Rui:PCR based protocol
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PCR based protocol (Tang 2009)[edit]
1. Single cell capture by mouth pipetting [up to ~0.1 ul]
- Maintain the integrity of living single cells before lysis (dissociation - transfer - wash - transfer)
- PBS alone will cause tight attachment of cells to dish/micropipette, leading to rupture/loss of cells.
2. Cell lysis
- Mild lysis buffer to ensure efficient lysis (thoroughly and completely lysed) w/o severely interfering with RT efficiency
- Positive control to establish the protocol (total RNA, 10pg, 50pg, 100pg, 500pg)
- Negative control to rule out the contamination from the start
P1 primer Original (48bp): 5' ATATGGATCCGGCGCGCCGTCGACTTTTTTTTTTTTTTTTTTTTTTTT 3' Rui-P1 (72nt) extra-T7promoter-BciVI-poly(dT): 5' AAACGACGGCCAGTGAATTGTAATACGACTCACTATAGGCGC-GTATCC-TTTTTTTTTTTTTTTTTTTTTTTT 3' Rui-P8 (51nt) T7promoter-BciVI-poly(dT): 5' TAATACGACTCACTATAGGG-GTATCC-TTTTTTTTTTTTTTTTTTTTTTTT 3' stock solution: 100 uM working solution for RT: 0.5 uM (1 ul to 199 ul n-f water)
Cell lysis buffer -------------------------------------------------------------- Componet Original [] Volume (ul) Final [] -------------------------------------------------------------- PCR buffer II 10* 0.45 0.9* MgCl2 25 mM 0.27 1.35 mM NP40 10% 0.225 0.45% DTT 0.1 M 0.225 4.5 mM SUPERase-In 20 U/ul 0.045 0.18 U/ul RNase inhibitor 40 U/ul 0.045 0.36 U/ul UP1 primer 0.5 uM 0.125 12.5 nM dNTP mix 2.5 mM each 0.09 0.045 mM each N-F water 2.975 Total 4.45 in 5ul -------------------------------------------------------------- use fresh made lysis buffer
2.1 Seed the cell into the 0.5 ml PCR tube with 4.45 ul lysis buffer 2.2 Centrifuge for 30s at 7,500g at 4C 2.3 Put on ice immediately 2.4 Incubate at 70C for 90s 2.5 Put on ice immediately 2.6 Centrifuge for 30s at 7,500g at 4C 2.7 Put on ice immediately for 1min
3. 1st strand cDNA synthesis
RT reaction mix ---------------------------------------------------------------------------------- Componet Original [] Volume (ul) Final [] ---------------------------------------------------------------------------------- SuperScript III reverse transcriptase 200 U/ul 0.33 12.2 U/ul RNase inhibitor 40 U/ul 0.05 0.4 U/ul T4 gene 32 protein 1-10 U/ul 0.07 0.07 U/ul Total 0.45 ---------------------------------------------------------------------------------- Prepare and maintain on ice before use
3.1 Prepare RT mix and add 0.45 to each tube 3.2 Incubate at 50C for 30min 3.3 Inactivate the reverse transcriptase at 70C for 15min 3.4 Centrifuge tubes for 30s at 7,500g at 4C 3.5 Put on ice immediately for 1min
4. Free primer removal
- Free primer removal followed Tang 2010 [up to 6 ul]
Exonulease I mix ---------------------------------------------------------------------------------- Componet Original [] Volume (ul) Final [] ---------------------------------------------------------------------------------- Exonuclease I buffer 10* 0.1 1* N-f Water 0.8 Exonuclease 5 U/ul 0.1 0.5 U/ul Total 1 ---------------------------------------------------------------------------------- Prepare and maintain on ice before use
- Free primer removal based on experimental evaluation on ExoI efficiency
Exonulease I mix ---------------------------------------------------------------------------------- Componet Original [] Volume (ul) Final [] ---------------------------------------------------------------------------------- N-f Water 0-fill up to 1 Exonuclease I (USB) 10 U/ul 0.2-0.5 2-5 U ----------------------------------------------------------------------------------
- Free primer removal based on ABi RiboAmp HS kit
Exonulease mix ---------------------------------------------------------------------------------- Componet Original [] Volume (ul) Final [] ---------------------------------------------------------------------------------- Exonuclease VIII Exonuclease I (USB) 10 U/ul 0.2-0.5 2-5 U ----------------------------------------------------------------------------------
4.1 Prepare Exonulease I mix and add 1 ul to each tube 4.2 Incubate at 37C for 30min 4.3 Inactivate the reaction at 80C for 25min 4.4 Centrifuge the tube for 30sec at 7,500g at 4C 4.5 Put on ice immediately for 1min
5. 3' poly(A) tailing
TdT reaction mix -------------------------------------------------------------- Componet Original [] Volume (ul) Final [] -------------------------------------------------------------- PCR buffer II 10* 0.6 1* MgCl2 25 mM 0.36 1.5 mM dATP 100 mM 0.18 3 mM RNase H 2 U/ul 0.3 0.1 U/ul TdT 15 U/ul 0.3 0.75 U/ul N-F water 4.26 Total 6 --------------------------------------------------------------
5.1 Prepare TdT mix and add 6ul to each tube 5.2 Incubate at 37C for 15min 5.3 Inactivate the TdT at 70C for 10min 5.4 Centrifuge for 30s at 7,500g at 4C 5.5 Put on ice immediately for 1 min
6. 2nd strand cDNA synthesis
P2 primer Original (48bp): 5' ATATCTCGAGGGCGCGCCGGATCCTTTTTTTTTTTTTTTTTTTTTTTT Modified (54bp) Anchor-BciVI-AdT: 5' ATATCTCGAGGGCGCGCCGGATCC-GTATCC-TTTTTATTTTTTTTTTTTTTTTTT stock solution: 100 uM
- PCR-based exponential amplification followed Tang 2010
PCR reaction mix with mP2 primer -------------------------------------------------------------- Componet Original [] Volume (ul) Final [] -------------------------------------------------------------- Ex Taq buffer 10* 7.6 1* dNTP mix 2.5 mM 7.6 0.25 mM mP2 primer 100 uM 0.76 1 uM Ex Taq HS 5 U/ul 0.76 0.05 U/ul N-F water 59.28 Total 76 --------------------------------------------------------------
- PCR-based exponential amplification by KAPA SYBR® FAST qPCR Kits
-------------------------------------------------------------- Componet Original [] Volume (ul) Final [] -------------------------------------------------------------- P1/8 primer 100 uM 0.76 1 uM Kapa-mix 2* 44 1* N-F water 31.24 Total 76 --------------------------------------------------------------
6.1 Divide TdT reaction mix into 4 tubes with 3 ul per tube 6.2 Prepare PCR mix and add 19 ul to each tube 6.3 PCR cycle: 95C 3min; 50C 2min; 72C 10min; 1 cycle 6.4 Put on ice for 1min 6.5 Centrifuge tube for 30s at 7,500g at 4C 6.6 Put on ice immediately for 1min
7. PCR Amplification
- PCR-based exponential amplification followed Tang 2010 [up to 41 ul per tube, 4 tubes]
PCR reaction mix with P1 or P8 primer -------------------------------------------------------------- Componet Original [] Volume (ul) Final [] -------------------------------------------------------------- Ex Taq buffer 10* 7.6 1* dNTP mix 2.5 mM 7.6 0.25 mM P1/8 primer 100 uM 0.76 1 uM Ex Taq HS 5 U/ul 0.76 0.05 U/ul N-F water 59.28 Total 76 --------------------------------------------------------------
- PCR-based exponential amplification by KAPA SYBR® FAST qPCR Kits
-------------------------------------------------------------- Componet Original [] Volume (ul) Final [] -------------------------------------------------------------- P1/8 primer 100 uM 0.76 1 uM Kapa-mix 2* 44 1* N-F water 31.24 Total 76 --------------------------------------------------------------
7.1 Prepare PCR mix and add 19 ul to each tube 7.2 PCR cycle: 95C 30s; 67C 1min; 72C 6min (+6s per cycle); 20 cycle; 4C hold 7.3 Centrifuge tube for 30s at 7,500g at 4C 7.4 Store at -80 up to 6 months
8. DNA precipitation, digestion and purification
8.1 Combine the 4 tubes for each sample 8.2 Purify the remaining PCR product by EtOH precipitation and suspend w/ 10 ul EB buffer Add 1/10 V 3M NaOAc, 0.05-1μg/μl glycogen, and 2.5 V EtOH, additional PCR primers to each tube Incubate at -80 for 1hr Centrifuge at 10,000g for 30min Wash w/ ice-cold 70% EtOH 8.3 BciVI digestion set up a digestion reaction around 15~20ul 8.4 USB SAP-IT treatment to remove the primers and de-phosphate ds DNA for half of hour 8.5 Beads purification (0.8*)