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

Animal experiments were authorized by the Institutional Animal Care and Use Committee of the University of Washington.

Small RNA library preparation

1. RNA isolation

1. 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.
2. Measure each sample’s RNA integrity on an instrument that can quantify RNA and provide an RNA integrity number (RIN). RINs should be >7.

2. 3' adaptor ligation

1. Prepare a ligation reaction in PCR strip tubes, by combining: 11 μL of RNA (1-3 μg, using the same amount for each sample), 1.5 μL of 10x T4 RNA ligase reaction buffer, ATP-free, 1 μL of poly-ethylene glycol (PEG), and 0.5 μL of 3'-linker (100 μM Universal miRNA cloning linker).
   NOTE: The absence of ATP helps enrich for miRNAs and minimizes cloning of mRNA degradation products. PEG acts as a molecular crowding agent, enhancing successful ligation. The Universal miRNA cloning linker has a 3' blocking group (amine) to prevent self-ligation, circularization, and ligation to RNA at the 5' end.
2. Heat the samples at 95 °C on a thermocycler for 30-40 s. Cool on ice for 1 min. Add 1 μL of T4 RNA ligase 2 and incubate at room temperature for 2 h. Prepare the gel (step 2.3) while the samples are incubating.
   NOTE: Incubation at room temperature helps prevent linker-linker ligation. We have also successfully used T4 RNA ligase 1.
3. Prepare 30 mL of a 15% polyacrylamide gel with 8 M urea (for a 20×20 cm gel): 14.4 g of urea, 3 mL of 10x Tris-buffered ethylenediaminetetraacetic acid (TBE), 11.2 mL of 40% 19:1 acrylamide, and H₂O to 30 mL. Solution is best dissolved at 42 °C. Immediately before casting, add 150 μL of 10% ammonium persulfate (APS) and 30 μL of tetramethylethylenediamine (TEMED) for polymerization.
4. Pour between 0.8 mm separated glass plates in a plastic cast and insert comb. Once the gel is solidified (about 20 min), add 0.5x TBE to tank and wash wells of residual urea by pipetting vigorously.
5. Pre-run the gel at a constant 375 V for 25 min without samples so urea can enter the gel, then wash the wells again.
   NOTE: The amount of voltage may need to be reduced depending on the type of power supply and electrophoresis system that is used.
6. Once the samples are done ligating, add 15 μL of acrylamide loading dye to the samples (for a 1:1 ratio), then denature for 5 min at 95 °C on a thermocycler.
7. Prepare 25 ng/μL of 37 and 44 bp size markers, diluted with one part acrylamide loading dye. Sequences are listed in Table 1.
8. Load the samples on the polyacrylamide gel, leaving at least one lane in between each sample. Load 20 μL of at least two sets of markers, in an asymmetrical pattern to keep track of gel orientation.
9. Run the gel at a constant 375 V for the first 15 min and then increase to a constant 425 V for the remaining run. Run until bromophenol blue is about 1-4 cm from the bottom, which takes approximately 2 h.
   NOTE: If necessary, the gel may be run at a lower constant voltage for a longer period of time until the bromophenol blue is about 1-4 cm from the bottom.
10. Remove the gel from the glass plates using a plate separator, and place the gel on a plastic page protector. Dilute 5 μL of ethidium bromide in 500 μL of distilled water, and pipette onto marker lanes just above the top light blue marker (see Figure 1A).
    CAUTION: Use gloves for ethidium bromide and dispose of waste in accordance with local regulations. Let sit for 5 min.
11. Under ultraviolet (UV) light, cut the gels from upper to lower marker in each lane using clean razor blade (see Figure 1A). Transfer to a 4 x 4 cm square of laboratory sealing film, then cut the gel with about 4 cuts horizontally and 3 vertically to produce 12 small squares (see Figure 1B).
12. Pipette 400 μL of 0.3 M NaCl on to the sealing film square, and funnel gel pieces into 1.5 mL siliconized tubes (see Figure 1C). Agitate the samples on a nutator at 4 °C overnight.
    NOTE: Other low-retention 1.5 mL tubes can be substituted for siliconized tubes.
13. After at least 12 h of agitation at 4 °C, retrieve the samples and put them on ice, along with a conical tube of 100% ethanol.
14. Transfer 400 μL of supernatant to a new tube, and then add 1 mL of 100% ethanol and 1 μL of 15 mg/mL glycogen coprecipitant. Ensure to collect as much supernatant as possible, spinning down at 4 °C and pipetting more as necessary. Place at -80 °C for 1 h, or -20 °C for 2 h or longer. Glycogen coprecipitant improves pellet visibility and recovery.
15. Spin at 4 °C at 17,000 x g for 20-30 min. Remove all traces of ethanol and let pellet air dry for 5 min.

3. 5' linker ligation

1. Re-suspend the pellet by pipetting in 6.5 μL of nuclease-free water. Letting the pellet sit in water for a few minutes first will help with re-suspension.
2. After spinning down the pellet and resuspending in water, add 0.5 μL of 100 μM 5'-linker (with barcodes; see Table 1), 1 μL of T4 RNA ligase buffer, 1 μL of 10 mM ATP, and 1 μL of PEG. Heat at 90 °C for 30 s, then place on ice. Add 1 μL of T4 RNA ligase 1 and let incubate at room temperature for 2 h.
3. Add 400 μL of 0.3 M NaCl, followed by 400 μL of acid phenol/chloroform. Vortex 30 s – 1 min (solution will look cloudy), and then spin at 4 °C for 10-15 min at max speed in a microcentrifuge (~17,000 x g). Draw off the top layer and place in new 1.5 mL tube.
   NOTE: Avoid pipetting any of the bottom layer.
4. Add 350 μL of chloroform, vortex briefly, and then spin at 4 °C for 10 min at max speed (~17,000 x g). Draw off the top later and place in new 1.5 mL tube. Add 1.5 μL of glycogen coprecipitant and 1 mL of 100% ethanol.
   NOTE: Again, avoid pipetting any of the bottom layer.
5. Vortex briefly, then place at -80 °C for at least 1 h, or -20 °C overnight.

4. Reverse transcription (RT)

1. Turn on the 42 °C heat block. Spin the samples at 4 °C and ~17,000 x g for 20-30 min. Remove all supernatant and let the pellet air dry for 5 min.
2. Re-suspend pelleted sample in 8.25 μL of nuclease-free water, then add: 0.5 μL of 100 μM RT primer (Table 1), and 5 μL of 2x RT Reaction Mix from a cDNA synthesis kit. Incubate at 42 °C for 3 min.
3. Add 1.5 μL of 10x RT enzyme to each sample and incubate at 42 °C for 30 min in a thermocycler. Place at -20 °C or continue with hydrolysis and neutralization.
   NOTE: Several RT kits can be utilized for steps 4.2 and 4.3.
4. Perform alkaline hydrolysis and neutralization: Make 1 mL of 150 mM potassium hydroxide (KOH) solution (150 μL of 1 M KOH, 20 μL of 1 M Tris Base pH 7.5, and 830 μL of H₂O) and 1 mL of 150 mM hydrochloric acid (HCl) (150 μL of 1 M HCl and 850 μL of H₂O).
5. Before adding to the samples, determine the amount of HCl needed to neutralize the KOH solution. Generally, around 20-24 μL of HCl will neutralize the 25 μL of KOH. Check the combination on a pH strip to ensure it is in the right range (pH 7.0 to 9.5).
6. Hydrolyze the samples by adding 25 μL of 150 mM KOH solution and incubate for 10 min at 95 °C.
7. Neutralize the samples by adding the amount of 150 mM HCl determined in step 4.4, to obtain a final sample pH between 7.0 and 9.5.

5. PCR amplification

1. After neutralization, prepare a PCR reaction with: 29.5 μL of water, 5 μL of 10x Taq buffer, 1 μL of dNTP, 2 μL of 25 μM forward primer (Table 1), 2 μL of 25 μM reverse primer (Table 1), 0.5 μL of Taq, and 10 μL of the reverse transcribed cDNA from step 4.6.
2. Run the following PCR reaction: 94 °C for 2 min, then 20 cycles of 94 °C for 45 s, 50 °C for 75 s and 72 °C for 60 s.
3. Run a second PCR reaction of about 2-4 more cycles using 5 μL of product from step 5.2. Mix: 34.8 μL of water, 5 μL of 10x Taq buffer, 1 μL of dNTP, 1 μL of 25 μM forward primer (Table 1), 1 μL of 25 μM reverse primer (Table 1), and 0.2 μL of Taq polymerase. Follow the same thermocycler parameters outlined in step 5.2.
   NOTE: The purpose of doing two PCR reactions – with the first for 20 cycles and the second for just 2-4 more – is to ensure that the amount of cDNA amplified is in a dynamic range (i.e., not a saturated amount).

6. Agarose gel purification

1. Prepare a 4% agarose gel with low-melting agarose. Load 40 μL or more of the PCR product on the gel, along with loading dye. Load 100 bp and 25 bp size markers.
   NOTE: The 25 bp ladder helps to distinguish amplified product from linker-linker ligation products. Low-melting agarose gels must be cast with greater care than traditional agarose gels, so closely follow the instructions from the manufacturer.
2. For gel extraction, select the cycle number that is visible on the gel but is not saturated (usually 22–24 cycles). Choose similar intensity bands when running multiple samples.
3. Cut the band that is above the 125 bp band (the darker band on 25 bp ladder; see Figure 1D). Using a gel extraction kit, follow the manufacturer’s instructions for adding buffer based on a 4% gel, then shake to dissolve agarose in buffer at room temperature.
   NOTE: Dissolving at 55 °C increases the potential for linker-linker ligation.
4. Follow the manufacturer’s gel extraction instructions and elute in 30 μL of elution buffer or water. If the product looked weak on the gel, then reduce elution to 20 μL.
5. Measure cDNA concentration using a sensitive technique, and prepare sample library for sequencing. Preparation will depend on the type of sequencing used.
   NOTE: Minimum requirements for a sequencing library are typically a 10 μL volume of 10 μM product. If concentrations are too low, pool and ethanol precipitate samples to bring library to the desired concentration.
6. Sequence the samples using available equipment. A common example would be to run samples using a kit for 50 bp single reads, to obtain approximately 15-25 million reads in a FASTQ output format.

Small RNA sequence alignment and bioinformatics

7. Data upload

1. Download FASTQ files generated from each sequencing run. Download a list of microRNA hairpin sequences from miRbase.org^8,9,10.
2. Generate a Galaxy account at www.usegalaxy.org and upload a FASTQ file of sequence reads to this account.
3. Upload a text file of barcode sequences to the Galaxy account, such as barcodes.txt, which is available as a text file (Supplementary Table 1).
4. Upload a FASTA file of microRNA hairpins to the Galaxy account from a database like miRBase.org. Examples of mouse (mousehairpins.fa) or human (humanhairpins.fa) microRNA precursors are provided in Supplementary Table 2 and Supplementary Table 3.

8. Adaptor removal, barcode sort, and trim

1. In the left-hand tab, navigate to Genomic file manipulation > FASTA/FASTQ > Clip adapter sequences.
2. In Input file in FASTA or FASTQ format, enter FASTQ file from the drop-down list. Change Minimum sequence length to 18. Change Source à Enter custom sequence. Enter CTGTAGGC. Keep all other default parameters. Click Execute.
   NOTE: Sequence reads that are shorter than 18 nucleotides are difficult to map uniquely to microRNAs and contain many degradation products.
3. In the left-hand tab, navigate to Genomic file manipulation > FASTA/FASTQ > Barcode Splitter.
   NOTE: Galaxy functions and headers are updated periodically, so the search function may be necessary to find an equivalent tool or its location. Commercial kits using indexed primers are often already sorted by barcode. Therefore, this step and the barcode trim step are not necessary if starting from a commercial kit.
4. For Barcodes to use, point to barcodes.txt. For Library to split, use Clip on data file produced in the previous step. In Number of allowed mismatches, enter 1. Click Execute.
5. Trim the first 4 nucleotides: navigate to Text Manipulations > Trim leading or trailing characters. For Input dataset, click on the folder icon, which is a dataset collection. Select the batch file of samples, which includes the label Barcode splitter on data. In Trim from the beginning up to this position, enter 5. In Is input dataset in FASTQ format? enter Yes. Click Execute. Execution may take several minutes.

9. Alignment of reads to microRNAs

1. In Galaxy, navigate to Genomics Analysis > RNA-Seq > Sailfish transcript quantification¹¹.
2. For the question Select a reference transcriptome from your history or use a built-in index? select Use one from the history. Enter the uploaded file mousehairpins.fa from the drop-down list. In FASTA/Q file, click the folder icon to use a dataset collection and select the file that includes Trim on collection. Click Execute. Execution may take several minutes.
3. In the history tab on the right, click on Sailfish on collection… which is a list with 19 items. Click on each individual file and click the disk icon to save to local computer. Individually downloaded files first need to be uncompressed. They also may need to be re-saved with a .txt extension for the purpose of importing into a spreadsheet.
4. Open each spreadsheet file in and re-name the NumReads column to the treatment condition. Merge the columns together to generate a matrix of microRNAs in the first column and read counts per condition in subsequent columns.
5. To calculate differentially expressed microRNAs for each treatment condition, use the file with raw microRNA read counts as input for programs such as DESeq2¹². DESeq2 is present in Galaxy in the Genomics Analysis > RNA-seq > DESeq2 tab.
6. Convert raw reads to normalized microRNA read counts. Counts are normalized to the library sequence depth of the library through the following calculation: [(raw reads/total microRNA reads) * (1,000,000 – number of microRNAs counted) + 1].
   NOTE: This calculation provides a normalized reads per million (RPM) mapped microRNAs that can be compared across datasets and biological conditions. The output is a tab delimited file. Sailfish provides a tpm output column, though this value is normalized by microRNA hairpin length, which is not necessary in this context.
7. If relevant, repeat alignment with custom input sequences (e.g., a vector) to identify reads that map to delivered constructs, like shRNAs.