Comments on: Agarose Gel – Olympia oyster Whole Body gDNA Integrity Check

By: Adaptor Ligation – Oly AlfI-Digested gDNA for RAD-seq | Sam's Notebook

Adaptor Ligation – Oly AlfI-Digested gDNA for RAD-seq | Sam's Notebook — Thu, 17 Dec 2015 23:03:03 +0000

[…] Digested DNA from yesterday was heat inactivated for 10mins @ 65C and was not run out on a gel due to the fact that the input gDNA was degraded and a shift in the high molecular weight band (indicating the digestion was successful) would not exist because a high molecular weight band is absent in these samples. […]

By: Restriction Digest – Oly gDNA for RAD-seq w/AlfI | Sam's Notebook

Restriction Digest – Oly gDNA for RAD-seq w/AlfI | Sam's Notebook — Thu, 17 Dec 2015 23:02:48 +0000

[…] performance of the test scale PCR was likely due to low numbers of adaptor-ligated fragments. Since the input DNA is so degraded, I’ve repeated this using 9μg of input DNA (instead of the recommended 1.2μg). This should […]

By: Adaptor Ligation – Oly AlfI-Digested gDNA for RAD-seq | Sam's Notebook

Adaptor Ligation – Oly AlfI-Digested gDNA for RAD-seq | Sam's Notebook — Thu, 17 Dec 2015 23:02:32 +0000

[…] Digested DNA from earlier today was not run out on a gel due to the fact that the input gDNA was degraded and a shift in the high molecular weight band (indicating the digestion was successful) would not exist because a high molecular weight band is absent in these samples. […]

By: PCR – Oly RAD-seq Test-scale PCR | Sam's Notebook

PCR – Oly RAD-seq Test-scale PCR | Sam's Notebook — Thu, 17 Dec 2015 23:02:12 +0000

[…] any bands in any samples (expected size of ~166bp). This is not particularly surprising, due to the level of degradation in these samples. As such, repeated the test scale PCR, but increased the number of […]

By: PCR – Oly RAD-seq Test-scale PCR | Sam's Notebook

PCR – Oly RAD-seq Test-scale PCR | Sam's Notebook — Mon, 12 Oct 2015 23:50:40 +0000

[…] One other aspect of this gel that is very interesting is the ligations. The three ligation samples all show an intact high molecular weight band! This is very surprising, since the input gDNA from these three samples does not look this. […]

By: Adaptor Ligation – Oly AlfI-Digested gDNA for RAD-seq | Sam's Notebook

Thu, 01 Oct 2015 23:39:04 +0000

[…] Digested DNA was not run out on a gel due to the fact that the input gDNA was degraded and a shift in the high molecular weight band (indicating the digestion was successful) would not exist because a high molecular weight band is absent in these samples. […]

By: Restriction Digest – Oly gDNA for RAD-seq w/AlfI | Sam's Notebook

Restriction Digest – Oly gDNA for RAD-seq w/AlfI | Sam's Notebook — Thu, 01 Oct 2015 19:49:09 +0000

[…] 20150916 to prepare RAD libraries. This will be done to assess whether or not these samples, which appear to be heavily degraded, are viable for […]