Fragment sizes of HLo ladder Gel 1 Pilar
- Slides: 6
Fragment sizes of H-Lo ladder
Gel 1: Pilar & Jim 1 2 3 4 L 5 6 7 8 High Molecular Weight DNA (extraction) Origin (wells) That’s how it ideally should look like: nice single band Here there is some HMW DNA, but also a lot of degraded DNA. This probably would still be ok for PCR This is RNA PCR product Probably overloaded (too much DNA). Could also be too much template DNA in the PCR. HMW DNA (top) 1 (Pilar)-Sockeye #10 -Salt 2 (Pilar)-Coho #2 -Salt 3 (Pilar)-Sockey #10 -Qiagen 4(Pilar)-Coho #2 -Qiagen L-Ladder 5 -(Jim)-Sockeye #10 -Salt 6 -(Jim)-Chinook #4 -Salt 7 -(Jim)-Sockeye #10 -Qiagen 8 -(Jim)-Chinook #4 -Qiagen PCR product (bottom) 1 -(Jim)-Chinook #4 -Salt 2 -(jim)-Chinook #4 -Qiagen 3(Jim)-Sockeye #10 -Salt 4 -(Jim)-Sockeye #10 -Qiagen L-Ladder 5 -(Pilar)-Sockeye #10 -Qiagen 6 -(Pilar)-Coho #2 -Qiagen 7 -(Pilar)-Sockeye #10 -Salt 8 -Negative control Conclusion: No obvious effect of salt vs Qiagen extraction, either in HMW or PCR product 1 2 3 4 L 5 6 7 8
Gel 2: Claudia, Kristi & Nick Good HMW DNA with little degradation, but the PCR didn’t work well L 1 2 3 4 5 6 7 8
Gel 3: Brian & Gang L 1 2 3 4 5 6 7 8 Weak HMW DNA with some degradation, but the PCR worked well in three samples (all Quiagen extractions!) HMW DNA L: ladder 1: DNA A Quiagen (GX) 2: DNA B Quaigen (GX) 3: Chinook 2 salt (GX) 4: Sockeye 7 salt (GX) 5: Coho 3 salt (BK) 6: sockeye 8 salt (BK) 7: Coho 3 Quiagen (BK) 8: Sockeye 8 Quiagen (BK) PCR product L: ladder 1: Sockeye 7 salt (GX) 2: Coho 3 salt (BK) 3: Sockeye 8 Quiagen (BK) 4: Coho 3 Quiagen (BK) 5: DNA A Quiagen (GX) 6: DNA B Quagen (GX) 7: Chinook 2 salt (GX) 8: control L 1 2 3 4 5
Gel 4: Alfred and Danny This is probably template DNA, i. e. there was too much in the PCR reaction – it still worked though Good PCR products in 5 of 7 samples Good HMW DNA in all samples (#8 a bit weak) Degraded DNA RNA PCR product HMW DNA 1 Sockeye 1 (Salt) 1 Hi-Lo Ladder 2 Nothing 2 Sockeye 1 (Salt) 3 Steelhead 1 (Salt) 4 Sockeye 1 (Qiagen) 5 Sockeye 4 (Salt) 6 Chinook 3 (Salt) 7 Sockeye 4 (Qiagen) 8 Chinook 3 (Qiagen) 9 Control 9 Steelhead 1 (Qiagen) 10 Hi-Lo Ladder 10
Gel 4: Bill & Thomas Gel broke to two pieces DNA looks ok in 4 samples Something strange going on here – you can’t see it on the picture, but on the gel the stain was only on the bottom surface of the gel – a lesson that you can’t see everything on a picture. PCR worked fine as well – this is actually the gel where we saw most straight away. DNA 1. Chinook 1 salt 2. Chinook 1 Qiagen 3. Sockeye 6 Qiagen 4. Steelhead 3 Qiagen 5. Sockeye 9 Qiagen 6. Steelhead 3 salt 7. Sockeye 9 salt 8. Ladder PCR product Ladder 1. Sockeye 9 salt 2. Steelhead 3 salt 3. Sockeye 9 Qiagen 4. Steelhead 3 Qiagen 5. Sockeye 6 Qiagen 6. Chinook 1 Qiagen 7. Negative control 8. Chinook 1 salt
