Continuing with the RAD-seq library prep. Following the Meyer Lab 2bRAD protocol.
After determining the minimum number of PCR cycles to run to generate a visible, 166bp band on a gel yesterday, ran a full library “prep scale” PCR.
REAGENT | SINGLE REACTION (μL) | x11 |
Template | 40 | NA |
ILL-HT1 (1μM) | 5 | 55 |
ILL-BC# (1μM) | 5 | NA |
NanoPure H2O | 5 | 55 |
dNTPs (1mM) | 20 | 220 |
ILL-LIB1 (10μM) | 2 | 22 |
ILL-LIB2 (10μM) | 2 | 22 |
5x Q5 Reaction Buffer | 20 | 220 |
Q5 DNA Polymerase | 1 | 11 |
TOTAL | 100 | 550 |
Combined the following for PCR reactions:
- 55μL PCR master mix
- 40μL ligation mix
- 5μL of ILL-BC# (1μM) – The barcode number and the respective sample are listed below.
SAMPLE | BARCODE | SEQUENCE |
Oly RAD 02 | 1 | CGTGAT |
Oly RAD 03 | 2 | ACATCG |
Oly RAD 04 | 3 | GCCTAA |
Oly RAD 06 | 4 | TGGTCA |
Oly RAD 07 | 5 | CACTGT |
Oly RAD 08 | 6 | ATTGGC |
Oly RAD 14 | 7 | GATCTG |
Oly RAD 17 | 8 | TCAAGT |
Oly RAD 23 | 9 | CTGATC |
Oly RAD 30 | 10 | AAGCTA |
Cycling was performed on a PTC-200 (MJ Research) with a heated lid:
STEP | TEMP (C) | TIME (s) |
Initial Denaturation |
|
|
17 cycles |
|
|
After cycling, added 16μL of 6x loading dye to each sample.
Loaded 10μL of ladder on each of the two gels.
Results:
Things looked fine. Excised the bands from each sample indicated by the green arrow. Before and after gel images show regions excised. Will purify the bands and quantify library yields.