Wagner Trout 3 (3Trout)

Setup Notes

~6 plates of trout to be prepared via the MseI and EcoRI GBS library prep protocol with some slight modifications:

Pool ~6*96 individuals per library
Cleanup each full pool via ultra purification
Size select for 300-366bp fragments size window via BluePippin or Pippin Prep
Send Out for Sequencing
5% PhiX spike

Check In Samples Against List from Will Rosenthal

Load Submission Data into MISO

Quantify and normalize samples:

Normalize plate reader with Buffer AE for all plates
Quantify all plates
Check for samples above 150 ng/ul
Transfer 20 ul from all wells of a plate needing normalization to new VWR plate
Add 20 ul TE to all wells above 150 ng/ul

Restriction Digestion

(Keep MM and reaction plates on ice)

Set Incubator to 37 C

Add 3 ul Digestion MM to 32 plates using the 8 channel

Reagent	ul/rxn	rxns	ul needed (1.5x)
10x T4 Buffer	1.15	800	920
5M NaCl	0.12	800	96
1 mg/ml BSA	0.6	800	480
H2O	0.73	800	584
MseI (enzyme)	0.12	800	96
EcoR1 (enzyme)	0.28	800	224
Total	3	800	2400

Add 6 ul template to each plate with Benchsmart. Cover and seal each plate, vortex, centrifuge and incubate at 37C for 8 hours. Followed by 65C in EcoBGC oven for 1 hour.

Adaptor Ligation

Spin down plates and add 1.4 ul Ligation MM to each well with 8 channel.

Reagent	ul/rxn	rxns	ul needed (1.6x)

Reagent	ul/rxn	rxns	ul needed (1.6x)
MseI oligo	1	800	800
H2O	0.112	800	89.6
10x T4 Buffer	0.1	800	80
5M NaCl	0.01	800	8
1 mg/ml BSA	0.05	800	40
T4 DNA ligase	0.1675	800	134
Total	1.4	800	1120

Add 1 ul of EcoR1 Adaptors with 96-channel and Track which template plate gets which MID plate.

Template	GTL Plate	EcoR1 MID plate	Pool Plate	Library

Template	GTL Plate	EcoR1 MID plate	Pool Plate	Library
YCT_library_22_6_3	3Trout1	1	3Trout_Pool1	1
Teton_Library_22_3_1	3Trout2	2	3Trout_Pool1	1
Teton_Library_Plate_22_3_2	3Trout3	3	3Trout_Pool2and4	1
Tetons_Library_Plate_22_5_4	3Trout4	4	3Trout_Pool2	2
YCT_Library_22_3_5	3Trout5	5	3Trout_Pool2	2
UMT_YCT_RBT_DNA to UWY	3Trout6	6	3Trout_Pool2and4	2

Label reaction plates with MID plate used.

Cover, vortex, and spin plates. Incubate plates at RT for 2 hours on benchtop.

Add 120 ul of low EDTA TE store at 4C for a month or -20C for longer.

PCR Amplification

PCR1:

Reagent	ul/rxn	rxns	ul needed (x1.4)

Reagent	ul/rxn	rxns	ul needed (x1.4)
H2O	9.52	350	3332
5x iProof buffer	4	350	1400
10 mM dNTPs	0.4	350	140
50 mM MgCl2	0.4	350	140
5 uM Illumina Primers	1.33	350	465
iProof TAQ	0.2	350	70
DMSO	0.15	350	52.5
total	16	350	5600

Add 16 ul of PCR1 MM to each well of four new hard shell PCR plates with 8 channel

Add 4uL of template from pooled plates with Benchsmart

Seal, Vortex, Spin down, and then run on Thermocycler program: GBS1:

Temp C	Cycles	Time

Temp C	Cycles	Time
95*	1X	3:00
98	30X	0:30
60	30X	0:30
72	30X	0:40
72	1X	10:00
4*	1X*	0:00*

*pause step

Extra PCR

Add 2.155 ul of the MM directly to the previous PCR

Reagent	ul/rxn	rxns	ul needed (x 1.6)
5x Iproof buffer	0.425	360	153
10 mM dNTPs	0.4	360	144
Primers	1.33	360	479
Total	2.155	360	776

Then continue with the last four unlisted steps for GBS1 from above:

Temp C	Cycles	Time

Temp C	Cycles	Time
98	1X	3:00
60	1X	2:00
72	1X	10:00
4	1X	0:00

Pool Using PCR Plates with Assist Plus

Organize plates by Library # above, vortex, and quick spin

Use 4GbsPoolx8

Use single channel to combine 48 ul from each well of a column into a separate labeled tube.

Pippin Prep Size Select (300-366 bp select):

Run Final Product on qPCR for check and quant

Result from qPCR check:

load =800 pM

dilute 1 nM PhiX to 500 pM

Genome Technologies Laboratory