF pellet. The RNA extraction protocol ensures a high yield of total RNA (including miRNAs) from adipocytes for downstream expression assays. Simultaneously, SVF cells are used to characterize macrophage subsets (pro- and anti-inflammatory phenotype) through flow cytometry analysis.

This protocol provides an efficient collagenase digestion method for isolation of viable adipocytes and stromal vascular fraction-SVF cells from human visceral fat in a single process, including methodology to obtain high-quality RNA from adipocytes and phenotypification of SVF-macrophages through staining of multiple membrane-bound markers for analysis by flow cytometry.

Isolierung lebensfähiger Adipozyten und stromaler vaskulärer Fraktion aus menschlichem viszeralem Fettgewebe, geeignet für RNA-Analyse und Makrophagen-Phänotypisierung

Visceral adipose tissue (VAT) is an active metabolic organ composed mainly of mature adipocytes and stromal vascular fraction (SVF) cells, which release ...

Medizin

Cryosectioning of Contiguous Regions of a Single Mouse Skeletal Muscle for Gene Expression and Histological Analyses

With this method, consecutive cryosections are collected to enable both microscopy applications for tissue histology and enrichment of RNA for gene expression using adjacent regions from a single mouse skeletal muscle. Typically, it is challenging to achieve adequate homogenization of small skeletal muscle samples because buffer volumes may be too low for efficient grinding applications, yet without sufficient mechanical disruption, the dense tissue architecture of muscle limits penetration of buffer reagents, ultimately causing low RNA yield. By following the protocol reported here, 30 &#956;m sections are collected and pooled allowing cryosectioning and subsequent needle homogenization to mechanically disrupt the muscle, increasing the surface area exposed for buffer penetration. The primary limitations of the technique are that it requires a cryostat, and it is relatively low throughput. However, high-quality RNA can be obtained from small samples of pooled muscle cryosections, making this method accessible for many different skeletal muscles and other tissues. Furthermore, this technique enables matched analyses (e.g., tissue histopathology and gene expression) from adjacent regions of a single skeletal muscle so that measurements can be directly compared across applications to reduce experimental uncertainty and to reduce replicative animal experiments necessary to source a small tissue for multiple applications.

Consecutive cryo-sections are collected to enable histological applications and enrichment of RNA for gene expression measurements using adjacent regions from a single mouse skeletal muscle. High-quality RNA is obtained from 20 - 30 mg of pooled cryosections and measurements are directly compared across applications.

Kryoschneiden von benachbarten Regionen eines einzelnen Maus Skelettmuskel für die Genexpression und histologische Analysen

With this method, consecutive cryosections are collected to enable both microscopy applications for tissue histology and enrichment of RNA for gene ...

Laser Capture Microdissection of Highly Pure Trabecular Meshwork from Mouse Eyes for Gene Expression Analysis

Laser capture microdissection (LCM) has allowed gene expression analysis of single cells and enriched cell populations in tissue sections. LCM is a great tool for the study of the molecular mechanisms underlying cell differentiation and the development and progression of various diseases, including glaucoma. Glaucoma, which comprises a family of progressive optic neuropathies, is the most common cause of irreversible blindness worldwide. Structural changes and damage within the trabecular meshwork (TM) can result in increased intraocular pressure (IOP), which is a major risk factor for developing glaucoma. However, the precise molecular mechanisms involved are still poorly understood. The ability to perform gene expression analysis will be crucial in obtaining further insights into the function of these cells and its role in the regulation of IOP and glaucoma development. To achieve this, a reproducible method for isolating highly enriched TM from frozen sections of mouse eyes and a method for downstream gene expression analysis, such as RT-qPCR and RNA-Seq is needed. The method described herein is developed to isolate highly pure TM from mouse eyes for downstream digital PCR and microarray analysis. In addition, this technique can be easily adapted for the isolation of other highly enriched ocular cells and cell compartments that have been difficult to isolate from mouse eyes. The combination of LCM and RNA analysis can contribute to a more comprehensive understanding of the cellular events underlying glaucoma.

Here, we describe a protocol for a reproducible laser capture microdissection (LCM) for isolating trabecular meshwork (TM) for downstream RNA analysis. The ability to analyze changes in gene expression in the TM will help in understanding the underlying molecular mechanisms of TM-related ocular diseases.

Laser Capture Microdissection von hochreinen trabekuläre Geflecht aus Maus Augen für Gene Expression Analysis

Laser capture microdissection (LCM) has allowed gene expression analysis of single cells and enriched cell populations in tissue sections. LCM is a great ...