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- Documentation
- A few important comments before you start
- Purify and Fragment mRNA
- Step 1: Capture mRNA
- Step 2: Clean Up and Fragment mRNA
- Generate cDNA
- Step 3: First strand cDNA synthesis
- Step 4: Second strand cDNA synthesis
- Step 5: cDNA clean-up
- Prepare and Amplify Libraries
- Step 6: Adenylate cDNA ends
- Step 7: Ligate Anchors
- Step 8: Clean Up Adapter-Ligated Fragments
- Step 9: Index and Amplify library
- Step 10: Clean Up Library
- Quality Checks
- Sequencing Guidelines
- Normalize and Pool
Documentation
Illumina's Stranded mRNA Sample Prep Guide. This method makes a cDNA library of the polyadenylated mRNA in your eukaryotic samples of interest. It requires high quality RNA with intact polyA tails. This is the updated version of Illumina’s TruSeq protocol.
A few important comments before you start
- The recommended starting amount of total RNA is 25-1000 ng, but we usually try to stay away from the extreme ends of this spectrum and use 100 ng input.
- This protocol can be performed in one day, or split into two or more days at the indicated safe stopping points.
- For 12 samples, you will need approximately 7 hours if completing the protocol in one day. This estimate is based on an experienced user with a multichannel pipette and vortexing at bead cleanup steps. An inexperienced user or one not using time-saving techniques should plan for more time.
- Do NOT put any reagents stored at 4C, especially beads, on ice.
- Have all beads at room temperature at least 30 minutes prior to use.
- Aliquot the reagents that arrive in large quantities (such as the resuspension buffer and the bead washing buffer) into 2 mL Eppendorf tubes.
- Use only filter pipette tips and clean your area so it is free of RNases.
- Ensure that the AMPureXP beads are mixed well immediately prior to use.
- There are many mixing steps in this protocol - we frequently use a multi-channel pipette to help speed up this process, particularly if many libraries are being prepared. Samples can also be mixed by sealing the plate and vortexing, as described in the Sample Prep Guide, linked above.
- We use a TapeStation to assay the input RNA quality. RNA Integrity Numbers (RIN) of 7 and higher are preferred.
- We quantify the input RNA using a Qubit fluorometer.
Purify and Fragment mRNA
The following items are included in the Illumina kit. We recommend kits be stored as received in the original manufacturer’s boxes and not unpacked to organize in a reagent box. When kits go bad, it is much easier to contain the damage if reagents were stored as received.
This kit has 1 box of reagents in the 4C fridge and 2 boxes of reagents in the -20C freezer, each labeled with a green dot saying "mRNA Ligation". Make sure you are using the correct boxes and return all reagents to the box they came from. Do not mix reagents with other boxes.
NAME | LOCATION | ACTION |
|---|---|---|
Bead Binding Buffer (BBB) | 4°C Fridge | Vortex briefly, leave at RT |
Bead Washing Buffer (BWB) | 4°C Fridge | Vortex briefly, leave at RT |
Elution Buffer (EB) | 4°C Fridge | Vortex briefly, leave at RT |
RNA Purification Beads (RPBX) | 4°C Fridge | Let stand at RT for 30 minutes to bring to RT, vortex and invert thoroughly before use |
Elute, Prime, Fragment High Mix (EPH3) | -20°C Freezer (cDNA synthesis box, gray sticker) | Thaw at RT, vortex briefly |
First Strand Synthesis Act D mix (FSA) | -20°C Freezer (cDNA synthesis box, brown tube) | Thaw and keep on ice, vortex briefly before use |
NAME | LOCATION | ACTION | VOLUME |
|---|---|---|---|
Ampure XP Beads/Homemade XP Beads | 4°C Fridge | Let stand at RT for 30 minutes to bring to RT, vortex and invert thoroughly before use | 174 uL per sample for entire prep |
Fresh 80% Ethanol (200 proof EtOH + MilliQ water) | RT Bench | Mix fresh each day. Low % EtOH negatively affects cleanups. | 1.2 mL per sample for entire prep |
RNAse Free RT-PCR Grade Water | -20°C Freezer | Thaw at RT | As needed for diluting RNA input |
Post-Style Magnetic Stand for 96 well plates | RT Bench |
Step 1: Capture mRNA
Dilute 25-1000 ng (we typically do 100 ng) total RNA in RT-PCR grade water to a total volume of 25 uL. Normalize inputs across all samples. Different inputs can be used, but samples may require different reagent volumes and cycle numbers in later steps based on input. Do this in a 96-well PCR plate (if only prepping a few samples, the plate can be cut).
Add 25 uL well-mixed RPBX to each well. Gently pipette up and down 10 times. Seal the plate with an adhesive seal.
Do not store RNA purification beads on ice! We have observed that the beads are very sensitive to cold temperatures. Beads stored at < 2°C may deteriorate, resulting in poor binding of mRNA, and therefore poor library prep that is heavily contaminated with excess adapter.
Place the sealed plate in the thermal cycler. Go to "CHMI —> STRANDED LIG" and run the "MRNA CAP" program (65°C for 5 min, 4°C for 30 sec, 23°C for 5 min, 23°C hold).
Return RNA samples to -80°C storage.
Remove the plate, keep it sealed, and centrifuge at 280 x g for 10 sec.
Place on the magnetic stand for 2 min.
Discard 45 µL supernatant from each well of the plate.
Remove the plate from the magnetic stand and add 100 uL BWB to each well. Pipette 10 times to mix.
Place the plate on the magnetic stand for 2 min.
Remove and discard 98 µL supernatant from each well.
Use a p20 pipette to remove residual BWB.
Remove the plate from the magnet stand and add 25 uL ELB.
Slowly pipette to completely resuspend beads.
Seal and centrifuge at 280 x g for 10 sec.
Place the plate in the thermal cycler. Run the program “MRNA ELT” (80°C for 2 min, 25°C hold, lid at 100°C).
Remove the plate when the thermal cycler reaches 25°C. Centrifuge the sealed plate at 280 x g for 10 sec.
Step 2: Clean Up and Fragment mRNA
On ice, in a microcentrifuge tube, prepare Fragmentation Master Mix with the following volumes per sample (overage already included):
Add 25 µL BBB to each well. Pipette 10 times to mix.
Incubate at room temperature for 5 minutes.
Place on the magnetic stand and wait 2 minutes.
Remove and discard 50 uL supernatant from each well.
Remove the plate from the magnetic stand and add 100 uL BWB to each well. Pipette 10 times to mix, fully resuspending the beads.
Place on the magnetic stand and wait 2 minutes.
Remove and discard 99 µL supernatant. With a p20 pipette, remove and discard any residual supernatant.
Remove from the magnetic stand.
Pipette Fragmentation Master Mix to mix, then add 19 uL to each well, slowing pipetting to mix until beads are fully resuspended.
Incubate at room temperature for 2 minutes.
Centrifuge at 280 x g for 10 seconds. Place on thermal cycler and run the "DEN94 8" program (94°C for 8min, 4°C hold).
Remove the plate once it reaches 4°C and centrifuge at 280 x g for 10 seconds
Remove the adhesive seal and place the plate on a magnetic stand at room temperature for 2 min.
Remove 17 uL supernatant from each well into corresponding wells in a new plate. This contains your purified mRNA.
Generate cDNA
Step 3: First strand cDNA synthesis
NAME | LOCATION | ACTION |
|---|---|---|
Ampure XP Beads/Homemade Beads | 4°C Fridge | Let stand at RT for 30 minutes to bring to RT, vortex and invert thoroughly before use |
Resuspension Buffer (RSB) | -20°C Freezer (cDNA synthesis box) | Thaw at RT, vortex briefly |
Reverse Transcriptase (RVT) | -20°C Freezer (cDNA synthesis box) | Store until needed. Flick to mix, centrifuge briefly |
Second Strand Marking Mix (SMM) | -20°C Freezer (cDNA synthesis box) | Thaw on ice, invert to mix, centrifuge briefly |
In a microcentrifuge tube on ice, prepare First Strand Synthesis Master Mix with the following volumes per sample (overage already included):
NAME | VOLUME (uL) |
|---|---|
First Strand Synthesis Act D mix (FSA) | 9 |
Reverse Transcriptase (RVT) | 1 |
Pipette First Strand Synthesis Master Mix to mix.
Centrifuge the First Strand Master Mix briefly. Add 8 uL First Strand Synthesis Master Mix to each well and pipette 10 times to mix.
Seal the plate and place in the thermocycler and run the “FSS” program (25°C for 10 min, 42°C for 15 min, 70°C for 15 min, hold at 4°C). Return RVT to the -20°C freezer immediately after use.
This step takes about 40 minutes and is your first large break.
Step 4: Second strand cDNA synthesis
When the first strand synthesis is completed, immediately proceed to the second strand synthesis.
Centrifuge the sealed plate at 280 x g for 10 seconds. Add 25 uL SMM to each well, being careful about bubbles. Pipette up and down 10 times.
Seal plate, centrifuge if needed, place plate in thermocycler and run the "SSS" program (16°C for 1 hr).
Make sure you have Ampure XP or homemade beads at room temp and fresh 80% ethanol for the next steps.
This step takes about 1 hour and is your second large break of the day.
Step 5: cDNA clean-up
When the reaction is complete, add 90 ul of well-mixed AMPure XP or homemade beads to each well containing cDNA and pipette to mix (or seal plate and vortex for 1 min. Check that the beads are not stuck to the sides of the wells. You may need to spin down the plate and vortex again). Incubate RT for 5 min.
During this time, make fresh 80% ethanol.
Place the plate on the magnet and let sit for 5 min.
Remove and discard 130 ul supernatant per well, being careful not to disturb the beads.
Wash beads on the magnet by adding 175 ul of 80% EtOH to each well, without disturbing the beads incubate 30 sec at RT.
Remove and discard the supernatant, repeat the wash step and remove the supernatant again.
Remove any residual supernatant with a p20 pipette. Let the plate stand on the magnet at RT for 2 minutes.
Remove from the magnet and add 19.5 ul of RSB to each well and pipette to fully resuspend the beads. Incubate for 2 min at RT.
Centrifuge at 280 x g for 10 seconds.
Place the plate on the magnetic stand for 2 minutes.
Transfer 17.5 ul of the supernatant (contains the ds cDNA) to a new plate.
This is a safe stopping point. You can seal the plate and store at -20°C for up to 7 days.
Prepare and Amplify Libraries
Step 6: Adenylate cDNA ends
NAME | LOCATION | ACTION |
|---|---|---|
Anchor Plate | -20°C Freezer | Thaw at RT, vortex, centrifuge briefly |
Index Adapter Plate | -20°C Freezer | Thaw at RT, vortex, centrifuge for 1 minute |
A-Tailing Mix (ATL4) | -20°C Freezer (Ligation box) | Thaw at RT, flick to mix, centrifuge briefly |
Stop Ligation Buffer (STL) | -20°C Freezer (Ligation box, red cap) | Thaw at RT, vortex, centrifuge briefly |
Ampure XP Beads/Homemade beads | 4°C Fridge | Let stand at RT for 30 minutes to bring to RT, vortex and invert thoroughly before use |
Resuspension Buffer (RSB) | -20°C Freezer (Ligation box) | Thaw at RT, vortex briefly |
Enhanced PCR Mix (EPM) | -20°C Freezer (Ligation box) | Thaw at RT, invert to mix, centrifuge briefly |
Ligation Mix (LIGX) | -20°C Freezer (Ligation box) | Store until needed, flick to mix, centrifuge briefly |
Add 12.5 ul of thawed A-tailing mix to each well. Using a p200 pipette set to 30 µL, pipette up and down 10 times.
Seal and put on the thermocycler for the "ATAIL" program (37°C for 30 min, 70°C for 5 min, 4°C hold).
This step takes about 35 minutes and is another break.
Step 7: Ligate Anchors
Each well of the anchor plate is single-use and contains the same RNA Index Anchors. They can be used in any order. Seal the used anchor wells with foil and label them before returning to freezer storage.
Order of Addition | Reagent | Vol for Sample Input < or = 100ng | Vol for Sample Input > 100ng |
|---|---|---|---|
1 | RSB | 2.5 uL | 0 uL |
2 | RNA Index Anchors | 2.5 uL | 5 uL |
3 | LIGX | 2.5 uL | 2.5 uL |
With a p200 pipette set to 35 µL, pipette to mix 10 times.
Seal and run on the thermocycler under the "LIG" program (30°C for 10 min, 4°C hold).
Return the LIGX to the -20°C freezer.
Briefly centrifuge plate. Immediately add 5 uL STL to each well, pipetting to mix 15 times.
Step 8: Clean Up Adapter-Ligated Fragments
Add 34 ul of AMPure XP or homemade beads to each reaction, mix well by pipetting, and incubate at RT for 15 min.
Place on the magnetic stand for 5 min at RT.
Spin down the index adaptors.
With the plate on the magnetic stand, remove 67 ul of supernatant from each sample, being careful not to disturb the beads.
With the plate on the magnetic stand, wash with 175 ul 80% EtOH for 30 sec, then remove the ethanol.
Perform the wash step again.
Use a p20 pipette to remove residual ethanol. Keep the plate on the magnet at RT for 2 minutes to dry.
Remove the plate from the magnetic stand, add 22 ul of Resuspension Buffer to each well, and mix well by pipetting to fully resuspend beads.
Incubate at RT for 2 minutes.
Centrifuge at 280 x g for 10 seconds.
Place the plate on the magnet for 5 min.
Keeping the plate on the magnet, recover 20 ul from each well and transfer to a new plate.
This is a safe stopping point. You can seal the plate and store at -20°C for up to 7 days.
Step 9: Index and Amplify library
Add 10 uL index adapter to each well.
Indexes come in a 96-well plate, each well containing a unique set of dual indexes. Although they are unique, certain patterns of index use are recommended to balance color channels during sequencing. See Illumina's Index Adapters Pooling Guide. Generally, moving in columns is fine. Seal the used wells with foil and label them before returning to freezer storage. Record which index plate (Set A or B) and which index well was used for each sample, as this is needed to demultiplex after sequencing.
Add 20 uL EPM. Pipette 10 times to mix.
Seal and place on thermocycler and run the "PCR" program, with cycle repeats according to the table below.
This is a 30-45 minute break, depending on cycle number
Step 10: Clean Up Library
Add 50 ul of AMPure or homemade beads to each well and mix well by pipetting. Incubate 15 min at RT.
Place on the magnet and incubate for 5 minutes.
Remove and discard 90 ul of supernatant from each well.
Wash the beads with 175 ul 80% EtOH, wait 30s, and remove the supernatant.
Repeat the ethanol wash step.
Use a p20 pipette to remove residual ethanol.
Keep the plate on the magnet at RT for 2 minutes to dry.
Remove the plate from the magnetic stand, add 17 ul of resuspension buffer and mix well by pipetting.
Incubate for 2 min at room temperature.
Place the plate back on the magnetic stand for 5 minutes.
Very slowly, remove 15 uL of supernatant from each sample and move it into a new plate. This is the final cDNA product.
Congratulations! You’re done!
Quality Checks
Perform quality control steps :
HS D1000 TapeStation to determine the library size.
HS RNA Qubit to quantify the libraries.
Libraries can be stored at -20°C for up to 30 days.
Sequencing Guidelines
Normalize and Pool
Quantify each of your libraries on Qubit. For most libraries, using the HS dsDNA Qubit assay with 2 uL of input will yield a reading. Record the concentration in ng/uL for each library.
Run your samples on TapeStation with either the D1000 or the HS D1000 assay. Remember to allow TapeStation reagents to sit at room temperature for at least 30 minutes before use. Save your TapeStation results by going to File -> Create Report -> Save as pdf. This file can then be emailed or uploaded to Asana. Calculate the average fragment size by using the Region settings. This is a more accurate way to size your library than the peak fragment size, which is listed by default.
Download our nM Conversion Calculator here. Enter the concentration (from Qubit) and the average base pair length (from TapeStation) in the appropriate cells and it will give you the nM concentration for each library. Normalize and pool all your libraries to 2 nM in a LoBind microcentrifuge tube. If you need to dilute your libraries, we recommend using at least 2 uL to minimize pipetting errors. The example sheet of the calculator provides further detail.
Quantify your pool on the TapeStation and Qubit and enter into the calculator sheet to check that your pool is close to the nM concentration you normalized to.