This work was mainly supported by the by USDA NIFA AFRI 2013-67015-21236, and in part by USDA NIFA AFRI 2015-67015-23216. This study was supported in part by an appointment to the Agricultural Research Service Research Participation Program administered by the Oak Ridge Institute for Science and Education (ORISE) through an interagency agreement between the US Department of Energy (DOE) and the US Department of Agriculture. ORISE is managed by Oak Ridge Associated Universities under DOE contract no. DE-AC05-06OR2310.
We would like to thank Dr. Kay Faaberg for the HP-PRRSV infectious clones, Dr. Susan Brockmeier for her help with animals involved in the experiment, and Sue Ohlendorf for secretarial assistance in preparation of the manuscript.

<ol>
	<li>Finotello, F., Di Camillo, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Measuring+differential+gene+expression+with+RNA-seq:+challenges+and+strategies+for+data+analysis.">Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis.</a> Briefings in Functional Genomics. 14 (2), 130-142 (2015).</li><li>Coble, D. J., 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=RNA-seq+analysis+of+broiler+liver+transcriptome+reveals+novel+responses+to+high+ambient+temperature.">RNA-seq analysis of broiler liver transcriptome reveals novel responses to high ambient temperature.</a> BMC Genomics. 15, 1084 (2014).</li><li>Koltes, J. E., 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+of+a+putative+quantitative+trait+nucleotide+in+guanylate+binding+protein+5+for+host+response+to+PRRS+virus+infection.">Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection.</a> BMC Genomics. 16, 412 (2015).</li><li>Miller, L. C., 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=Comparative+analysis+of+signature+genes+in+PRRSV-infected+porcine+monocyte-derived+cells+to+different+stimuli.">Comparative analysis of signature genes in PRRSV-infected porcine monocyte-derived cells to different stimuli.</a> PLoS One. 12 (7), 0181256 (2017).</li><li>Head, S. 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=Library+construction+for+next-generation+sequencing:+overviews+and+challenges.">Library construction for next-generation sequencing: overviews and challenges.</a> Biotechniques. 56 (2), 61-64 (2014).</li><li>Wang, Z., Gerstein, M., Snyder, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA-Seq:+a+revolutionary+tool+for+transcriptomics.">RNA-Seq: a revolutionary tool for transcriptomics.</a> Nature reviews. Genetics. 10 (1), 57-63 (2009).</li><li>Dominic, O. N., Heike, G., Martin, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ribosomal+RNA+Depletion+for+Efficient+Use+of+RNA-Seq+Capacity.">Ribosomal RNA Depletion for Efficient Use of RNA-Seq Capacity.</a> Current Protocols in Molecular Biology. 103 (1), 11-14 (2013).</li><li>Fleming, D. S., Miller, L. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+small+non-coding+RNA+classes+expressed+in+swine+whole+blood+during+HP-PRRSV+infection.">Identification of small non-coding RNA classes expressed in swine whole blood during HP-PRRSV infection.</a> Virology. 517, 56-61 (2018).</li><li>Fleming, D. S., Miller, L. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Small+non-coding+RNA+expression+status+in+animals+faced+with+highly+pathogenic+porcine+reproductive+and+respiratory+syndrome+virus+(HP-PRRSV).">Small non-coding RNA expression status in animals faced with highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV).</a> Proceedings of the World Congress on Genetics Applied to Livestock Production. (11), (2018).</li><li>Bivens Nathan, J., Zhou, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA-Seq+Library+Construction+Methods+for+Transcriptome+Analysis.">RNA-Seq Library Construction Methods for Transcriptome Analysis.</a> Current Protocols in Plant Biology. 1 (1), 197-215 (2016).</li><li>Cui, 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=A+comparison+between+ribo-minus+RNA-sequencing+and+polyA-selected+RNA-sequencing.">A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing.</a> Genomics. 96 (5), 259-265 (2010).</li><li>Guo, 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=RNAseq+by+Total+RNA+Library+Identifies+Additional+RNAs+Compared+to+Poly(A)+RNA+Library.">RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library.</a> BioMed Research International. 2015, 9 (2015).</li><li>Choi, I., 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=Increasing+gene+discovery+and+coverage+using+RNA-seq+of+globin+RNA+reduced+porcine+blood+samples.">Increasing gene discovery and coverage using RNA-seq of globin RNA reduced porcine blood samples.</a> BMC Genomics. 15, 954 (2014).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=TruSeq&#174;+Stranded+Total+RNA+Sample+Preparation+Guide.">TruSeq&#174; Stranded Total RNA Sample Preparation Guide.</a> Illumina. , (2018).</li><li>. New England Biolabs Inc. Protocol for use with NEBNext Multiplex Small RNA Library Prep Kit for Illumina (Index Primers 1-48) (E7560) Available from: <a target="_blank" href="https://www.neb.com/~/media/Catalog/All-Protocols/758F75A29CDE4D03954E1EF75E78EA3D/Content/manualE7560_Figure_1.jpg">https://www.neb.com/~/media/Catalog/All-Protocols/758F75A29CDE4D03954E1EF75E78EA3D/Content/manualE7560_Figure_1.jpg</a> (2018)</li><li>Shin, H., 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=Variation+in+RNA-Seq+transcriptome+profiles+of+peripheral+whole+blood+from+healthy+individuals+with+and+without+globin+depletion.">Variation in RNA-Seq transcriptome profiles of peripheral whole blood from healthy individuals with and without globin depletion.</a> PLoS One. 9 (3), 91041 (2014).</li><li>Costa, V., Angelini, C., De Feis, I., Ciccodicola, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Uncovering+the+complexity+of+transcriptomes+with+RNA-Seq.">Uncovering the complexity of transcriptomes with RNA-Seq.</a> Journal of Biomedicine and Biotechnology. 2010, 853916 (2010).</li><li>Martens-Uzunova, E. 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The authors have nothing to disclose.
Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer.

The first critical step in the protocol that made it optimized included the added globin depletion steps, which made it possible to get quality reads from whole blood samples. One of the largest limitations on using whole blood in sequencing studies are the high numbers of reads in the sample that will map to globin molecules and reduce the reads that could map to other molecules of interest18. Therefore, in optimizing the protocol for our sample type, we needed to incorporate a globin depletion s...

Next generation sequencing (NGS) has emerged as a powerful tool for the investigation of the changes that occur at the genomic level of biological organisms. Sample preparation for NGS methods can be varied depending on the organism, tissue type, and more importantly the questions the researchers are keen to address. Many studies have turned to NGS as a means of studying the differences in gene expression between states such as healthy and sick individuals1,2,3,4. The sequencing take place on a whole genome basis and allows a researcher to capture the most, if not all, of the genomic information for a particular genetic marker at a time point.
The most common markers of expression observed are the messenger RNAs (mRNAs). The most used procedures for prepping libraries for RNA-seq are optimized for the recovery of mRNA molecules through the use of a series of purifications, fragmentations, and ligations5,6. However, the decision on how a protocol is to be performed relies heavily on the sample type and the questions being posed about said sample. In most cases total RNA is extracted; yet, not all RNA molecules are of interest and in cases such as mRNA expression studies overly abundant RNA species, like ribosomal RNAs (rRNA) need to be removed to increase the number of detectable transcripts associated with the mRNAs. The most popular and widely used method for removing the abundant rRNA molecules is the reduction of polyadenylated RNA transcripts referred to as polyA depletion7. This approach works well for the analysis of mRNA expression as it does not affect the mRNA transcripts. However, in studies that are interested in non-coding or viral RNAs, polyA depletion also removes these molecules.
Many studies choose to focus on the RNA sequence library preparation to examine either mRNA expression (coding) or a particular class of small or large non-coding RNA. Although there are other procedures8 like ours that allow for the dual sample preparation, many studies prepare libraries from separate samples for separate studies when available. For a study like ours, this would normally require multiple blood samples increasing time, consumables, and animal stress. The goal of our study was to be able to use whole blood from animals to identify and quantify the different classes of both mRNA and non-coding RNA expressed between healthy and highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) challenged pigs9,10 despite having only a single whole blood sample (2.5 mL) from each pig. In order to do this, we needed to optimize the typical extraction and library creation protocols to generate the proper data to allow for analysis of both mRNA and non-coding RNA (ncRNA) expression11 from a single sample.
This prompted a need for a protocol that allowed for mRNA and non-coding RNA analysis because the available standard kits and methods for RNA-extraction and library creation were intended chiefly for mRNA and use a poly-A depletion step12. This step would have made it impossible to recover non-coding RNA or viral transcripts from the sample. Therefore, an optimized method was needed that allowed for total RNA extraction without sample polyA depletion. The method presented in this manuscript has been optimized to allow for the use of whole blood as a sample type and to build sequencing libraries for both mRNA and ncRNAs of small and large sizes. The method has been optimized to allow for the analysis of all detectable non-coding RNAs as well as retain viral RNAs for later investigation13. In all, our optimized library preparation protocol allows for the investigation of multiple RNA molecules from a single whole blood sample.
The overall goal behind the use of this method was to develop a process that allowed for the collection of both non-coding RNA and mRNA from one sample of whole blood. This allows us to have mRNA, ncRNA, and viral RNA for each animal in our study sourced from a single sample9. This, ultimately, allows for more scientific discovery without additional animal costs and gives a more complete picture of the expression of each individual sample. The described method allows for the examination of the regulators of gene expression as well as allowing for completion of correlative studies comparing both mRNA and non-coding RNA expression using a single whole blood sample. Our study used this protocol to examine the changes in gene expression and possible epigenetic regulators in virally infected 9-week old male commercial pigs.

<table><tbody><tr><td>PAXgene Tubes</td><td>PreAnalytix</td><td>762165</td><td></td></tr><tr><td>Molecular Biology Grade Water</td><td>ThermoFisher</td><td>10977-015</td><td></td></tr><tr><td>mirVana miRNA Isolation Kit</td><td>ThermoFisher</td><td>AM1560</td><td></td></tr><tr><td>Rneasy MinElute Clean Up Kit</td><td>QIAGEN</td><td>74204</td><td></td></tr><tr><td>100% Ethanol</td><td>Decon Labs, Inc.</td><td>2716</td><td></td></tr><tr><td>0.2 mL thin-walled tubes</td><td>ThermoFisher</td><td>98010540</td><td></td></tr><tr><td>1.5 mL RNase/DNase - free tubes</td><td>Any supplier</td><td></td><td></td></tr><tr><td>Veriti 96-well Thermocycler</td><td>ThermoFisher</td><td>4375786R</td><td></td></tr><tr><td>Globin Reduction Oligo (&amp;alpha; 1)</td><td>Any supplier</td><td></td><td>Sequence GAT CTC CGA GGC TCC AGC TTA ACG GT</td></tr><tr><td>Globin Reduction Oligo (&amp;alpha; 2)</td><td>Any supplier</td><td></td><td>Sequence TCA ACG ATC AGG AGG TCA GGG TGC AA</td></tr><tr><td>Globin Reduction Oligo (&amp;beta; 1)</td><td>Any supplier</td><td></td><td>Sequence AGG GGA ACT TAG TGG TAC TTG TGG GT</td></tr><tr><td>Globin Reduction Oligo (&amp;beta; 2)</td><td>Any supplier</td><td></td><td>Sequence GGT TCA GAG GAA AAA GGG CTC CTC CT</td></tr><tr><td>10X Oligo Hybridization Buffer</td><td></td><td></td><td></td></tr><tr><td>-Tris-HCl, pH 7.6</td><td>Fisher Scientific</td><td>BP1757-100</td><td></td></tr><tr><td>-KCl</td><td>Millipore Sigma</td><td>60142-100ML-F</td><td></td></tr><tr><td>10X RNase H Buffer</td><td></td><td></td><td></td></tr><tr><td>&amp;nbsp;-Tris-HCl, pH 7.6</td><td>Fisher Scientific</td><td>BP1757-100</td><td></td></tr><tr><td>&amp;nbsp;-DTT</td><td>ThermoFisher</td><td>Y00147</td><td></td></tr><tr><td>&amp;nbsp;-MgCl&lt;sub&gt;2&lt;/sub&gt;</td><td>Promega</td><td>A351B</td><td></td></tr><tr><td>&amp;nbsp;-Molecular Biology Grade Water</td><td>ThermoFisher</td><td>10977-015</td><td></td></tr><tr><td>RNase H</td><td>ThermoFisher</td><td>AM2292</td><td></td></tr><tr><td>SUPERase-IN</td><td>ThermoFisher</td><td>AM2694</td><td>Rnase inhibitor</td></tr><tr><td>EDTA</td><td>Millipore Sigma</td><td>E7889</td><td></td></tr><tr><td>Microcentrifuge</td><td>Any supplier</td><td></td><td></td></tr><tr><td>&amp;nbsp;2100 Electrophoresis BioAnalyzer Instrument</td><td>Agilent Technologies</td><td>G2938C</td><td></td></tr><tr><td>Agilent RNA 6000 Nano Kit</td><td>Agilent Technologies</td><td>5067-1511</td><td></td></tr><tr><td>Agilent High Sensitivity DNA&amp;nbsp; Kit</td><td>Agilent Technologies</td><td>5067-4626</td><td></td></tr><tr><td>TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero&amp;nbsp;</td><td>Illumina</td><td>RS-122-2201</td><td>mRNA kit; Human/Mouse/Rat Set A&amp;nbsp; (48 samples, 12 indexes)</td></tr><tr><td>TruSeq Stranded Total RNA Sample Preparation Guide</td><td>Illumina</td><td></td><td>Available on-line</td></tr><tr><td>RNAClean XP Beads</td><td>BeckmanCoulter</td><td>A63987</td><td></td></tr><tr><td>AMPure XP Beads</td><td>BeckmanCoulter</td><td>A63880</td><td></td></tr><tr><td>MicroAmp Optical 8-tube Strip</td><td>ThermoFisher</td><td>N8010580</td><td>0.2 ml thin-walled tubes</td></tr><tr><td>MicroAmp Optical 8-tube Strip Cap</td><td>ThermoFisher</td><td>N801-0535</td><td></td></tr><tr><td>RNase/DNase - free reagent reservoirs</td><td>Any supplier</td><td></td><td></td></tr><tr><td>SuperScript II Reverse Transcriptase</td><td>ThermoFisher</td><td>18064-014</td><td></td></tr><tr><td>MicroAmp Optical 96 well plates</td><td>ThermoFisher</td><td>N8010560</td><td>These were used in place of .3mL plates as needed</td></tr><tr><td>MicroAmp Optical adhesive film</td><td>ThermoFisher</td><td>4311971</td><td></td></tr><tr><td>NEBNext Multiplex Small RNA Library Prep Set for Illumina&amp;reg; (Set 1)&amp;nbsp;</td><td>New England Biolabs</td><td>E73005</td><td>small RNA kit</td></tr><tr><td>NEBNext Multiplex Small RNA Library Prep Set for Illumina&amp;reg; (Set 2)&amp;nbsp;</td><td>New England Biolabs</td><td>E75805</td><td>small RNA kit</td></tr><tr><td>QIAQuick PCR Purification Kit</td><td>QIAGEN</td><td>28104</td><td></td></tr><tr><td>96S Super Magnet Plate</td><td>ALPAQUA</td><td>A001322</td><td></td></tr></tbody></table>

identification of coding and non-coding rna classes expressed in swine whole blood

The advent of innovative and increasingly powerful next generation sequencing techniques has opened new avenues into the ability to examine the underlying gene expression related to biological processes of interest. These innovations not only allow researchers to observe expression from the mRNA sequences that code for genes that effect cellular function, but also the non-coding RNA (ncRNA) molecules that remain untranslated, but still have regulatory functions. Although researchers have the ability to observe both mRNA and ncRNA expression, it has been customary for a study to focus on one or the other. However, when studies are interested in both mRNA and ncRNA expression, many times they use separate samples to examine either coding or non-coding RNAs due to the difference in library preparations. This can lead to the need for more samples which can increase time, consumables, and animal stress. Additionally, it may cause researchers to decide to prepare samples for only one analysis, usually the mRNA, limiting the number of biological questions that can be investigated. However, ncRNAs span multiple classes with regulatory roles that effect mRNA expression. Because ncRNA are important to fundamental biologic processes and disorder of these processes in during infection, they may, therefore, make attractive targets for therapeutics. This manuscript demonstrates a modified protocol for the generation mRNA and non-coding RNA expression libraries, including viral RNA, from a single sample of whole blood. Optimization of this protocol, improved RNA purity, increased ligation for recovery of methylated RNAs, and omitted&#160;size selection, to allow capture of more RNA species.

The representative samples in our study are the globin and ribo-depleted whole blood samples. The representative outcome of the protocol consists of a globin depleted library sample with an RNA integrity number (RIN) above 7 (Figure 1a) and 260/280 nm concentration ratios at or above 2 (Figure 1b and 1c). Validation of the sample outcome was performed using spectrophotometer to give the final con...

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Identification of Coding and Non-coding RNA Classes Expressed in Swine Whole Blood

Here, we present a protocol optimized for the processing of coding (mRNA) and non-coding&#160;(ncRNA) globin reduced RNA-seq libraries from a single whole blood sample.

The advent of innovative and increasingly powerful next generation sequencing techniques has opened new avenues into the ability to examine the underlying ...

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Research

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Immunology and Infection

7.3K Views.  USDA, Agricultural Research Service. Here, we present a protocol optimized for the processing of coding (mRNA) and non-coding (ncRNA) globin reduced RNA-seq libraries from a single whole blood sample.

Video: Identification of Coding and Non-coding RNA Classes Expressed in Swine Whole Blood

Isolation of High-density Lipoproteins for Non-coding Small RNA Quantification

The diversity of small non-coding RNAs (sRNA) is rapidly expanding and their roles in biological processes, including gene regulation, are emerging. Most interestingly, sRNAs are also found outside of cells and are stably present in all biological fluids. As such, extracellular sRNAs represent a novel class of disease biomarkers and are likely involved in cell signaling and intercellular communication networks. To assess their potential as biomarkers, sRNAs can be quantified in plasma, urine, and other fluids. Nevertheless, to fully understand the impact of extracellular sRNAs as endocrine signals, it is important to determine which carriers are transporting and protecting them in biological fluids (e.g., plasma), which cells and tissues contribute to extracellular sRNA pools, and cells and tissues capable of accepting and utilizing extracellular sRNA. To accomplish these goals, it is critical to isolate highly pure populations of extracellular carriers for sRNA profiling and quantification. We have previously demonstrated that lipoproteins, particularly high-density lipoproteins (HDL), transport functional microRNAs (miRNA) between cells and HDL-miRNAs are significantly altered in disease. Here, we detail a new protocol that utilizes tandem HDL isolation with density-gradient ultracentrifugation (DGUC) and fast-protein-liquid chromatography (FPLC) to obtain highly pure HDL for downstream profiling and quantification of all sRNAs, including miRNAs, using both high-throughput sequencing and real-time PCR approaches. This protocol will be a valuable resource for the investigation of sRNAs on HDL.

This protocol describes the isolation and quantification of high-density lipoprotein small RNAs.

The diversity of small non-coding RNAs (sRNA) is rapidly expanding and their roles in biological processes, including gene regulation, are emerging. Most ...

Biochemistry

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Sequencing in remote locations and resource-poor settings presents unique challenges. Nanopore sequencing can be successfully used under such conditions, and was deployed to West Africa during the recent Ebola virus epidemic, highlighting this possibility. In addition to its practical advantages (low cost, ease of equipment transport and use), this technology also provides fundamental advantages over second-generation sequencing approaches, particularly the very long read length, ability to directly sequence RNA, and real-time availability of data. Raw read accuracy is lower than with other sequencing platforms, which represents the main limitation of this technology; however, this can be partially mitigated by the high read depth generated. Here, we present a field-compatible protocol for sequencing of the mRNAs encoding for Niemann-Pick C1, which is the cellular receptor for ebolaviruses. This protocol encompasses extraction of RNA from animal blood samples, followed by RT-PCR for target enrichment, barcoding, library preparation, and the sequencing run itself, and can be easily adapted for use with other DNA or RNA targets.

Nanopore sequencing is a novel technology that allows cost-effective sequencing in remote locations and resource-poor settings. Here, we present a protocol for sequencing of mRNAs from whole blood that is compatible with such conditions.

Sequencing in remote locations and resource-poor settings presents unique challenges. Nanopore sequencing can be successfully used under such conditions, ...

Genetics

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA

The growing role attributed nowadays to long non-coding RNAs (lncRNA) in physiology and pathophysiology makes it crucial to characterize their interactome by identifying their molecular partners, DNA, proteins and/or RNAs. The latter can interact with lncRNA through networks involving proteins, but they can also be engaged in direct RNA/RNA interactions. We, therefore, developed an easy-to-use RNA pull-down procedure that allowed identification of RNAs engaged in direct RNA/RNA interaction with a lncRNA using psoralen, a molecule that cross-links only RNA/RNA interactions. Bioinformatics modeling of the lncRNA secondary structure allowed the selection of several specific antisense DNA oligonucleotide probes with a strong affinity for regions displaying a low probability of internal base pairing. Since the specific probes that were designed targeted accessible regions throughout the length of the lncRNA, the RNA-interaction zones could be delineated in the sequence of the lncRNA. When coupled with a high throughput RNA sequencing, this protocol can be used for the whole direct RNA interactome studies of a lncRNA of interest.

An easy-to-use RNA pull-down protocol is designed for the identification of RNAs engaged in direct RNA/RNA interaction with a long non-coding RNA. The protocol uses psoralen as a fixative to cross-link only RNA/RNA interactions and provides the whole direct RNA interactome of a long non-coding RNA when coupled with RNA sequencing.

The growing role attributed nowadays to long non-coding RNAs (lncRNA) in physiology and pathophysiology makes it crucial to characterize their interactome ...

Genome-wide Analysis of HDAC Inhibitor-mediated Modulation of microRNAs and mRNAs in B Cells Induced to Undergo Class-switch DNA Recombination and Plasma Cell Differentiation

Antibody responses are accomplished through several critical B cell-intrinsic processes, including somatic hypermutation (SHM), class-switch DNA recombination (CSR), and plasma cell differentiation. In recent years, epigenetic modifications or factors, such as histone deacetylation and microRNAs (miRNAs), have been shown to interact with B-cell genetic programs to shape antibody responses, while the dysfunction of epigenetic factors has been found to lead to autoantibody responses. Analyzing genome-wide miRNA and mRNA expression in B cells in response to epigenetic modulators is important for understanding the epigenetic regulation of B-cell function and antibody response. Here, we demonstrate a protocol for inducing B cells to undergo CSR and plasma cell differentiation, treating these B cells with histone deacetylase (HDAC) inhibitors (HDIs), and analyzing mRNA and microRNA expression. In this protocol, we directly analyze complementary DNA (cDNA) sequences using next-generation mRNA sequencing (mRNA-seq) and miRNA-seq technologies, mapping of the sequencing reads to the genome, and quantitative reverse transcription (qRT)-PCR. With these approaches, we have defined that, in B cells induced to undergo CSR and plasma cell differentiation, HDI, an epigenetic regulator, selectively modulates miRNA and mRNA expression and alters CSR and plasma cell differentiation.

Epigenetic factors can interact with genetic programs to modulate gene expression and regulate B cell function. By combining in vitro B-cell stimulation, qRT-PCR, and high-throughput microRNA-sequence and mRNA-sequence approaches, we can analyze the epigenetic modulation of miRNA and gene expression in B cells.

Antibody responses are accomplished through several critical B cell-intrinsic processes, including somatic hypermutation (SHM), class-switch DNA ...

RNA-seq Analysis of Transcriptomes in Thrombin-treated and Control Human Pulmonary Microvascular Endothelial Cells

The characterization of gene expression in cells via measurement of mRNA levels is a useful tool in determining how the transcriptional machinery of the cell is affected by external signals (e.g. drug treatment), or how cells differ between a healthy state and a diseased state. With the advent and continuous refinement of next-generation DNA sequencing technology, RNA-sequencing (RNA-seq) has become an increasingly popular method of transcriptome analysis to catalog all species of transcripts, to determine the transcriptional structure of all expressed genes and to quantify the changing expression levels of the total set of transcripts in a given cell, tissue or organism1,2 . RNA-seq is gradually replacing DNA microarrays as a preferred method for transcriptome analysis because it has the advantages of profiling a complete transcriptome, providing a digital type datum (copy number of any transcript) and not relying on any known genomic sequence3.
Here, we present a complete and detailed protocol to apply RNA-seq to profile transcriptomes in human pulmonary microvascular endothelial cells with or without thrombin treatment. This protocol is based on our recent published study entitled "RNA-seq Reveals Novel Transcriptome of Genes and Their Isoforms in Human Pulmonary Microvascular Endothelial Cells Treated with Thrombin,"4 in which we successfully performed the first complete transcriptome analysis of human pulmonary microvascular endothelial cells treated with thrombin using RNA-seq. It yielded unprecedented resources for further experimentation to gain insights into molecular mechanisms underlying thrombin-mediated endothelial dysfunction in the pathogenesis of inflammatory conditions, cancer, diabetes, and coronary heart disease, and provides potential new leads for therapeutic targets to those diseases.
The descriptive text of this protocol is divided into four parts. The first part describes the treatment of human pulmonary microvascular endothelial cells with thrombin and RNA isolation, quality analysis and quantification. The second part describes library construction and sequencing. The third part describes the data analysis. The fourth part describes an RT-PCR validation assay. Representative results of several key steps are displayed. Useful tips or precautions to boost success in key steps are provided in the Discussion section. Although this protocol uses human pulmonary microvascular endothelial cells treated with thrombin, it can be generalized to profile transcriptomes in both mammalian and non-mammalian cells and in tissues treated with different stimuli or inhibitors, or to compare transcriptomes in cells or tissues between a healthy state and a disease state.

This protocol presents a complete and detailed procedure to apply RNA-seq, a powerful next-generation DNA sequencing technology, to profile transcriptomes in human pulmonary microvascular endothelial cells with or without thrombin treatment. This protocol is generalizable to various cells or tissues affected by different reagents or disease states.

The characterization of gene expression in cells via measurement of mRNA levels is a useful tool in determining how the transcriptional machinery of the ...

Biology

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis

Hematopoietic stem cells (HSCs) are used clinically for transplantation treatment to rebuild a patient&#39;s hematopoietic system in many diseases such as leukemia and lymphoma. Elucidating the mechanisms controlling HSCs self-renewal and differentiation is important for application of HSCs for research and clinical uses. However, it is not possible to obtain large quantity of HSCs due to their inability to proliferate in vitro. To overcome this hurdle, we used a mouse bone marrow derived cell line, the EML (Erythroid, Myeloid, and Lymphocytic) cell line, as a model system for this study.
RNA-sequencing (RNA-Seq) has been increasingly used to replace microarray for gene expression studies. We report here a detailed method of using RNA-Seq technology to investigate the potential key factors in regulation of EML cell self-renewal and differentiation. The protocol provided in this paper is divided into three parts. The first part explains how to culture EML cells and separate Lin-CD34+ and Lin-CD34- cells. The second part of the protocol offers detailed procedures for total RNA preparation and the subsequent library construction for high-throughput sequencing. The last part describes the method for RNA-Seq data analysis and explains how to use the data to identify differentially expressed transcription factors between Lin-CD34+ and Lin-CD34- cells. The most significantly differentially expressed transcription factors were identified to be the potential key regulators controlling EML cell self-renewal and differentiation. In the discussion section of this paper, we highlight the key steps for successful performance of this experiment.
In summary, this paper offers a method of using RNA-Seq technology to identify potential regulators of self-renewal and differentiation in EML cells. The key factors identified are subjected to downstream functional analysis in vitro and in vivo.

RNA-sequencing and bioinformatics analyses were used to identify significantly and differentially expressed transcription factors in Lin-CD34+ and Lin-CD34- subpopulations of mouse EMLcells. These transcription factors might play important roles in determining the switch between self-renewing Lin-CD34+ and partially differentiated Lin-CD34- cells.

Hematopoietic stem cells (HSCs) are used clinically for transplantation treatment to rebuild a patient&#39;s hematopoietic system in many diseases such as ...

Low-input Nucleus Isolation and Multiplexing with Barcoded Antibodies of Mouse Sympathetic Ganglia for Single-nucleus RNA Sequencing

The cardiac autonomic nervous system is crucial in controlling cardiac function, such as heart rate and cardiac contractility, and is divided into sympathetic and parasympathetic branches. Normally, there is a balance between these two branches to maintain homeostasis. However, cardiac disease states such as myocardial infarction, heart failure, and hypertension can induce the remodeling of cells involved in cardiac innervation, which is associated with an adverse clinical outcome.
Although there are vast amounts of data for the histological structure and function of the cardiac autonomic nervous system, its molecular biological architecture in health and disease is still enigmatic in many aspects. Novel technologies such as single-cell RNA sequencing (scRNA-seq) hold promise for the genetic characterization of tissues at single-cell resolution. However, the relatively large size of neurons may impede the standardized use of these techniques. Here, this protocol exploits droplet-based single-nucleus RNA sequencing (snRNA-seq), a method to characterize the biological architecture of cardiac sympathetic neurons in health and disease. A stepwise approach is demonstrated to perform snRNA-seq of the bilateral superior cervical (SCG) and stellate ganglia (StG) dissected from adult mice.
This method enables long-term sample preservation, maintaining an adequate RNA quality when samples from multiple individuals/experiments cannot be collected all at once within a short period of time. Barcoding the nuclei with hashtag oligos (HTOs) enables demultiplexing and the trace-back of distinct ganglionic samples post sequencing. Subsequent analyses revealed successful nuclei capture of neuronal, satellite glial, and endothelial cells of the sympathetic ganglia, as validated by snRNA-seq. In summary, this protocol provides a stepwise approach for snRNA-seq of sympathetic extrinsic cardiac ganglia, a method that has the potential for broader application in studies of the innervation of other organs and tissues.

This protocol describes the detailed, low-input sample preparation for single-nucleus sequencing, including the dissection of mouse superior cervical and stellate ganglia, cell dissociation, cryopreservation, nucleus isolation, and hashtag barcoding.

The cardiac autonomic nervous system is crucial in controlling cardiac function, such as heart rate and cardiac contractility, and is divided into ...

Medicine

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

The analysis of single cell gene expression across thousands of individual cells within a tissue or microenvironment is a valuable tool for identifying cell composition, discrimination of functional states, and molecular pathways underlying observed tissue functions and animal behaviors. However, the isolation of intact, healthy single cells from adult mammalian tissues for subsequent downstream single cell molecular analysis can be challenging. This protocol describes the general processes and quality control checks necessary to obtain high-quality adult single cell preparations from the nervous system or skin that enabled subsequent unbiased single cell RNA sequencing and analysis. Guidelines for downstream bioinformatic analysis are also provided.

This protocol describes the general processes and quality control checks necessary for preparing healthy adult mammalian single cells for droplet-based, high throughput single cell RNA-Seq preparations. Sequencing parameters, read alignment, and downstream single-cell bioinformatic analysis are also provided.

The analysis of single cell gene expression across thousands of individual cells within a tissue or microenvironment is a valuable tool for identifying ...

Cell Type-specific Gene Expression Profiling in the Mouse Liver

Liver repopulation after injury is a crucial feature of mammals which prevents immediate organ failure and death after exposure of environmental toxins. A deeper understanding of the changes in gene expression that occur during repopulation could help identify therapeutic targets to promote the restoration of liver function in the setting of injuries. Nonetheless, methods to isolate specifically the repopulating hepatocytes are inhibited by a lack of cell markers, limited cell numbers, and the fragility of these cells. The development of translating ribosome affinity purification (TRAP) technology in conjunction with the Fah-/- mouse model to recapitulate repopulation in the setting of liver injury allows gene expression profiling of the repopulating hepatocytes. With TRAP, cell type-specific translating mRNA is rapidly and efficiently isolated. We developed a method that utilizes TRAP with affinity-based isolation of translating mRNA from hepatocytes that selectively express the green fluorescent protein (GFP)-tagged ribosomal protein (RP), GFP:RPL10A. TRAP circumvents the long time period required for fluorescence-activated cell sorting that could change the gene expression profile. Furthermore, since only the repopulating hepatocytes express the GFP:RPL10A fusion protein, the isolated mRNA is devoid of contamination from the surrounding injured hepatocytes and other cell types in the liver. The affinity-purified mRNA is of high quality and allows downstream PCR- or high-throughput sequencing-based analysis of gene expression.

Translating ribosome affinity purification (TRAP) enables rapid and efficient isolation of cell type-specific translating mRNA. Here, we demonstrate a method that combines hydrodynamic tail-vein injection in a mouse model of liver repopulation and TRAP to examine the expression profile of repopulating hepatocytes.

Liver repopulation after injury is a crucial feature of mammals which prevents immediate organ failure and death after exposure of environmental toxins. A ...

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

As well as the typical analysis of RNA-Seq to measure differential gene expression (DGE) across experimental/biological conditions, RNA-seq data can also be utilized to explore other complex regulatory mechanisms at the exon level. Alternative splicing and polyadenylation play a crucial role in the functional diversity of a gene by generating different isoforms to regulate gene expression at the post-transcriptional level, and limiting analyses to the whole gene level can miss this important regulatory layer. Here, we demonstrate detailed step by step analyses for identification and visualization of differential exon and polyadenylation site usage across conditions, using Bioconductor and other packages and functions, including DEXSeq, diffSplice from the Limma package, and rMATS.

Alternative splicing (AS) and alternative polyadenylation (APA) expand the diversity of transcript isoforms and their products. Here, we describe bioinformatic protocols to analyze bulk RNA-seq and 3' end sequencing assays to detect and visualize AS and APA varying across experimental conditions.

As well as the typical analysis of RNA-Seq to measure differential gene expression (DGE) across experimental/biological conditions, RNA-seq data can also ...