Blue:RNA-Seq Experiments:smart-seq2: Difference between revisions
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| align="center" style="background:#f0f0f0;"|'''Input RNA''' | | align="center" style="background:#f0f0f0;"|'''Input RNA''' | ||
| align="center" style="background:#f0f0f0;"|'''ERCC Dilution | | align="center" style="background:#f0f0f0;"|'''ERCC Dilution''' | ||
| align="center" style="background:#f0f0f0;"|'''T30 Primer''' | | align="center" style="background:#f0f0f0;"|'''T30 Primer''' | ||
| align="center" style="background:#f0f0f0;"|'''TSO Primer''' | | align="center" style="background:#f0f0f0;"|'''TSO Primer''' | ||
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| align="center" style="background:#f0f0f0;"|'''Protocol''' | | align="center" style="background:#f0f0f0;"|'''Protocol''' | ||
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|1ng UHRR||1: | |1ng UHRR||1:10e4||Smart2_T30VN||Smart2_TSO||IS PCR Primer||15||Smart-Seq2 | ||
|- | |- | ||
|100pg UHRR||1: | |100pg UHRR||1:10e5||Smart2_T30VN||Smart2_TSO||IS PCR Primer||18||Smart-Seq2 | ||
|- | |- | ||
|10pg UHRR||1: | |10pg UHRR||1:10e6||Smart2_T30VN||Smart2_TSO||IS PCR Primer||21||Smart-Seq2 | ||
|- | |- | ||
|} | |} |
Revision as of 23:08, 26 September 2014
RNA-Seq Library Information
Input RNA | ERCC Dilution | T30 Primer | TSO Primer | PCR Primer | PCR Cycles | Protocol |
1ng UHRR | 1:10e4 | Smart2_T30VN | Smart2_TSO | IS PCR Primer | 15 | Smart-Seq2 |
100pg UHRR | 1:10e5 | Smart2_T30VN | Smart2_TSO | IS PCR Primer | 18 | Smart-Seq2 |
10pg UHRR | 1:10e6 | Smart2_T30VN | Smart2_TSO | IS PCR Primer | 21 | Smart-Seq2 |
Smart-seq 2 Protocol
- RNA
Volume UHRR/ERCC 1ul 10uM T30 1ul dNTP (10mM) 1ul Total 3ul
- Incubate @ 72C 3 min
- Transfer to ice
- Reverse Transcription
Volume 5xRT Buffer 2ul 100mM DTT 0.25ul 100mM MgCl2 0.6ul Betaine (5M) 2ul TSO 1ul dH20 0.4ul RNase Inhibitor (40U/ul) 0.25ul Smarter MMLV (200U/ul) 0.5ul Total 10ul
- Incubate @ 42C 90 min
- Incubate @ 70C 10 min
- PCR (Advantage)
Volume 10x Advantage 2 PCR Buffer 5ul dNTP Mix (10mM) 2ul STRT Primer (10uM) 2ul 50X Advantage 2 Polymerase Mix 2ul H2O 29ul Total 50ul
95C 1 min 95C 15s -> 65C 30s -> 68C 6min 12x 72C, 10min
Smart-seq 2 Protocol with Poly(A) Tailing
- RNA
Volume UHRR 2ng/ul 0.5ul ERCC 1:10E4 0.2ul 5x ePAP Buffer 0.6ul 25mM MnCl2 0.3ul dH2O 0.9ul Total 2.5ul
- Incubate @ 72C 3 min
- Transfer to ice
Volume 1mM ATP or 1:1 ATP/dATP 0.25ul ePAP 2u/ul 0.25ul Total 3ul
- Incubate @ 37C 10 min
Volume 10uM T30 1ul dNTP (10mM) 1ul Total 5ul
- Reverse Transcription
Volume 5xRT Buffer 2ul 100mM DTT 0.25ul 100mM MgCl2 0.3ul Betaine (5M) 2ul RNase Inhibitor (40U/ul) 0.25ul Smarter MMLV (200U/ul) 0.5ul Total 10.3ul
- Incubate @ 42C 90 min
- Beads Purification
- Add 25ul beads per well
- Allow to bind 15 min
- Remove supernatant and wash 2x with 1ml 80% EtOH
- Air Dry until cracking first occurs
- Resuspend beads in TSO reaction:
- TSO
Volume dH2O 3ul 5x RT buffer [MMLV] 2ul 10mM dNTP mix 1ul 100mM DTT 0.25ul 10uM TSO 1ul Betaine (5M) 2ul RNase Inhibitor 0.25ul Smarter MMLV 0.5ul Total 10ul
- Incubate @42C 10min
- Incubate @70C 10min
- PCR (Advantage)
Volume 10x Advantage 2 PCR Buffer 5ul dNTP Mix (10mM) 2ul STRT Primer (10uM) 2ul 50X Advantage 2 Polymerase Mix 2ul H2O 29ul Total 50ul
95C 1 min 95C 15s -> 65C 30s -> 68C 6min 12x 72C, 10min
Results of Amplification
- Run 5ul on gel: