NGS Sequencing Support—Getting Started
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Ion PGM™ System
The Ion PGM™ System supports the Ion 3 series chips, including the Ion Torrent™ Ion 314™ Chip Kit v2 (Cat. No. 4482261), Ion Torrent™ Ion 316™ Chip Kit v2 (Cat. Nos. 4483188 and 4483324), and Ion Torrent™ Ion 318™ Chip Kit v2 (Cat. Nos. 4484354 and 4484355). The Ion 314 Chip Kit v2 is available in an 8-pack; the Ion 316 Chip Kit v2 and Ion 318 Chip Kit v2 are available in 4-packs and 8-packs.
For Ion PGM™ 3 series chip performance specifications, please see the Ion PGM System Specification Sheet.
Each Ion PGM™ sequencing kit includes reagents and materials for four initializations. The number of runs per initialization will depend on the desired read length.
The Ion PGM™ Sequencing 200 Kit v2 (Cat. No. 4482006) supports two runs per initialization (or eight runs per kit) for 200-base read sequencing. For ≤100-base read sequencing, there are enough reagents to support three runs per initialization (or twelve runs per kit).
The Ion PGM™ Sequencing 400 Kit (Cat. No. 4482002) supports one run per initialization (or four runs per kit) for 300- and 400-base read sequencing.
Firmware updates for Ion instruments are included with the latest version of Torrent Suite Software. First, download and install the latest version of Torrent Suite Software on your Torrent Server. Once completed, your Ion PGM™ System should alert you that an update is available. You can also start the update process from the Options menu. From the Main menu, select Options, then Updates, Released Updates, and Check. Once your Ion PGM™ system has detected the update, press the Update button to begin the process. Instructions to update the Ion PGM™ Sequencer can also be found in the Appendix of the Ion PGM™ sequencing kit user guides.
The number of samples that can be multiplexed in a single sequencing run depends on the capacity of the chip, the size of the library, and the required coverage. A table of approximate capacities based on the size of the library and chip can be found in the Ion AmpliSeq Preparation User Guide within the section “Strategies for combining Ion AmpliSeq libraries.”
When performing two sequencing runs from the same initialization, the second run must be started within 27 hours after initialization.
No, the Ion PI Hi-Q sequencing chemistry is only compatible with the Ion PI Chip v3. Using the Ion PI Chip v2 will result in lower loading and data throughput.
Yes, an Ion PI v2 chip can be used for the initialization. Ensure that the PI Hi-Q initialization program is selected, and an Ion PI Chip v3 is used for the sequencing run.
No. The Ion PI™ Chips v2 are not optimized for use with the Ion PI™ Hi-Q™ Chef Kit chemistry. We recommend using the Ion PI™ Chips v3, which have been pretreated during manufacturing and optimized for use with the Ion PI™ Hi-Q™ Chef Kit chemistry.
The Ion PI™ Chips v3 have a shelf life of 9 months from manufacturing. However, please be aware that when you order the chips, time may have passed since manufacturing. To request the chips with the longest expiration date available, please contact Customer Care by phone to see which lots are in stock.
The initialization is stable for 24 hours after initialization. However, we still recommend that you begin the second sequencing run right after the first run is completed.
Yes, up to 3 barcoded exome libraries can be run on an Ion P1™ Chip depending on the coverage and depth desired. As the number of libraries on a single chip increases, the average coverage depth decreases.
The recommendation is 2 exomes per chip. We can confidently call germ line mutations at 20 X coverage. You need ~ 30 M mapped reads per library, so since the minimum number of reads per chip is 60 million reads, that is 2 exomes per chip.
Ion S5™ and Ion™ S5™ XL Systems
Initialization takes 35 minutes for both the Ion S5™ and Ion™ S5™ XL Systems.
No, the Ion S5™ and Ion™ S5™ XL Systems have an onboard air compressor and tank to store pressurized air.
No, the instrument will give a warning message regarding the expired reagents, but will not prevent you from running the instrument.
We expect that applications currently supported on the Ion PGM™ and Ion Proton™ Systems will be supported on the Ion S5™ and Ion™ S5™ XL Systems. However, not all applications have been tested or demonstrated yet.
For 200 bp sequencing, it will yield 0.6 - 1.0 Gb. For 400 bp sequencing, it will yield 1.2-2 Gb.
For 200 bp sequencing, it will yield 3-4 Gb. For 400 bp sequencing, it will yield 6-8 Gb.
For 200 bp sequencing, it will yield 10-15 Gb. 400 bp sequencing is not supported on the Ion 540™ Chip.
No, the W2 solution in the Ion S5™ and Ion™ S5™ XL Systems is supplied at the correct pH, so the auto pH step is not necessary.
Unlike the Ion PGM™ and Ion Proton™ Systems, the sequencing reagents for the Ion S5™ and Ion™ S5™ XL Systems come with a cleaning solution bottle, which the instrument uses to automatically clean itself after each run.
You can perform either one or two runs per initialization on the Ion S5 and Ion S5 XL systems, depending on the read length of each run. Two runs per initialization are compatible with 200 bp reads whereas only one run per initialization is compatible with 400 bp reads.
- For two 200 bp runs per initialization on the Ion S5/S5XL and Ion Chef systems, using the Ion 520 or Ion 530 chip, we recommend using the Ion 520 & Ion 530 Kit-Chef (2 sequencing runs per initialization), Cat. No. A30010.
- For two 200 bp runs per initialization on the Ion S5/S5XL and Ion Chef Systems, using the Ion 540 chip, we recommend using the Ion 540 Kit-Chef (2 sequencing runs per initialization), Cat. No.A30011.
- For one 200 bp or one 400 bp run per initialization on the Ion S5/S5XL and Ion Chef systems, using the Ion 520 or Ion 530 chip, we recommend using the Ion 520 & Ion 530 Kit-Chef, Cat. No. A27757.
- For one 200 bp or one 400 bp run per initialization on the Ion S5/S5XL and Ion Chef systems, using the Ion 540 chip, we recommend using the Ion 540 Kit-Chef, Cat. No. A27759.
- For one 400 bp run or two 200 bp runs per initialization on the Ion S5/S5XL and Ion OneTouch2 systems, using the Ion 520 or Ion 530 chip, we recommend using the Ion 520 & Ion 530 Kit-OT2, Cat. No. A27751.
- For one or two 200 bp runs per initialization on the Ion S5/S5XL and Ion OneTouch2 systems, using the Ion 540 chip, we recommend using the Ion 540 Kit-OT2, Cat. No. A27753.
Note: 400 bp runs are not compatible with the Ion 540 chip.
For Research Use Only. Not for use in diagnostic procedures.