User:Tara K. Luckau/Notebook/Team ConGen/2011/03/31

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 * style="background-color: #BCED91"|[[Image:owwnotebook_icon.png|128px]] Tara's Lab Notebook
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H2O

 * water has large peak at 160bp
 * Buffer F [[Image:20110323_Frag_H2O-F.jpg|600 px]]
 * Buffer G [[Image:20110323_Frag_H2O-G.jpg|600 px]]
 * Buffer H [[Image:20110323_Frag_H2O-H.jpg|600 px]]

SCOC RAJ X01

 * RAJ has only water peaks :(
 * Buffer F [[Image:20110323_Frag_RAJ-F.jpg|600 px]]
 * Buffer G [[Image:20110323_Frag_RAJ-G.jpg|600 px]]
 * Buffer H [[Image:20110323_Frag_RAJ-H.jpg|600 px]]

SCOC HOL X01

 * HOL has only water peaks :(
 * Buffer F [[Image:20110323_Frag_HOL-F.jpg|600 px]]
 * Buffer G [[Image:20110323_Frag_HOL-G.jpg|600 px]]
 * Buffer H [[Image:20110323_Frag_HOL-H.jpg|600 px]]

SCOC SYR2 X01

 * Buffer F [[Image:20110323_Frag_SYR2-F.jpg|600 px]]
 * Buffer G [[Image:20110323_Frag_SYR2-G.jpg|600 px]]
 * Buffer H [[Image:20110323_Frag_SYR2-H.jpg|600 px]]
 * 2 peaks!  at 115.36, 119.38
 * they're 4 bp apart, with very small (leading?) peak at 111.36 bp

SCOC CPN X01

 * Buffer F [[Image:20110323_Frag_CPN-F.jpg|600 px]]
 * Buffer G [[Image:20110323_Frag_CPN-G.jpg|600 px]]
 * multiple peaks!  at 115.45, 119.5, 123.57, 127.84
 * all are 4 bp apart, with (leading) peak at 111.43


 * Buffer H [[Image:20110323_Frag_CPN-H.jpg|600 px]]
 * multiple peaks!  at 78.35, 99.09, 103.09, 115.43, 119.47, 123.54
 * pairs of peaks are 4bp apart, with only one (leading) peak at 111.24

SCOC TP1 X01

 * Buffer F [[Image:20110323_Frag_TP1-F.jpg|600 px]]
 * multiple peaks!  at 99.09, 103.12, 111.31, 115.35, 123.50, 127.79
 * all are 4bp apart, with small (leading) peak at 119.41


 * Buffer G [[Image:20110323_Frag_TP1-G.jpg|600 px]]
 * multiple peaks!  at 107.24, 111.24, 119.47, 123.54, 127.82
 * all are 4bp apart, with small (leading) peaks at 103.09, 115.26
 * ladder lane is very short


 * Buffer H [[Image:20110323_Frag_TP1-H.jpg|600 px]]
 * multiple peaks!  at 103.27, 107.42, 111.41, 119.63, 123.68, 127.92
 * all are 4bp apart, with small (leading) peaks at 115.42
 * ladder lane is very short

SCOC TP3 X01

 * TP3 has only water peaks :(
 * Buffer F [[Image:20110323_Frag_TP3-F.jpg|600 px]]
 * Buffer G [[Image:20110323_Frag_TP3-G.jpg|600 px]]
 * Buffer H [[Image:20110323_Frag_TP3-H.jpg|600 px]]

SCOC LOM X01

 * LOM has only water peaks :(
 * Buffer F [[Image:20110323_Frag_LOM-F.jpg|600 px]]
 * Buffer G [[Image:20110323_Frag_LOM-G.jpg|600 px]]
 * Buffer H [[Image:20110323_Frag_LOM-H.jpg|600 px]]

Diversity Panel Frag Conclusions

 * these are much smaller than the expected 131 to 191 bp reported in Lance, et al.
 * peaks are 4 peaks apart, consistent with 4bp motif
 * of the 3 samples that yielded amplicons, Buffer H worked for all three - but profiles were not consistent across Buffers

Next Steps

 * Why didn't some of the DNA work? Look up quantification values - are SCOC RAJ X01, HOL X01, TP3 X01, LOM X01 low?
 * What are the differences between the DNAs that worked?
 * [[Image:20110323 FragScun2Diversity.jpg|700 px]]
 * green cells indicate a shorter (leading?) peak


 * }