Fragment sizes of H-Lo ladder

Gel 1: Pilar & JimHigh Molecular Weight DNA

(extraction)

PCR product

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

Probably overloaded (too much DNA). Could also be too much template DNA in the PCR.

1 2 3 4 L 5 6 7 8

1 2 3 4 L 5 6 7 8

Origin (wells)

This is RNA

HMW DNA (top)1 (Pilar)-Sockeye #10-Salt2 (Pilar)-Coho #2-Salt3 (Pilar)-Sockey #10-Qiagen4(Pilar)-Coho #2-QiagenL-Ladder5-(Jim)-Sockeye #10-Salt6-(Jim)-Chinook #4-Salt7-(Jim)-Sockeye #10-Qiagen8-(Jim)-Chinook #4-Qiagen

PCR product (bottom)1-(Jim)-Chinook #4-Salt2-(jim)-Chinook #4-Qiagen3(Jim)-Sockeye #10-Salt4-(Jim)-Sockeye #10-QiagenL-Ladder5-(Pilar)-Sockeye #10-Qiagen6-(Pilar)-Coho #2-Qiagen7-(Pilar)-Sockeye #10-Salt8-Negative control

Conclusion: No obvious effect of salt vs Qiagen extraction, either in HMW or PCR product

L 1 2 3 4 5 6 7 8

Good HMW DNA with little degradation, but the PCR didn’t work well

Gel 2: Claudia, Kristi & Nick

Gel 3: Brian & Gang

Weak HMW DNA with some degradation, but the PCR worked well in three samples (all Quiagen extractions!)

L 1 2 3 4 5 6 7 8

L 1 2 3 4 5

PCR productL: ladder1: 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

HMW DNAL: ladder1: 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)

Gel 4: Alfred and Danny

Good HMW DNA in all samples (#8 a bit weak)

Good PCR products in 5 of 7 samples

This is probably template DNA, i.e. there was too much in the PCR reaction – it still worked though

RNA

Degraded DNA

PCR product   

HMW DNA 

1 Sockeye 1 (Salt)   1 Hi-Lo Ladder

2 Nothing   2 Sockeye 1 (Salt)

3 Steelhead 1 (Salt)   3 Steelhead 1 (Salt)

4Sockeye 1 (Qiagen)  

4Sockeye 1 (Qiagen)

5 Sockeye 4 (Salt)   5 Sockeye 4 (Salt)

6 Chinook 3 (Salt)   6 Chinook 3 (Salt)

7Sockeye 4 (Qiagen)  

7Sockeye 4 (Qiagen)

8 Chinook 3 (Qiagen)   8 Chinook 3 (Qiagen)

9 Control 

9Steelhead 1

(Qiagen)

10 Hi-Lo Ladder   10  

DNA looks ok in 4 samples

Gel 4: Bill & Thomas

Gel broke to two pieces

PCR worked fine as well – this is actually the gel where we saw most straight away.

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.

DNA1.Chinook 1 salt2.Chinook 1 Qiagen3. Sockeye 6 Qiagen4. Steelhead 3 Qiagen5. Sockeye 9 Qiagen6. Steelhead 3 salt7. Sockeye 9 salt8. Ladder

PCR productLadder1. Sockeye 9 salt2.Steelhead 3 salt3. Sockeye 9 Qiagen4. Steelhead 3 Qiagen5. Sockeye 6 Qiagen6. Chinook 1 Qiagen7. Negative control8. Chinook 1 salt