03/17/11
- ✓ qRT-PCR: Pc-TF -/+ dox, plate 5, 6
- ✓ RT-PCR: optimize more primers with KAH126-1 +dox cDNA
qRT-PCR
> Plate 5
--> 750 nM Primers (& cDNA dilution)
- mCh1 (1:1000)
- GAPDH 21A (1:1000)
- ACTC1 35A (1:10)
- GRLH2 37C (1:10)
--> Templates, use 2 μL
- KAH126-1, 2/21/10
- KAH126-1 +dox, 2/21/10
- KAH128-8, 2/21/10
- KAH128-8 +dox, 2/21/10
- KAH129-4, 2/21/10
- KAH129-4 +dox, 2/21/10
- FTRx, 7/26/10
- FTRx +dox, 7/26/10
> Plate 6
--> 750 nM Primers (& cDNA dilution)
- NPPA 40A (1:10)
- CDKN2A 7C (1:10)
- MMP12 31B (1:10)
- THPO 33A (1:10)
--> Templates (same), use 2 μL
- KAH126-1, 2/21/10
- KAH126-1 +dox, 2/21/10
- KAH128-8, 2/21/10
- KAH128-8 +dox, 2/21/10
- KAH129-4, 2/21/10
- KAH129-4 +dox, 2/21/10
- FTRx, 7/26/10
- FTRx +dox, 7/26/10
Reagent |
1 rxn |
Primer mix (x25)
|
diluted cDNA |
2.0 |
---
|
SYBR Green mix |
7.5 |
187.5
|
750 nM primers |
3.0 |
75.0
|
dH2O |
2.5 |
62.5
|
|
15.0
|
--> Aliquot 39.0 primer mix into 1st well of each 3x set
--> Add 6.0 (2.0 x3) DNA to 39.0 primer mix
--> Aliquot 15.0 rxn mix to other 2 wells in each 3x set
Bio-Rad CFX96 qPCR (Kirschner lab)
--> Use Bio-Rad 96-well low profile plate MLL-9601 + Microseal "B" film
- 95°C/ 5 min.
- [95°C/ 15 sec, 58°C/ 15 sec, 72°C/ 15 sec] x45
- Melt curve range 58°C -> 95°C/ 0.5°C per step
RT-PCR
> Test new RT-PCR primers on KAH126-1 (36 rxns total)
> Primers:
1-4. CASP10 41A-D (80, 84, 80, 93 bp)
5-8. EOMES 42A-D (101, 106, 102, 120 bp)
9-12. OTX2 43A-D (102, 108, 105, 88 bp)
13-16. PRKACG 44A-D (88, 99, 90, 86 bp)
17-20. SST 45A-D (106, 82, 102, 81 bp)
21-24. ATOH1 46A-D (119, 116, 93, 100 bp)
25-28. HHEX 47A-D (86, 80, 87, 113 bp)
29-32. IL4 48A-D (97, 102, 106, 94 bp)
33-36. SLC6A4 49A-D (84, 86, 80, 83 bp)
> Template:
- KAH126-1 -dox 1:1
Reagent |
1 rxn |
Template mix (37x)
|
cDNA |
0.5 |
18.5
|
10 μM primers |
1.0 |
---
|
2x GoTaq Green |
10.0 |
370.0
|
dH2O |
8.5 |
314.5
|
|
20.0 μL
|
--> 1 template mix: aliquot 19.0 μL
--> Add 1.0 μL primers
--> PCR (96-well)
- 95°C/ 3 min.
- [95°C/ 15 sec., 58°C/ 15 sec., 72°C/ 15 sec.] x32
- 72°C/ 3 min.
- 4°C/ ∞
--> Conclusions:
- CASP10: qPCR test 41A, D
- EOMES: qPCR test 42A, D
- OTX2: qPCR test 43D
- PRKACG: too non-specific
- SST: qPCR test 45C, D
- ATOH1: qPCR test 46A, D
- HHEX: failed
- IL4: failed
- SLC6A4: non-specific (49C)
Next: Do qRT-PCR test with 1:10, 1:100 dilutions of 126-1 (+dox bulk cDNA)
|