This work was supported by grants from the Natural Science Foundation of China (82070450 to C.T.and 82170466 to L.Z.) and the fellowship of China Postdoctoral Science Foundation (7121102223 to F.L.).

All animal procedures described below were approved by the Institutional Animal Care and Use Committee of Soochow University.
1. Reagents and materials preparation
<ol>
	<li>Utilize 1x PBS without calcium and magnesium and 2.5 U/mL heparin sodium salt to prepare the perfusion solution. Store at 4 &#176;C, and precool on ice when used.</li>
	<li>Prepare dissociation reagent A that contains 125 CDU/mL collagenase II and 60 U/mL DNase I by diluting 1250 CDU/mL collagenase II and 3000 U/mL DNase I with HBSS. Store at 4 &#176;C until use.</li>
	<li>Prepare dissociation reagent B that contains a final concentration of 0.12% trypsin by diluting 1 mL of 0.25% EDTA-free trypsin (without phenol red) into 1 mL of 1x PBS. Store at 4 &#176;C until use.</li>
	<li>Prepare 10 mL of 1.5% FBS and 10 mL of 5% FBS in 1x PBS. Use 1.5% FBS to pool carotid arteries and keep on ice before use. Use 5% FBS to neutralize digestion and store at room temperature (RT).</li>
	<li>Get the experimental materials, including 1 mL syringes, 20 mL syringes with 26-G needles, six-well cell culture plates, 1.5 mL centrifuge tubes, 40 &#181;m sterile cell strainers, and ice containers.</li>
</ol>
2. Equipment preparation
<ol>
	<li>Sterilize all the surgical equipment, including a stereoscopic microscope, dissecting scissors, micro-dissecting scissors, and fine-tip forceps.</li>
	<li>Turn on the automated cell counter and maintain it at RT.</li>
	<li>Turn on the water bath to 37 &#176;C in advance.</li>
	<li>Precool the microcentrifuge to 4 &#176;C before use.</li>
</ol>
3. Isolation of the mouse carotid artery
<ol>
	<li>Anesthetize the mouse using 1.25% tribromoethanol by intraperitoneal injection (0.24 mL for every 10 g of body weight) and flip the mouse to check if there is a righting reflex after 3 min. Then, euthanize the mouse by cervical dislocation and lay it on its back. Spray the mouse&#39;s skin with 75% alcohol.</li>
	<li>Use sterilized dissecting scissors to open up the skin and expose the chest cavity. Cut open the diaphragm.</li>
	<li>Continue cutting upward to the lower jaw and carefully remove excess connective tissues and fat, exposing the carotid artery.</li>
	<li>Cut the inferior vena cava of the mouse to make blood flow out of the closed circulation.</li>
	<li>Inject 20 mL of prechilled perfusion solution into the left ventricle with a syringe slowly and continuously. 
	NOTE: If perfusion is successful, blood-rich organs such as the liver, spleen, and kidneys will turn gray-white.</li>
	<li>Peel off all the fat and connective tissues around the carotid artery with micro-dissecting scissors under a stereoscopic microscope. 
	NOTE: This step should be done slowly and carefully to prevent damage to the carotid artery.</li>
	<li>Isolate the carotid artery from the mouse, wash with 1x PBS to flush the blood again, and transfer to six-well plates containing 1.5% FBS on ice.</li>
</ol>
4. Digestion of the carotid artery into single-cell suspension
<ol>
	<li>Use micro-dissecting scissors to dissect the carotid artery longitudinally and lay flat in another 6-well cell culture plate containing 1 mL of 1.5% FBS on ice.</li>
	<li>Flush the intima carefully with 1.5% FBS to remove the residual blood. 
	NOTE: Flushing should be gentle and slow to avoid injuring endothelial cells.</li>
	<li>Cut each carotid artery into approximately 2 mm2 tissue pieces using microdissecting scissors in 1.5% FBS.</li>
	<li>Transfer these tissue pieces into a 1.5 mL centrifuge tube with 1 mL wide bore tips, centrifuge at 400 x g for 5 min at 4 &#176;C to sink the tissues to the bottom.</li>
	<li>Discard the supernatant and resuspend the tissues in 500 &#181;L of dissociation reagent A.</li>
	<li>Place the tube in a 37 &#176;C water bath for 1 h. Pipette gently with a 1 mL pipette every 10 min.</li>
	<li>Add 500 &#181;L of 5% FBS into the tube and mix well with a 1 mL pipette.</li>
	<li>Filter the cell suspension through a 40 &#181;m sterile cell strainer into a new 1.5 mL centrifuge tube and centrifuge at 400 x g for 5 min at 4 &#176;C.</li>
	<li>Remove the supernatant carefully and resuspend the cell pellet in 200 &#181;L of dissociation reagent B.</li>
	<li>Place in a 37 &#176;C water bath and digest for another 5 min. Gently pipette every 2 min during digestion to fully dissociate into a single-cell suspension.</li>
	<li>Use 200 &#181;L of 5% FBS to terminate the digestion reaction, and centrifuge at 400 x g for 5 min at 4 &#176;C.</li>
	<li>Discard the supernatant and resuspend the cell pellet in 100 &#181;L of 1x PBS on ice.</li>
</ol>
5. Cell suspension examination and single-cell RNA sequencing
<ol>
	<li>Add 10 &#181;L of AO/PI solution into 10 &#181;L of single-cell suspension and gently mix with a 20 &#181;L pipette.</li>
	<li>Pipette 20 &#181;L of the mixture into the chamber slide and wait for 1 min.</li>
	<li>Load the slide into the automated cell counter instrument.</li>
	<li>Select the AO/PI Viability assay, then wait for the quality report.</li>
	<li>Use a single-cell 3&#697; reagent kit to generate single-cell gel beads in the emulsion on a single-cell controller and amplify the barcoded cDNA in a thermal cycler following the manufacturer&#39;s protocol. 
	NOTE: Here, Chromium Single Cell 3&#697;Reagent Kits v3 was used.</li>
	<li>Perform sequencing on a sequencer with a paired-end 150 bp (PE150) reading strategy. Use a software application (Cell Ranger) to convert raw base call files to fastq files using the mkfastq pipeline. Then, use the Count Pipeline of Cell Ranger for performing alignment, filtering, barcode counting, and unique molecular identifier (UMI) counting to generate feature-barcode matrices13.</li>
	<li>Perform data dimensionality reduction and visualization with the R package Seurat14.
	<ol>
		<li>First, the Read10X() function of Seurat reads in the output of the Cell Ranger pipeline and then uses the count matrix to create a Seurat object. Then, filter out the cells with expression of &#60;200 or &#62;4000 genes or a mitochondrial gene ratio that was more than 10% by the subset() function of Seurat.</li>
		<li>Use NormalizeData() and FindVariableFeatures() to normalize the data and identify 2000 highly variable features, respectively.</li>
		<li>Perform principal component analysis (PCA) on the scaled data, and cluster the cells with dims = 30 and resolution = 0.5. Finally, use the RunUMAP() function to visualize the single-cell datasets and FindAllMarkers() to find each cluster biomarker.</li>
	</ol>
	</li>
</ol>

Two-Step Cell Digestion of Mouse Carotid Artery

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The authors have no conflicts of interest to disclose.

Here we provide a detailed protocol for the preparation of a high-quality single-cell suspension from the carotid artery of wild-type mice, in which a two-step digestion method integrating the digestion process of collagenase/DNase and trypsin was constructed. After the quality check of the single-cell suspension, we found that it satisfied the requirements for single-cell sequencing, with the viability of cells over 85% and a high cell concentration. Moreover, a variety of cell types in the carotid artery, including VSM...

Atherosclerosis is a chronic inflammatory disease associated with risk factors such as high blood pressure, hyperlipidemia, and hemodynamics1. Carotid artery bifurcations are prone to hemodynamic changes and lead to carotid plaque formation. The clinical presentation of carotid atherosclerosis can be acute such as stroke and transient cerebral ischemia, or chronic such as recurrent transient cerebral ischemia and vascular dementia2. Mechanically, carotid plaque is the outcome of the interaction between different vessel wall cells and various blood cells under pathological conditions. Therefore, revealing the single-cell atlas of carotid vessels under physiological and pathological conditions is particularly important for preventing and treating carotid plaque development.
Single-cell RNA sequencing is one of the most powerful technologies of biological research because of its ultrahigh resolution and detection of cell heterogeneity from the same cell type of organisms3,4. Researchers have used single-cell RNA sequencing to conduct research in many fields, such as cardiovascular disease5 and cancer6. However, quickly and accurately separating tissues into single cells is still one of the main challenges. Enzymatic dissociation is a commonly used method that dominantly includes collagenase, papain, trypsin, DNase, and hyaluronidase. Specifically, collagenases are the major enzyme species for single-cell digestion, mainly hydrolyzing collagen components in connective tissues. Different collagenase types are applicable for the dissociation of different tissues, such as the mammary gland7, glomerulus8, iridocorneal angle9, knee joint10, aorta11, and lung12. Due to the unique physiological properties of different tissues, dissociation using the same method may cause many troubles in acquiring single cells, such as low cell viability, low cell number, and large cell debris. Therefore, the invention of digestion methods for different tissues is essential for preparing high-quality single-cell suspensions.
This protocol aims to develop a two-step cell digestion method to prepare a single-cell suspension of the carotid artery of wild-type mice. According to the characteristics of the carotid artery, we combined collagenase/DNase with trypsin to obtain a high-quality single-cell suspension of the mouse carotid artery because collagenase can hydrolyze collagen of the carotid tissues, which was further digested by trypsin into a single-cell suspension. Acridine orange/propidium iodide (AO/PI) dual-fluorescence counting was used to detect cell viability and concentration, and it was found that the single-cell suspension satisfied the requirements for single-cell sequencing, with the viability of cells over 85% and a high cell concentration. After single-cell data processing, four cell types, including vascular smooth muscle cells (VSMCs), fibroblasts, endothelial cells (ECs), and macrophages and dendritic cells (M&#966;/DCs), were identified in normal mouse carotid arteries after digestion. The advantages of this protocol are that: 1) multiple cell types in the carotid artery can be identified, 2) cell viability is well preserved, and 3) it can be easily repeated without special equipment. This protocol is suitable for researchers who are interested in studying single-cell multiomics of the mouse carotid arteries. This protocol may also be helpful in the dissociation of other blood vessels with appropriate modifications.

<table><tbody><tr><td>0.25% EDTA-free trypsin</td><td>Beyotime</td><td>C0205</td><td>Dilute 1 mL of 0.25% EDTA-free trypsin into 1 mL of 1x PBS.</td></tr><tr><td>0.9% NaCl saline solution</td><td>Beyotime</td><td>ST341</td><td>Dilute the heparin sodium solution into a final concentration of 10 mg/mL</td></tr><tr><td>1 mL syringes</td><td>&amp;nbsp;SKJYLEAN</td><td>sk-r009</td><td>To perform cardiac perfusion</td></tr><tr><td>1.5 mL centrifuge tubes</td><td>KIRGEN</td><td>KG2211W</td><td>To centrifuge the tissue piece and cell suspension</td></tr><tr><td>20 mL syringes</td><td>SKJYLEAN</td><td>sk-r013</td><td>To perform cardiac perfusion</td></tr><tr><td>40 &amp;micro;m cell strainer</td><td>JETBIOFIL</td><td>css010040</td><td>To filter undigested tissue fragments</td></tr><tr><td>AO/PI kit</td><td>Hengrui Biological</td><td>RE010212</td><td>To identify whether the cell is alive or dead</td></tr><tr><td>Automated cell counter</td><td>Countstar</td><td>Mira FL</td><td>To analyze the cell morphology and cell viability of digested carotid vascular cells</td></tr><tr><td>Cell Ranger software</td><td>10&amp;times; Genomics</td><td>3.0.2</td><td>To process Chromium single-cell RNA-seq output and perform clustering and gene expression analysis</td></tr><tr><td>Chromium Single Cell 3&#039;Reagent Kits v3</td><td>10&amp;times; Genomics</td><td>1000075</td><td>To prepare single-cell RNA-seq libraries of single-cell suspension</td></tr><tr><td>Collagenase II</td><td>Sigma-Aldrich</td><td>C6885</td><td>Dilute with HBSS to a final concentration of 125 CDU/mL</td></tr><tr><td>Deoxyribonuclease I</td><td>Worthington</td><td>LS002140</td><td>Dilute with HBSS to a final concentration of 60 U/mL</td></tr><tr><td>Fetal bovine serum&amp;nbsp;</td><td>HyClone</td><td>SH30088.03</td><td>Termination of the digestion reaction</td></tr><tr><td>Hank&#039;s balanced salt solution&amp;nbsp;</td><td>Gibco</td><td>14175095</td><td>Store at the room temperture</td></tr><tr><td>Heparin sodium salt</td><td>Solarbio Life Science</td><td>H8060</td><td>Dilute with 0.9% NaCl to a final concentration of 10 mg/mL</td></tr><tr><td>Microcentrifuge</td><td>Thermo Fisher Scientific</td><td>75002560</td><td>Applied for spining down the tissues and cell pellets</td></tr><tr><td>NovaSeq 6000&amp;nbsp;</td><td>Illumina</td><td>N/A</td><td>Sequencer</td></tr><tr><td>Phosphate-buffered saline</td><td>Solarbio Life Science</td><td>P1000</td><td>Used for cardiac perfusion and resuspension of cells</td></tr><tr><td>Seurat package- R</td><td>Satija Lab</td><td>3.1.2</td><td>To performed dimensionality reduction, visualization, and analysis of scRNA-sequencing data</td></tr><tr><td>Six-well cell culture plates</td><td>NEST</td><td>703002</td><td>Place the vascular tissue</td></tr><tr><td>Water bath</td><td>Jinghong</td><td>DK-S22</td><td>Keep the digestion temperature at 37 &amp;deg;C</td></tr></tbody></table>

preparation of a single-cell suspension from mouse carotid arteries for single-cell sequencing

Carotid arteries are major blood vessels in the neck that supply blood and oxygen to the brain, but carotid stenosis occurs when carotid arteries are clogged by plaque. Revealing the cellular composition of the carotid artery at the single-cell level is essential for treating carotid atherosclerosis. However, there is no ready-to-use protocol for the preparation of single-cell suspensions from carotid arteries. To obtain a suitable protocol for the dissociation of normal carotid arteries at the single-cell level with less damage to cells, we designed a two-step digestion method by integrating the digestion process of collagenase/DNase and trypsin. Acridine orange/propidium iodide (AO/PI) dual-fluorescence counting was used to detect cell viability and concentration, and it was found that the single-cell suspension satisfied the requirements for single-cell sequencing, with the viability of cells over 85% and a high cell concentration. After single-cell data processing, a median of ~2500 transcripts per cell were detected in each carotid artery cell. Notably, a variety of cell types of the normal carotid artery, including vascular smooth muscle cells (VSMCs), fibroblasts, endothelial cells (ECs), and macrophages and dendritic cells (M&#966;/DCs), were concurrently detectable. This protocol may be applied to prepare a single-cell suspension of blood vessels from other tissues with appropriate modifications.

This protocol describes a two-step cell digestion method for preparing a single-cell suspension of mouse carotid arteries (Figure 1). This two-step cell digestion method combines collagenase/DNase with trypsin to effectively dissociate the mouse carotid vascular wall to obtain high-quality single-cell suspensions for single-cell sequencing. After dissociation, the cell concentration and cell viability were calculated by an automated cell counter. The bright field showed the morphology of car...

Watch this Scientific Journal Video about Vascular Tissue Dissociation and Exploring Single-Cell Subclusters for Targeted Therapy at JoVE.com

Author Spotlight: Vascular Tissue Dissociation and Exploring Single-Cell Subclusters for Targeted Therapy 

Here we describe a two-step cell digestion protocol for preparing a single-cell suspension of mouse carotid arteries.

Preparation of a Single-Cell Suspension from Mouse Carotid Arteries for Single-Cell Sequencing

Carotid arteries are major blood vessels in the neck that supply blood and oxygen to the brain, but carotid stenosis occurs when carotid arteries are ...

preparation-single-cell-suspension-from-mouse-carotid-arteries-for

Research

JoVE Journal

Biology

2.7K Views.  Soochow University. Here we describe a two-step cell digestion protocol for preparing a single-cell suspension of mouse carotid arteries.

Video: Author Spotlight: Vascular Tissue Dissociation and Exploring Single-Cell Subclusters for Targeted Therapy 

A Model of Disturbed Flow-Induced Atherosclerosis in Mouse Carotid Artery by Partial Ligation and a Simple Method of RNA Isolation from Carotid Endothelium

Despite the well-known close association, direct evidence linking disturbed flow to atherogenesis has been lacking. We have recently used a modified version of carotid partial ligation methods [1,2] to show that it acutely induces low and oscillatory flow conditions, two key characteristics of disturbed flow, in the mouse common carotid artery. Using this model, we have provided direct evidence that disturbed flow indeed leads to rapid and robust atherosclerosis development in Apolipoprotein E knockout mouse [3]. We also developed a method of endothelial RNA preparation with high purity from the mouse carotid intima [3]. Using this mouse model and method, we found that partial ligation causes endothelial dysfunction in a week, followed by robust and rapid atheroma formation in two weeks in a hyperlipidemic mouse model along with features of complex lesion formation such as intraplaque neovascularization by four weeks. This rapid in vivo model and the endothelial RNA preparation method could be used to determine molecular mechanisms underlying flow-dependent regulation of vascular biology and diseases. Also, it could be used to test various therapeutic interventions targeting endothelial dysfunction and atherosclerosis in considerably reduced study duration.

This describes a partial carotid ligation surgery, which causes disturbed flow conditions and subsequent atherosclerosis development (in two weeks) with intraplaque neo-vascularization (in four weeks) in the mouse common carotid artery. We also describe a novel method of RNA isolation from the carotid intima, providing high purity endothelial RNA.

Despite the well-known close association, direct evidence linking disturbed flow to atherogenesis has been lacking. We have recently used a modified ...

Medicine

Generation of Single-Cell Suspensions from Mouse Neural Tissue

Within the nervous system, hundreds of neuronal and glial cell types have been described. Each specific cell type in the brain or spinal cord has a repertoire of cell surface molecules, or molecular determinants, through which it can be identified and characterized. Currently, robust cell identification and separation technologies require single-cell preparations to be generated while simultaneously limiting cell death and destruction of characteristic surface protein. The gentleMACS Dissociator, when used in combination with trypsin or papain-based dissociation kits, can effectively and gently dissociate brain tissue while preserving antigen epitopes and limiting cell loss. Standardized preparation of single-cell suspensions is achieved using C Tubes and optimized, preset gentleMACS Programs. Once generated, single-cell suspensions can be treated with monoclonal conjugates like Anti-Prominin-1 MicroBeads, which identify neural progenitors, or purified further using Myelin Removal Beads.

Dissociating cells from specific tissue types requires specific parameters for tissue aggitation to obtain a high volume of viable, culturable cells. The Miltenyi gentleMACS Dissociator optimizes this task with a simple, practical protocol. In this publication the use of this apparatus on nerual tissue is explained.

Within the nervous system, hundreds of neuronal and glial cell types have been described. Each specific cell type in the brain or spinal cord has a ...

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells

Single cell mRNA sequencing has made significant progress in the last several years and has become an important tool in the field of developmental biology. It has been successfully used to identify rare cell populations, discover novel marker genes, and decode spatial and temporal developmental information. The single cell method has also evolved from the microfluidic based Fluidigm C1 technology to the droplet-based solutions in the last two to three years. Here we used the heart as an example to demonstrate how to profile the mouse embryonic tissue cells using the droplet based scRNA-Seq method. In addition, we have integrated two strategies into the workflow to profile multiple samples in a single experiment. Using one of the integrated methods, we have simultaneously profiled more than 9,000 cells from eight heart samples. These methods will be valuable to the developmental biology field by providing a cost-effective way to simultaneously profile single cells from different genetic backgrounds, developmental stages, or anatomical locations.

Here we presented a multiplexed single cell mRNA sequencing method to profile gene expression in mouse embryonic tissues. The droplet-based single cell mRNA sequencing (scRNA-Seq) method in combination with multiplexing strategies can profile single cells from multiple samples simultaneously, which significantly reduces reagent costs and minimizes experimental batch effects.

Single cell mRNA sequencing has made significant progress in the last several years and has become an important tool in the field of developmental ...

Developmental Biology

Nuclei Isolation from Mouse Cardiac Progenitor Cells at Single-Cell Resolution

Nuclei Isolation from Mouse Cardiac Progenitor Cells for Epigenome and Gene Expression Profiling at Single-Cell Resolution

The developing heart is a complex structure containing various progenitor cells controlled by complex regulatory mechanisms. The examination of the gene expression and chromatin state of individual cells allows the identification of the cell type and state. Single-cell sequencing approaches have revealed a number of important characteristics of cardiac progenitor cell heterogeneity. However, these methods are generally restricted to fresh tissue, which limits studies with diverse experimental conditions, as the fresh tissue must be processed at once in the same run to reduce the technical variability. Therefore, easy and flexible procedures to produce data from methods such as single-nucleus RNA sequencing (snRNA-seq) and the single-nucleus assay for transposase-accessible chromatin with high-throughput sequencing (snATAC-seq) are needed in this area. Here, we present a protocol to rapidly isolate nuclei for subsequent single-nuclei dual-omics (combined snRNA-seq and snATAC-seq). This method allows the isolation of nuclei from frozen samples of cardiac progenitor cells and can be combined with platforms that use microfluidic chambers.

Author Spotlight: Nuclei Isolation from Mouse Cardiac Progenitor Cells for Epigenome and Gene Expression Profiling at Single-Cell Resolution  

Here, we present a protocol describing cell nuclei preparation. After microdissection and enzymatic dissociation of cardiac tissue into single cells, the progenitor cells were frozen, followed by isolation of pure viable cells, which were used for single-nucleus RNA sequencing and the single-nucleus assay for transposase-accessible chromatin with high-throughput sequencing analyses.

The developing heart is a complex structure containing various progenitor cells controlled by complex regulatory mechanisms. The examination of the gene ...

Single Cell Transcriptional Profiling of Adult Mouse Cardiomyocytes

While numerous studies have examined gene expression changes from homogenates of heart tissue, this prevents studying the inherent stochastic variation between cells within a tissue. Isolation of pure cardiomyocyte populations through a collagenase perfusion of mouse hearts facilitates the generation of single cell microarrays for whole transcriptome gene expression, or qPCR of specific targets using nanofluidic arrays. We describe here a procedure to examine single cell gene expression profiles of cardiomyocytes isolated from the heart. This paradigm allows for the evaluation of metrics of interest which are not reliant on the mean (for example variance between cells within a tissue) which is not possible when using conventional whole tissue workflows for the evaluation of gene expression (Figure 1). We have achieved robust amplification of the single cell transcriptome yielding micrograms of double stranded cDNA that facilitates the use of microarrays on individual cells. In the procedure we describe the use of NimbleGen arrays which were selected for their ease of use and ability to customize their design. Alternatively, a reverse transcriptase - specific target amplification (RT-STA) reaction, allows for qPCR of hundreds of targets by nanofluidic PCR. Using either of these approaches, it is possible to examine the variability of expression between cells, as well as examining expression profiles of rare cell types from within a tissue. Overall, the single cell gene expression approach allows for the generation of data that can potentially identify idiosyncratic expression profiles that are typically averaged out when examining expression of millions of cells from typical homogenates generated from whole tissues.

Single cell expression profiling allows the detailed gene expression analysis of individual cells. We describe methods for the isolation of cardiomyocytes, and preparing the resulting lysates for either whole transcriptome microarray or qPCR of specific targets.

While numerous studies have examined gene expression changes from homogenates of heart tissue, this prevents studying the inherent stochastic variation ...

Isolation of Adult Spinal Cord Nuclei for Massively Parallel Single-nucleus RNA Sequencing

Probing an individual cell&#39;s gene expression enables the identification of cell type and cell state. Single-cell RNA sequencing has emerged as a powerful tool for studying transcriptional profiles of cells, particularly in heterogeneous tissues such as the central nervous system. However, dissociation methods required for single cell sequencing can lead to experimental changes in the gene expression and cell death. Furthermore, these methods are generally restricted to fresh tissue, thus limiting studies on archival and bio-bank material. Single nucleus RNA sequencing (snRNA-Seq) is an appealing alternative for transcriptional studies, given that it accurately identifies cell types, permits the study of tissue that is frozen or difficult to dissociate, and reduces dissociation-induced transcription. Here, we present a high-throughput protocol for rapid isolation of nuclei for downstream snRNA-Seq. This method enables isolation of nuclei from fresh or frozen spinal cord samples and can be combined with two massively parallel droplet encapsulation platforms.

Here, we present a protocol to rapidly isolate high-quality nuclei from the fresh or frozen tissue for downstream massively parallel RNA sequencing. We include detergent-mechanical and hypotonic-mechanical tissue disruption and cell lysis options, both of which can be used for isolation of nuclei.

Probing an individual cell&#39;s gene expression enables the identification of cell type and cell state. Single-cell RNA sequencing has emerged as a ...

Neuroscience

Isolation of Region-specific Microglia from One Adult Mouse Brain Hemisphere for Deep Single-cell RNA Sequencing

As resident macrophages in the central nervous system, microglia actively control brain development and homeostasis, and their dysfunctions may drive human diseases. Considerable advances have been made to uncover the molecular signatures of homeostatic microglia as well as alterations of their gene expression in response to environmental stimuli. With the advent and maturation of single-cell genomic methodologies, it is increasingly recognized that heterogenous microglia may underlie the diverse roles they play in different developmental and pathological conditions. Further dissection of such heterogeneity can be achieved through efficient isolation of microglia from a given region of interest, followed by sensitive profiling of individual cells. Here, we provide a detailed protocol for the rapid isolation of microglia from different brain regions in a single adult mouse brain hemisphere. We also demonstrate how to use these sorted microglia for plate-based deep single-cell RNA sequencing. We discuss the adaptability of this method to other scenarios and provide guidelines for improving the system to accommodate large-scale studies.

We provide a protocol for isolation of microglia from different dissected regions of an adult mouse brain hemisphere, followed by semi-automated library preparation for deep single-cell RNA sequencing of full-length transcriptomes. This method will help to elucidate functional heterogeneity of microglia in health and disease.

As resident macrophages in the central nervous system, microglia actively control brain development and homeostasis, and their dysfunctions may drive ...

Preparation of a Non-Cardiomyocyte Cell Suspension for Single-Cell RNA Sequencing from a Post-Myocardial Infarction Adult Mouse Heart

Myocardial infarction (MI) is one of the most common cardiovascular diseases, with increasing mortality worldwide. Non-cardiomyocytes account for more than half of the total cardiac cell population, and they contribute to adaptive compensations upon myocardial injury, including inflammatory responses, tissue repair, and scar formation. To study the post-MI cardiac microenvironment, single-cell RNA sequencing (scRNA-seq) is widely used to identify different cardiac cell types and intercellular communications. Among the procedures of scRNA-seq sample preparation, preparing the cell suspension is one of the most critical steps, because the cell viability can affect the quality of the scRNA-seq results. Therefore, we designed an experimental protocol for preparing a non-cardiomyocyte cell suspension from post-MI mouse hearts with an extra focus on improving the cell viability by choosing mild digestive enzymes, controlling the digestion time, and applying fluorescence-activated cell sorting (FACS). Finally, we isolated CD45+ cells from the non-cardiomyocyte cell suspension obtained through this protocol, and then we performed scRNA-seq.

Here, we describe a protocol to isolate a sufficient amount of single non-cardiomyocytes with high viability from a post-myocardial infarction (MI) mouse heart. This can be used for subsequent single-cell sequencing, flow cytometry analysis, and primary cell culture.

Myocardial infarction (MI) is one of the most common cardiovascular diseases, with increasing mortality worldwide. Non-cardiomyocytes account for more ...

Isolation of Endothelial Cells from the Lumen of Mouse Carotid Arteries for Single-Cell Multi-Omics Experiments

Atherosclerosis is an inflammatory disease of the arterial regions exposed to disturbed blood flow (d-flow). D-flow regulates the expression of genes in the endothelium at the transcriptomic and epigenomic levels, resulting in proatherogenic responses. Recently, single-cell RNA sequencing (scRNAseq) and single-cell Assay for Transposase Accessible Chromatin sequencing (scATACseq) studies were performed to determine the transcriptomic and chromatin accessibility changes at a single-cell resolution using the mouse partial carotid ligation (PCL) model. As endothelial cells (ECs) represent a minor fraction of the total cell populations in the artery wall, a luminal digestion method was used to obtain EC-enriched single-cell preparations. For this study, mice were subjected to PCL surgery to induce d-flow in the left carotid artery (LCA) while using the right carotid artery (RCA) as a control. The carotid arteries were dissected out two days or two weeks post PCL surgery. The lumen of each carotid was subjected to collagenase digestion, and endothelial-enriched single cells or single nuclei were obtained. These single-cell and single-nuclei preparations were subsequently barcoded using a 10x Genomics microfluidic setup. The barcoded single-cells and single-nuclei were then utilized for RNA preparation, library generation, and sequencing on a high-throughput DNA sequencer. Post bioinformatics processing, the scRNAseq and scATACseq datasets identified various cell types from the luminal digestion, primarily consisting of ECs. Smooth muscle cells, fibroblasts, and immune cells were also present. This EC-enrichment method aided in understanding the effect of blood flow on the endothelium, which could have been difficult with the total artery digestion method. The EC-enriched single-cell preparation method can be used to perform single-cell omics studies in EC-knockouts and transgenic mice where the effect of blood flow on these genes has not been studied. Importantly, this technique can be adapted to isolate EC-enriched single cells from human artery explants to perform similar mechanistic studies.

We present a method for isolating endothelial cells and nuclei from the lumen of mouse carotid arteries exposed to stable or disturbed flow conditions to perform single-cell omics experiments.

Atherosclerosis is an inflammatory disease of the arterial regions exposed to disturbed blood flow (d-flow). D-flow regulates the expression of genes in ...

Single-Cell Suspension Preparation from Nile Tilapia Intestine for Single-Cell Sequencing

Nile tilapia is one of the most commonly cultured freshwater fish species worldwide and is a widely used research model for aquaculture fish studies. The preparation of high-quality single-cell suspensions is essential for single-cell level studies such as single-cell RNA or genome sequencing. However, there is no ready-to-use protocol for aquaculture fish species, particularly for the intestine of tilapia. The effective dissociation enzymes vary depending on the tissue type. Therefore, optimizing the tissue dissociation protocol by selecting the appropriate enzyme or enzyme combination to obtain enough viable cells with minimum damage is essential. This study illustrates an optimized protocol to prepare a high-quality single-cell suspension from Nile tilapia intestine with an enzyme combination of collagenase/dispase. This combination is highly effective for dissociation with the utilization of bovine serum albumin and DNase to reduce cell aggregation after digestion. The cell output satisfies the requirements for single-cell sequencing, with 90% cell viability and a high cell concentration. This protocol can also be modified to prepare a single-cell suspension from the intestines of other fish species. This research provides an efficient reference protocol and reduces the need for additional trials in the preparation of single-cell suspensions for aquaculture fish species.

Here, we demonstrate the preparation of a high-quality single-cell suspension of tilapia intestine for single-cell sequencing.

Nile tilapia is one of the most commonly cultured freshwater fish species worldwide and is a widely used research model for aquaculture fish studies. The ...