BigHornSheep 16S 2021 (5CM)

MasterMix (make for 8 plates in 15mL conical tube)

*Add 11 ul to each well of a hard shell, full skirt plate. Seal with bubble strips and store in refrigerator until needed label “NovaSeq4 PCR”. (If doing manually, one needs 2 ul of template and 2 ul of the primers).

Run on Thermocycler Program GSAF36:

MagBead Cleanup:

Some plates were cleaned up using the Nimbus platform protocol “AxyPrep MagBead PCR1 No MM”

Manually, it was done:

• Equilibrate Beads to room Temperature

• Add 24 ul of MagBeads to each well and 15 ul of replicate to same well of replicate

• Pipette mix up and down 10 times.

• Incubate at RT for 5 minutes

• Secure plate on magnet plate; incubate at RT for 5 minutes (until wells are clear)

• Remove 65 ul from each well; keep tips to left or right depending on the column to avoid bead pellet.

• Add 100 ul Fresh 80% EtOH to each well. Incubate 30 seconds. Remove 100 ul from each well

• Add 100 ul Fresh 80% EtOH to each well. Incubate 30 seconds. Remove 100 ul from each well

• Reaspirate from each well to assure maximum EtOH removal

• Allow plate to air dry for 7 minutes.

• Remove sample plate from magnet plate.

• Add 40 ul TE; pipette mix 10+ times. Incubate 2 minutes at RT.

• Place sample plate back on magnet for 5 minutes or until all wells are cleared.

• Transfer 40 ul to labeled transparent plate (Plate name_PCR_MIDs)

qPCR NovaSeq5_Plate1

• Make 1:1000 dilutions of column 3 from the PCR plates by adding 1 ul to 999 ul TE in a deep well plate:

• Make a 1:1000 dilution of HMax_PP Final Pool to check quality of pippin elution before sending out for RFS.

• Add 16 ul of Illumina Library Quantification MasterMix to each well:

• Add 4 ul of template, pool, or standards to each well:

Results:

Average results for the following plates (column 3):

5CM1_16S: 6.03 nanomoles

5CM2_16S: 9.32 nanomoles

5CM3_16S: 3.52 nanomoles

5CM4_16S: 9.77 nanomoles

Results for HMax_PP_Final can be viewed in result report below and have been added to the HMax page here.

Full result report can be viewed below:

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Pooling and Shipping:

The client, Chris MacGlover, is concerned about the nasal swabs not sequencing as occurred with his last attempt. We will send 3 nasal, one excontrol, and one other sample to be fragment analyzed at CU:

5CM1 A4 (18-143N), 5CM1 H12 (SB33N), 5CM2 A4 ( 18-143T), 5CM3 H12 (51N), and 5CM1 A3 (excontrol)

Fragment Analysis returned from the Genomics Core lead us to allow sequencing to proceed.

Open