Directional-RNAseq Prep

The modifications we adapted are those from Parkhomchuk et al. (Nucl. Acids Res., 2009, doi: 10.1093/nar/gkp596). This was determined by Levin et al. (Nat Methods 2010, 7:709-715) to be one of the most reliable strand-specific sequencing method tested. While our method is optimized for the Illumina TruSeq RNA sample preparation kit, it can likely be used for any library construction method that procedes via polymerase-mediated double-stranded cDNA/second strand synthesis.

Materials required for making Strand-Specific mRNAseq Illumina Libraries via dUTP

• 48 well plate or RNase-free, non-sticky 1.5 mL tubes

• Sera-Mag Oligo(dT)₁₄ beads, Seradyn #2815-2103-010150 (Now from Thermo-Forma; 20 µL per sample)

• Illumina TruSeq RNA Sample preparation kit(catalog RS930-2001, manual 15008136 Rev. A, November 2010)

• Bead Washing Buffer (10mM Tris-HCl PH 7.5, 0.15M LiCl, 1mM EDTA; user supplied, 700 µL per sample)

These steps replace or are added to the Illumina TruSeq RNA Sample preparation guide

---- First Strand Synthesis (page 44) ---

1. Perform First Strand Synthesis (FSS) reaction as directed.

2. When the FSS reaction is complete, precipitate RNA with ethanol and ammonium acetate. Per 50 ul FSS reaction, mix:

    •	5 ul 5M NH4OAc (ammonium is used because it does not precipitate nucleotides).
    •	2 ul GlycoBlue (or similar co-precipitant)
    •	110 ul 100% Ethanol

3. incubate 1 hour to overnight at -80°C

4. centrifuge 30 min x 20,000g, 4°C

5. Remove supernatant; add 200 ul of ice-cold 70% EtOH

6. centrifuge 5 min x 20,000g, 4°C

7. Remove supernatant; air dry 10 minutes.

---- Resuspend pellet in FSS buffer w/o dNTPs or RT (new step) ---

1. Per sample, mix:

• 2 ul10X RT buffer (superscript kit)

• 4 ul 25 mM MgCl2 (superscript kit)

• 2 ul 0.1 M DTT (superscript kit)

• 1 ul random hexamers (superscript kit)

• 49 ul dH2O (superscript kit)

    •	5 ul 5M NH4OAc (ammonium is used because it does not precipitate nucleotides).
    •	2 ul GlycoBlue (or similar co-precipitant)
    •	110 ul 100% Ethanol

2. mix well; add 58 ul to each pellet and resuspend by pipetting gently. The final volume should be 58 ul.

---- Perform Second Strand Synthesis (SSS) with dUTP/dNTP mix (new step) ---

1. Per sample, mix:

• 8 ul of 10X Second Strand buffer mix w/o dNTPs (NEB buffer)

• 10 ul dUTP/dNTP mixture

• 4 ul second strand enzyme mix (NEB)

2. mix well. Pipette 22 ul to each resuspended RNA to give a final volume 80 ul.

3. Incubate 2.5 hours at 16C.

---- Clean the SSS product with AMPure, as directed (page 48) ---

---- Continue protocol as directed through the AMPure cleaning step following adapter ligation (page 48) ---

---- Prior to PCR enrichment, degrade the dUTP in the coding strand (new step) ---

1. Per sample, add 1 ul of USER enzyme mixture.

2. Incubate at 37C for 15 minutes, then place on ice

---- Continue to PCR enrichment step (page 62) ---

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