Sacks:RAD-seq

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Contents

Overview

This is a protocol for generating RAD libraries for Illumina sequencing. With this technique, 96 samples can be multiplexed into one sequencing library, and only tags adjacent to PstI sites are sequenced. This is a cheap way to both mine and genotype large numbers of SNPs. This is the protocol developed in Erik Sacks' lab at UIUC by Lindsay Clark, based on protocols from Pat Brown and Megan Hall.

Materials

Reagents

  • Quant-iT Picogreen kit (Invitrogen)
  • Qiagen gel purification kit
  • Qiagen PCR cleanup kit
  • From New England Biolabs:
    • PstI-HF, 20,000 U/mL
    • MspI, 20,000 U/mL
    • T4 DNA ligase, 2,000,000 U/mL
    • ATP
    • Phusion High Fidelity PCR master mix

Note: MspI is not a heat-inactivated enzyme, but I have found that the protocol works anyway. Between the ligation and gel extraction steps, I keep the sample on ice to prevent any residual digestion activity.

  • You will also need a black microtiter plate for the Picogreen assay.

Oligonucleotides

PstI adapters

This is the most expensive part of the protocol other than the sequencing itself, since 192 oligonucleotides must be ordered.

Adapter 1 top: 5'GATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTxxxxTGCA3'

Adapter 1 bottom: 5'yyyyAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATC3'

Where xxxx and yyyy are the barcode and its reverse complement, respectively.

Barcodes and oligo sequences are from Pat Brown's lab.

Media:PstI-barcodes.txt

Other oligos

MspI adapters:

  • A2top: 5'CGCTCAGGCATCACTCGATTCCTCCGAGAACAA3'
  • A2bot: 5'CAAGCAGAAGACGGCATACGACGGAGGAATCGAGTGATGCCTGAG3'

Illumina PCR primers:

  • PCR1: 5'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT3'
  • PCR2: 5'CAAGCAGAAGACGGCATACGA3'

Equipment

  • Nanodrop spectrophotometer
  • BioTek Synergy plate reader (for reading fluorescence)
  • Ordinary PCR machine
  • Agarose gel rig
  • Bioanalyzer
  • real-time PCR machine (we just pay the core facility to do that part)

Procedure

Adapter prep

Top and bottom strands of adapters need to be annealed 1X Annealing Buffer, which is 10 mM Tris, 50 mM NaCl.

The annealing program is:

  • 95°C 5 minutes
  • Ramp down -0.1°C every 2 seconds (or -1°C every 20 seconds) to 25°C.

My protocol:

  • Pat Brown provided us with a plate of PstI adapters that are at 1 μM. I took a bottle of autoclaved 1X Annealing Buffer, added 45 μl to each well of a 96-well plate, then transferred 5 μl from the 1 μM plate to make a 0.1 μM working stock.
  • MspI adapters are ordered like normal oligos, and I have 100 μM concentrated stocks in TE. To make a 10 μM stock:
    • 20 μl A2top, 100 μM
    • 20 μl A2bot, 100 μM
    • 20 μl 500 mM NaCl
    • 2 μl 1M Tris
    • 138 μl nuclease-free water
    • Mix well, add 100 μl to each of two PCR tubes, and run them on the annealing program ("Adapt" on the PCR machine).

DNA quantification and dilution

Nanodrop first:

  1. Quantify your DNA using the Nanodrop spectrophotometer.
  2. If the DNA concentration is greater than 200 ng/ul, dilute to 200 ng/ul. I find it useful to set up these dilutions on a 96-well plate. If the DNA is between 50 and 200 ng/ul, just put an aliquot directly on your dilution plate. If it is less than 50 ng/ul, you need to redo the extraction or find a way to concentrate the DNA.

Quantify your ≤200 ng/ul dilution plate using Picogreen:

  1. Take the tube of bright orange Picogreen reagent out ahead of time to thaw. Wrap it in aluminum foil to protect it from light. It is in DMSO instead of water, so it takes a long time to thaw and will immediately freeze solid if you put it on ice.
  2. The Quant-iT Picogreen kit comes with a lambda DNA standard at 100 ug/ml. Dilute some of the 20X TE that comes with the kit to 1X TE, and use it to make a 2 ug/ml dilution of the lambda DNA. (1:50 dilution.)
  3. For one plate (88 samples, 8 standards) make up 20 mL of 1X TE. (1 mL of the TE that comes with the kit, plus 19 mL sterilized filtered water.)
  4. The plate you need for the assay is a black, flat-well plastic plate. (Corning makes these.)
  5. Set up a standard curve in column 1 (or column 12, doesn’t matter). Pipette 100 ul of TE into wells B-H. Add 100 ul of your 2 ug/ml lambda standard each to well A and B. Pipette well B up and down to mix, then transfer 100 ul to well C. Pipette well C up and down to mix, then transfer 100 ul to well D. Continue through well G, and leave well H as a blank. (After mixing well G, you will simply throw out 100 ul.)
  6. Add 99 ul TE to the other 88 (or however many samples you are doing) wells . Add 1 ul of ≤200 ng/ul sample DNA to each well.
  7. Add 50 ul of Quant-iT reagent to 10 mL of 1X TE. This solution needs to be used within a few hours, even if it is protected from light. Add 100 ul of the solution to each well (both sample, standard, and blank).
  8. Picogreen bonded to dsDNA has an excitation maximum at 480 nm and emission maximum at 520 nm. The plate readers in IGB (BioTek Synergy HT) probably already have a picogreen program on them.
  9. Read fluorescence intensity on the plate reader, and export it to Microsoft Excel.
  10. Make a scatterplot of fluorescence intensity of the standard vs. the standard concentration. Given that the samples were diluted 200X, the standard concentration is multiplied by 200:
    1. Well A 200 ng/ul
    2. Well B 100
    3. Well C 50
    4. Well D 25
    5. Well E 12.5
    6. Well F 6.25
    7. Well G 3.125
    8. Well H 0
  11. In Excel, fit a trendline to the scatterplot and display the equation on the chart. Use this equation to estimate the concentration of the samples.

Image:lvc_picogreen.jpg

In most cases, the concentration estimate via Picogreen should be lower than the concentration estimate via Nanodrop. This is because Nanodrop measures DNA + RNA, whereas Picogreen only measures DNA. Why didn’t we just use Picogreen to begin with? Because it can measure a much narrower range of concentrations than Nanodrop can. If the standard curve were any more concentrated, it would not be linear.

Based on the Picogreen concentration estimates, dilute the DNA to 50 ng/μL in 10 mM Tris (and 0.1 mM EDTA, optional).

Restriction digestion and ligation

Cleanup and amplification

Quality control

Bioinformatics

Notes

Please feel free to post comments, questions, or improvements to this protocol. Happy to have your input!

  1. List troubleshooting tips here.
  2. You can also link to FAQs/tips provided by other sources such as the manufacturer or other websites.
  3. Anecdotal observations that might be of use to others can also be posted here.

Please sign your name to your note by adding '''*~~~~''': to the beginning of your tip.

References

  • Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, and Mitchell SE (2011) "A robust, simple Genotyping-by-Sequencing (GBS) approach for high diversity species." PLoS One 6(5): e19379. doi:10.1371/journal.pone.0019379

Contact

  • Who has experience with this protocol?

or instead, discuss this protocol.

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