■CHAPTER 4 Clean and initialize ....................................... 21
Condition the Wash 2 Bottle for first use .......................................... 21
Clean the Ion PGM™ System ..................................................... 21
Materials required ......................................................... 21
Cleaning schedule ......................................................... 22
Cleaning setup ............................................................ 22
18 MΩ water cleaning ...................................................... 22
Chlorite cleaning .......................................................... 23
Initialize the Ion PGM™ System ................................................... 24
Materials required ......................................................... 24
Initialization guidelines ..................................................... 25
Before initialization ........................................................ 25
Prepare the Wash 2 Bottle .................................................. 25
Prepare the Wash 1 and Wash 3 Bottles ....................................... 27
Begin the initialization ...................................................... 28
Prepare the 50‑mL Reagent Bottles with dNTPs ............................... 30
Attach the sipper tubes and Reagent Bottles .................................. 30
■CHAPTER 5 Load the chip and start the sequencing run ............ 32
Materials required ............................................................. 32
Before starting ................................................................ 32
Add controls to the enriched, template-positive ISPs ............................... 33
Anneal the Sequencing Primer .................................................. 33
Perform Chip Check ............................................................ 34
Bind the Sequencing Polymerase to the ISPs ...................................... 36
Prepare and load the chip ....................................................... 37
Remove liquid from the chip ................................................. 37
Load the chip .............................................................. 38
Select the Planned Run and perform the run ...................................... 41
Select the Planned Run ..................................................... 41
Perform the run ........................................................... 42
■APPENDIX A Troubleshooting ......................................... 43
Chip Check .................................................................... 43
Chip calibration (before loading sample) .......................................... 44
Chip calibration (after loading sample) ............................................ 46
Initialization—General errors .................................................... 47
Initialization—Auto pH errors .................................................... 48
Initialization—Reagent pH verification ............................................ 53
Troubleshooting using Control Ion Sphere™ Particles and control libraries ............ 54
Contents
4
Ion PGM
™
Hi‑Q
™
View Sequencing Kit User Guide