Name: a complete pipeline for isolating and sequencing micrornas, and analyzing them using open source tools
Uploaded: 2019-08-21T13:30:00
Description: Watch this Scientific Journal Video about A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools at JoVE.com

We would like to thank members of the laboratories of Andrew Fire and Mark Kay for guidance and suggestions.

Animal experiments were authorized by the Institutional Animal Care and Use Committee of the University of Washington.
Small RNA library preparation
1. RNA isolation
<ol>
	<li>Isolate RNA from a biological source using a standard RNA isolation reagent, or a kit that enriches for microRNAs. For tissues, it is best to start with samples snap-frozen in liquid nitrogen and ground to a powder using a pre-chilled mortar and pestle.</li>
	...

<ol>
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P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+abundant+class+of+tiny+RNAs+with+probable+regulatory+roles+in+Caenorhabditis+elegans.">An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans.</a> Science. 294 (5543), 858-862 (2001).</li><li>Kim, V. N., Han, J., Siomi, M. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biogenesis+of+small+RNAs+in+animals.">Biogenesis of small RNAs in animals.</a> Nature Reviews Molecular Cell Biology. 10 (2), 126-139 (2009).</li><li>Gu, S., 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=The+loop+position+of+shRNAs+and+pre-miRNAs+is+critical+for+the+accuracy+of+dicer+processing+in+vivo.">The loop position of shRNAs and pre-miRNAs is critical for the accuracy of dicer processing in vivo.</a> Cell. 151 (4), 900-911 (2012).</li><li>Valdmanis, P. N., 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+interference-induced+hepatotoxicity+results+from+loss+of+the+first+synthesized+isoform+of+microRNA-122+in+mice.">RNA interference-induced hepatotoxicity results from loss of the first synthesized isoform of microRNA-122 in mice.</a> Nature Medicine. 22 (5), 557-562 (2016).</li><li>Valdmanis, P. N., 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=miR-122+removal+in+the+liver+activates+imprinted+microRNAs+and+enables+more+effective+microRNA-mediated+gene+repression.">miR-122 removal in the liver activates imprinted microRNAs and enables more effective microRNA-mediated gene repression.</a> Nature Communications. 9 (1), 5321 (2018).</li><li>Griffiths-Jones, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+microRNA+Registry.">The microRNA Registry.</a> Nucleic Acids Research. 32, D109-D111 (2004).</li><li>Griffiths-Jones, S., Grocock, R. J., van Dongen, S., Bateman, A., Enright, A. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=miRBase:+microRNA+sequences,+targets+and+gene+nomenclature.">miRBase: microRNA sequences, targets and gene nomenclature.</a> Nucleic Acids Research. 34 (Database issue), D140-D144 (2006).</li><li>Griffiths-Jones, S., Saini, H. K., van Dongen, S., Enright, A. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=miRBase:+tools+for+microRNA+genomics.">miRBase: tools for microRNA genomics.</a> Nucleic Acids Research. 36 (Database issue), D154-D158 (2008).</li><li>Patro, R., Mount, S. M., Kingsford, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sailfish+enables+alignment-free+isoform+quantification+from+RNA-seq+reads+using+lightweight+algorithms.">Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.</a> Nature Biotechnology. 32 (5), 462-464 (2014).</li><li>Love, M. I., Huber, W., Anders, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Moderated+estimation+of+fold+change+and+dispersion+for+RNA-seq+data+with+DESeq2.">Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.</a> Genome Biology. 15 (12), 550 (2014).</li><li>Fire, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Potent+and+specific+genetic+interference+by+double-stranded+RNA+in+Caenorhabditis+elegans.">Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans.</a> Nature. 391 (6669), 806-811 (1998).</li><li>Etheridge, A., Wang, K., Baxter, D., Galas, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Preparation+of+Small+RNA+NGS+Libraries+from+Biofluids.">Preparation of Small RNA NGS Libraries from Biofluids.</a> Methods in Molecular Biology. 1740, 163-175 (2018).</li><li>Yamane, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Differential+hepatitis+C+virus+RNA+target+site+selection+and+host+factor+activities+of+naturally+occurring+miR-122+3+variants.">Differential hepatitis C virus RNA target site selection and host factor activities of naturally occurring miR-122 3 variants.</a> Nucleic Acids Research. 45 (8), 4743-4755 (2017).</li><li>Giraldez, M. D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comprehensive+multi-center+assessment+of+small+RNA-seq+methods+for+quantitative+miRNA+profiling.">Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling.</a> Nature Biotechnology. 36 (8), 746-757 (2018).</li><li>Dard-Dascot, 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=Systematic+comparison+of+small+RNA+library+preparation+protocols+for+next-generation+sequencing.">Systematic comparison of small RNA library preparation protocols for next-generation sequencing.</a> BMC Genomics. 19 (1), 118 (2018).</li><li>Yeri, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evaluation+of+commercially+available+small+RNASeq+library+preparation+kits+using+low+input+RNA.">Evaluation of commercially available small RNASeq library preparation kits using low input RNA.</a> BMC Genomics. 19 (1), 331 (2018).</li><li>Coenen-Stass, A. M. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evaluation+of+methodologies+for+microRNA+biomarker+detection+by+next+generation+sequencing.">Evaluation of methodologies for microRNA biomarker detection by next generation sequencing.</a> RNA Biology. 15 (8), 1133-1145 (2018).</li><li>Baran-Gale, 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=Addressing+Bias+in+Small+RNA+Library+Preparation+for+Sequencing:+A+New+Protocol+Recovers+MicroRNAs+that+Evade+Capture+by+Current+Methods.">Addressing Bias in Small RNA Library Preparation for Sequencing: A New Protocol Recovers MicroRNAs that Evade Capture by Current Methods.</a> Frontiers in Genetics. 6, 352 (2015).</li><li>Jayaprakash, A. D., Jabado, O., Brown, B. D., Sachidanandam, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+and+remediation+of+biases+in+the+activity+of+RNA+ligases+in+small-RNA+deep+sequencing.">Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing.</a> Nucleic Acids Research. 39 (21), e141 (2011).</li><li>Van Nieuwerburgh, F., 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=Quantitative+bias+in+Illumina+TruSeq+and+a+novel+post+amplification+barcoding+strategy+for+multiplexed+DNA+and+small+RNA+deep+sequencing.">Quantitative bias in Illumina TruSeq and a novel post amplification barcoding strategy for multiplexed DNA and small RNA deep sequencing.</a> PLoS One. 6 (10), e26969 (2011).</li><li>Valdmanis, P. N., 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=Upregulation+of+the+microRNA+cluster+at+the+Dlk1-Dio3+locus+in+lung+adenocarcinoma.">Upregulation of the microRNA cluster at the Dlk1-Dio3 locus in lung adenocarcinoma.</a> Oncogene. 34 (1), 94-103 (2015).</li><li>Schwarzenbach, H., da Silva, A. M., Calin, G., Pantel, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Data+Normalization+Strategies+for+MicroRNA+Quantification.">Data Normalization Strategies for MicroRNA Quantification.</a> Clinical Chemistry. 61 (11), 1333-1342 (2015).</li><li>Viollet, S., Fuchs, R. T., Munafo, D. B., Zhuang, F., Robb, G. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=T4+RNA+ligase+2+truncated+active+site+mutants:+improved+tools+for+RNA+analysis.">T4 RNA ligase 2 truncated active site mutants: improved tools for RNA analysis.</a> BMC Biotechnology. 11, 72 (2011).</li><li>Chiang, H. 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=Mammalian+microRNAs:+experimental+evaluation+of+novel+and+previously+annotated+genes.">Mammalian microRNAs: experimental evaluation of novel and previously annotated genes.</a> Genes &amp; Development. 24 (10), 992-1009 (2010).</li><li>Fromm, B., 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+Uniform+System+for+the+Annotation+of+Vertebrate+microRNA+Genes+and+the+Evolution+of+the+Human+microRNAome.">A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome.</a> Annual Review of Genetics. 49, 213-242 (2015).</li></ol>

Despite the identification of microRNAs over 20 years ago13, the process of microRNA sequencing remains laborious and requires specialized equipment, hindering laboratories from routinely adopting in-house protocols14. Other techniques can simultaneously evaluate microRNAs, like microRNA microarrays and multiplexed expression panels; however, these approaches are limited in that they only quantify the microRNAs present in their probe set. Because of this, they miss importan...

First discovered in 19931, it is now estimated that nearly 2000 microRNAs are present in the human genome2. MicroRNAs are small non-coding RNAs that are typically 21-24 nucleotides long. They are post-transcriptional regulators of gene expression, often binding to complementary sites in the 3-untranslated region (3-UTR) of target genes to repress protein expression and degrade mRNA. Quantifying microRNAs can give valuable insight into gene expression and several protocols have been developed for this purpose3.
We have developed a defined, reproducible, and long-standing protocol for small RNA sequencing, and for analyzing normalized reads using open source bioinformatics tools. Importantly, our protocol enables the simultaneous identification of both endogenous microRNAs and exogenously delivered constructs that produce microRNA-like species, while minimizing reads that map to other small RNA species, including ribosomal RNAs (rRNAs), transfer RNA-derived small RNAs (tsRNAs), repeat-derived small RNAs, and mRNA degradation products. Fortunately, microRNAs are 5-phosphorylated and 2-3 hydroxylated4, a feature that can be leveraged to separate them from these other small RNAs and mRNA degradation products. Several commercial options exist for microRNA cloning and sequencing that are often quicker and easier to multiplex; however, the proprietary nature of kit reagents and their frequent modifications makes comparing sample runs challenging. Our strategy optimizes collecting only the correct size of microRNAs through acrylamide and agarose gel purification steps. In this protocol, we also describe a procedure for aligning sequence reads to microRNAs using open source tools. This set of instructions will be especially useful for novice informatics users, regardless of whether our library preparation method or a commercial method is used.
This protocol has been used in several published studies. For example, it was used to identify the mechanism by which the Dicer enzyme cleaves small hairpin RNAs at a distance of two nucleotides from the internal loop of the stem-loop structure - the so-called &#34;loop-counting rule&#34;5. We also followed these methods to identify the relative abundance of delivered small hairpin RNAs (shRNA) expressed from recombinant adeno-associated viral vectors (rAAVs), to identify the threshold of shRNA expression that can be tolerated prior to liver toxicity associated with excess shRNA expression6. Using this protocol, we also identified microRNAs in the liver that respond to the absence of microRNA-122 - a highly expressed hepatic microRNA - while also characterizing the degradation pattern of this microRNA7. Because we have used our protocol consistently in numerous experiments, we have been able to observe sample preparations longitudinally, and see that there are no discernible batch effects.
In sharing this protocol, our goal is to enable users to generate high quality, reproducible quantification of microRNAs in virtually any tissue or cell line, using affordable equipment and reagents, and free bioinformatics tools.

<table>
	<tbody>
		<tr>
			<td>100 bp DNA ladder</td>
			<td>NEB</td>
			<td>N3231</td>
			<td></td>
		</tr>
		<tr>
			<td>19:1 bis-acrylamide</td>
			<td>Millipore Sigma</td>
			<td>A9926</td>
			<td></td>
		</tr>
		<tr>
			<td>25 bp DNA step ladder</td>
			<td>Promega</td>
			<td>G4511</td>
			<td></td>
		</tr>
		<tr>
			<td>Acid phenol/chloroform</td>
			<td>ThermoFisher</td>
			<td>AM9720</td>
			<td></td>
		</tr>
		<tr>
			<td>Acrylamide RNA loading dye</td>
			<td>ThermoFisher</td>
			<td>R0641</td>
			<td></td>
		</tr>
		<tr>
			<td>Ammonium persulfate (APS)</td>
			<td>Biorad</td>
			<td>161-0700</td>
			<td></td>
		</tr>
		<tr>
			<td>Bioanalyzer instrument</td>
			<td>Agilent</td>
			<td>G2991AA</td>
			<td>For assessing RNA quality and concentration</td>
		</tr>
		<tr>
			<td>Chloroform</td>
			<td>Fisher Scientific</td>
			<td>C298-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethanol (100%)</td>
			<td>Sigma</td>
			<td>E7023</td>
			<td></td>
		</tr>
		<tr>
			<td>Gel Loading Buffer II</td>
			<td>ThermoFisher</td>
			<td>AM8547</td>
			<td></td>
		</tr>
		<tr>
			<td>GlycoBlue</td>
			<td>ThermoFisher</td>
			<td>AM9516</td>
			<td>Blue color helps in visualizing pellet</td>
		</tr>
		<tr>
			<td>HCl</td>
			<td>Sigma</td>
			<td>320331</td>
			<td></td>
		</tr>
		<tr>
			<td>KOH</td>
			<td>Sigma</td>
			<td>P5958</td>
			<td></td>
		</tr>
		<tr>
			<td>Maxi Vertical Gel Box 20 x 20cm</td>
			<td>Genesee</td>
			<td>45-109</td>
			<td></td>
		</tr>
		<tr>
			<td>miRVana microRNA isolation kit</td>
			<td>ThermoFisher</td>
			<td>AM1560</td>
			<td></td>
		</tr>
		<tr>
			<td>miSeq system</td>
			<td>Illumina</td>
			<td>SY-410-1003</td>
			<td>For generating small RNA sequencing data</td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Fisher Scientific</td>
			<td>S271-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Nusieve low-melting agarose</td>
			<td>Lonza</td>
			<td>50081</td>
			<td></td>
		</tr>
		<tr>
			<td>Parafilm (laboratory sealing film)</td>
			<td>Millipore Sigma</td>
			<td>P7793</td>
			<td></td>
		</tr>
		<tr>
			<td>Poly-ethylene glycol 8000</td>
			<td>NEB</td>
			<td>included with M0204</td>
			<td></td>
		</tr>
		<tr>
			<td>ProtoScript II First strand cDNA Synthesis Kit</td>
			<td>NEB</td>
			<td>E6560S</td>
			<td></td>
		</tr>
		<tr>
			<td>QIAquick Gel Extraction kit</td>
			<td>Qiagen</td>
			<td>28704</td>
			<td></td>
		</tr>
		<tr>
			<td>Qubit Fluorometer</td>
			<td>ThermoFisher</td>
			<td>Q33226</td>
			<td>For quantifying DNA concentration</td>
		</tr>
		<tr>
			<td>Qubit RNA HS Assay kit</td>
			<td>ThermoFisher</td>
			<td>Q32855</td>
			<td></td>
		</tr>
		<tr>
			<td>Razor Blades</td>
			<td>Fisher Scientific</td>
			<td>12640</td>
			<td></td>
		</tr>
		<tr>
			<td>Siliconized Low-Retention 1.5 ml tubes</td>
			<td>Fisher Scientific</td>
			<td>02-681-331</td>
			<td></td>
		</tr>
		<tr>
			<td>T4 RNA ligase 1</td>
			<td>NEB</td>
			<td>M0204</td>
			<td></td>
		</tr>
		<tr>
			<td>T4 RNA Ligase 2, truncated</td>
			<td>NEB</td>
			<td>M0242S</td>
			<td></td>
		</tr>
		<tr>
			<td>TapeStation</td>
			<td>Agilent</td>
			<td>G2939BA</td>
			<td>For assessing RNA quality and concentration</td>
		</tr>
		<tr>
			<td>Taq DNA Polymerase</td>
			<td>NEB</td>
			<td>M0273X</td>
			<td></td>
		</tr>
		<tr>
			<td>TEMED</td>
			<td>Biorad</td>
			<td>161-0800</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris Base pH 7.5</td>
			<td>Sigma</td>
			<td>10708976001</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris-buffered EDTA</td>
			<td>Sigma</td>
			<td>T9285</td>
			<td></td>
		</tr>
		<tr>
			<td>Trizol</td>
			<td>ThermoFisher</td>
			<td>15596026</td>
			<td></td>
		</tr>
		<tr>
			<td>UltraPure Ethidium bromide (10 mg/ml)</td>
			<td>Invitrogen</td>
			<td>15585-011</td>
			<td></td>
		</tr>
		<tr>
			<td>Universal miRNA cloning linker</td>
			<td>NEB</td>
			<td>S1315S</td>
			<td></td>
		</tr>
		<tr>
			<td>Urea</td>
			<td>Sigma</td>
			<td>U5378</td>
			<td></td>
		</tr>
	</tbody>
</table>

a complete pipeline for isolating and sequencing micrornas, and analyzing them using open source tools

Half of all human transcripts are thought to be regulated by microRNAs. Therefore, quantifying microRNA expression can reveal underlying mechanisms in disease states and provide therapeutic targets and biomarkers. Here, we detail how to accurately quantify microRNAs. Briefly, this method describes isolating microRNAs, ligating them to adaptors suitable for high-throughput sequencing, amplifying the final products, and preparing a sample library. Then, we explain how to align the obtained sequencing reads to microRNA hairpins, and quantify, normalize, and calculate their differential expression. Versatile and robust, this combined experimental workflow and bioinformatic analysis enables users to begin with tissue extraction and finish with microRNA quantification.

Schematic of steps involved in library preparation 
An overall schematic of small RNA extraction, sequencing, and alignment is outlined in Figure 2. 
Liver samples from one male and one female mouse were collected and snap frozen in liquid nitrogen. Total RNA was extracted and evaluated for quality and concentration.
Small RNA sequencing yields sufficient RNA for s...

Watch this Scientific Journal Video about A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools at JoVE.com

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools

Here, we describe a step-by-step strategy for isolating small RNAs, enriching for microRNAs, and preparing samples for high-throughput sequencing. We then describe how to process sequence reads and align them to microRNAs, using open source tools.

Half of all human transcripts are thought to be regulated by microRNAs. Therefore, quantifying microRNA expression can reveal underlying mechanisms in ...

We have developed a defined, reproducible, and longstanding protocol for small RNA sequencing and for analyzing normalized reads using opensource bioinformatics tools. The main advantages of our strategy are that it accurately collects microRNAs through gel purification and that the bioinformatics analysis can be applied regardless of how the microRNAs are collected. High throughput sequencing of microRNAs can reveal insight into disease mechanisms, the processing of microRNAs, and the accurate quantification of gene therapy approaches that deliver small RNAs.Make sure to work in a RNase free environment and to keep all of the RNA products on ice throughout the procedure. Visualizing the gel cutting steps will help viewers to identify the correct size of the products required for downstream applications. For three prime adaptor ligation, combine 11 microliters of RNA with 1.5 microliters of ATP free 10X T4RNA ligase reaction buffer, one microliter of polyethylene glycol, and 0.5 microliters of three prime linker.Heat the samples at 95 degrees Celsius on a thermocycler for 30 to 40 seconds, followed by cooling on ice for one minute. Add one microliter of T4RNA ligase two and incubate the reaction at room temperature for two hours. While the samples are incubating, pour a 15%polyacyrilamide gel between 0.8 millimeter separated glass plates in a plastic cast and insert a comb.When the gel has solidified, add 0.5 5X TBE to the tank and pipette vigorously to wash the wells of residual urea. After pre-running the polyacrylamide gel for 25 minutes at 375 volts, load the samples leaving at least one lane in between each sample. Load 20 microliters of at least two sets of markers in an asymmetrical pattern to keep track of the gel orientation and run the gel at a constant 375 volts.After 15 minutes, increase to a constant 425 volts for the rest of the run and run the gel for about two hours. At the end of the run, use a plate separator to remove the gel from the glass plates and place the gel on a plastic page protector. Dilute five microliters of ethidium bromide in 500 microliters of distilled water and add the dye onto the marker lanes just above the top light blue marker.Next, use a clean razor blade to cut the gels from the upper to lower marker in each lane under ultraviolet light and transfer the pieces to a four by four centimeter square of laboratory sealing film. Cut the gel with about three cuts horizontally and two cuts vertically to produce 12 small squares. Add 400 microliters of 0.3 molar sodium chloride onto the sealing film and guide the gel pieces into 1.5 milliliter siliconized tubes.Agitate the samples on a nutator at four degrees Celsius overnight. The next morning, transfer 400 microliters of each supernatant into new tubes. Add one milliliter of 100%ethanol and one microliter of 15 milligrams per milliliter glycogen co-precipitant per tube.Then store the tubes at minus 80 degrees Celsius for one hour. For five prime linker ligation, first spin down the thawed samples and resuspend the pellets in water. Next, add 0.5 microliters of 100 micromolar five prime linker, one microliter of T4RNA ligase buffer, one microliter of 10 millimolar ATP, and one microliter of polyethylene glycol to each sample.Heat the reactions at 90 degrees Celsius for 30 seconds before placing them on ice. Then add one microliter of T4RNA ligase one to each tube and incubate the reactions at room temperature for two hours. For reverse transcription, collect the samples by centrifugation and resuspend the air dried pellet in 8.25 microliters of nuclease free water.Add 0.5 microliters of 100 micromolar reverse transcriptase primer and five microliters of 2X reverse transcriptase reaction mix from a complementary DNA synthesis kit. After three minutes at 42 degrees Celsius, add 1.5 microliters of 10X reverse transcriptase enzyme to each sample for a 30 minute incubation at 42 degrees Celsius in a thermocycler. After neutralization, prepare a PCR reaction with 29.5 microliters of water, five microliters of 10X taq buffer, one microliter of nucleoside triphosphate, two microliters of 25 micromolar forward primer, two microliters of 25 micromolar reverse primer, 0.5 microliters of taq polymerase, and 10 microliters of the reverse transcribed complementary DNA.Then run two PCR reactions. For agarose gel purification, prepare a 4%agarose gel with low melting agarose and load 40 microliters or more of the PCR product onto the gel with loading dye and 100 base pair and 25 base pair size markers. After running the gel, cut the band above the 125 base pair band and use a gel extraction kit according to the manufacturer's instructions.Shake to dissolve the gel band in buffer at room temperature before using the appropriate equipment to quantify the final sequence library. Then use the appropriate opensource bioinformatics tools to analyze the sequence data. In this representative PCR reaction on low melt agarose gel, the acquisition of the correct cloned product compared to the obtained linker linker product and unsaturated versus saturated samples can be observed.After alignment to human microRNA hairpins, a strong concordance between the microRNA read counts in each replicate can be observed. A total of 306 microRNA species were detected with the greatest number of reads mapping to microRNA 122. It is important to remember to cut the gels at the appropriate size to enable an accurate recovery of the microRNAs.After sequencing the microRNAs, users can apply a bioinformatics analysis to characterize the distribution of microRNAs within their tissues of interest. This technique has been used to identify how microRNAs are processed and which sets of microRNAs are altered in certain cancers. Be sure to exercise care when handling the ethidium bromide and when looking at the gels under ultraviolet light.

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Cell Biology

Genetics

Unit 1

Control of Gene Expression

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