Instruments

Next Generation Sequencers (NGS) - Ion Proton™ & Ion PGM™with Ion OneTouch2 Systemfrom Thermo Fisher Scientific, USA.

The Ion Proton™ combines semiconductor sequencing technology with biochemistry to directly translate chemical information into digital data. The System offers a complete workflow from sample through analysis, and variant calling or RNA analysis. It is used with the Ion OneTouch2 System to enable automated, high-throughput template preparation and reproducible chip loading for users of any experience level. It generates reads up to 200-base fragment read and perform fragment, mate-paired and paired-end runs for a variety of applications.

Ion Proton™ System performance specifications with Ion PI™ Chip: Output Up to 10 Gb, Reads 60–80 million reads, Read length Up to 200-base reads, Run time 2-4 hours.

Research areas:

Cancer, Genetic disorders, Agriculture, Stem cells, Epigenetics.

Key applications:

Human-scale whole genome sequencing, Exome sequencing, Transcriptome sequencing, Copy number analysis, ChIP sequencing, Targeted RNA sequencing.

Library solutions:

Ion AmpliSeq™ Library Kit, Ion AmpliSeq™Exome RDY Kit, Ion TargetSeq™ Exome Kit, Ion Xpress™ Plus Fragment Library Kit, Ion Total RNA-Seq Kit v2, Ion Xpress™ RNA-Seq Barcode Kit, Ion AmpliSeq™ Transcriptome Human Gene Expression Kit.

Barcoding solutions:

384 barcodes supported by Torrent Suite™ Software, 96 off-the-shelf barcodes for DNA, 16 off-the-shelf barcodes for RNA.

Data analysis solutions:

Torrent Suite™ Software processes signals, calls bases, aligns sequences, and performs basic variant calling as the primary analysis software for the Ion Proton™ Sequencer. Optimized data analysis workflows have been developed for genome sequencing, targeted RNA and DNA sequencing, transcriptome sequencing, exome sequencing, and other research applications using third-party software solutions and freely downloadable plugins. Ion Reporter™ Software performs controlled analysis, annotation, and reporting of variants along with application-specific workflows to support single, paired (tumor-normal), and trio analysis.

Specifications for the Ion Proton™ Sequencer:

Working environment (for indoor use only):- Temperature: 68–77°F (20–25°C), Humidity: 40–60%, noncondensing Altitude: <6,500ft. Gas supply: Connection: 0.25 in push-to-connect fitting, Pressure: 30 psi, Composition: nitrogen (grade 4.8, 99.998% or better). Other connections: Ethernet: 1 GigE, USB: 2x USB 2.0. Power: Voltage: 100 V (min) to 240 V (max) Current: 14 A (max), Frequency: 50/60 Hz Power draw: 1,350 W. Dimensions: Width: 21.3 in/54.2 cm, Depth: 30.5 in/77. 5 cm, Height: 18.7 in/47.4 cm. Weight Crated for shipment: 200 lb/90.7 kg, Free-standing: 130 lb/59 kg. Instrument computer hardware Processor: Dual 8-core Intel® Xeon® Sandy Bridge Memory: 128 GB RAM FPGA: Dual Altera® Stratix® V GPU processor: 1x NVIDIA® Tesla® C2075 Storage: 11 TB (SSD and HDD) Operating system: Ubuntu® 11.10.

Specifications for the Ion Proton™ Torrent Server:

Product configuration: A single free-standing tower computer, included with the purchase of the Ion Proton™ System. Includes Torrent Suite™ Software with all necessary software components to deliver signal processing, base calling, read alignment, and variant calling. Processor Dual 8-core 2.9 GHz CPUs, Memory 128 GB RAM, GPU processor 2x NVIDIA® Tesla® GPUs, Storage (approx.) 27 TB (sufficient for storage of >50 Ion PI™ Chip runs), Operating system Ubuntu® 10.04, Dimensions (approx.) Width: 8.5 in/21.8 cm Depth: 28 in/71.4 cm Height: 17 in/43 cm. Weight (approx.) 120 lb/55 kg. Power Voltage: 100 V (min) to 240 V (max), Current: 12 A (max), Frequency: 50/60 Hz Power Draw: 1,100 W.

The PGM™ System makes affordable, high-quality next-generation sequencing accessible to human diseaseresearchers and microbiologists around the world. The Ion PGM System is a reliable sequencing platform thatcombines simple sample preparation and data analysis solutions with flexible chip output for ultimate project flexibility.

Ion PGM System performance specifications:

Chip specifications and data output: Ion 314™ Chip v2(200 base, 30-50 Mb, Reads:400-550 thousand, Run time: 2.3hr) or Ion 314 Chip v2 BC(400 base, 60-100 Mb, Reads: 400-550 thousand, Run time: 3.7hr), Ion 316™ Chip v2(200 base, 300-600 Mb, Reads: 2-3 million, Run time: 3.0hr) or Ion 316 Chip v2 BC(400 base, 600 Mb-1Gb, Reads: 2-3 million, Run time: 4.9hr), Ion 318™ Chip v2(200 base, 600 Mb-1Gb, Reads: 4-5.5 million, Run time: 4.4hr) or Ion 318 Chip v2 BC(400 base, 1.2-2 Gb, Reads: 4-5.5 million, Run time: 7.3hr).

Research Areas: Cancer research, inherited disease research, microbial genomics, stem cell research, agriculture, epigenomics, metagenomics, forensic science, and ancient DNA genomics.

Key applications: Targeted DNA sequencing, copy number analysis, targeted RNA sequencing, small RNA sequencing, de novo microbial sequencing, bacterial typing research, viral typing research, ChIP sequencing, methylation analysis, SNP verification, and genotyping by sequencing.

Target Selection Solutions: Ion AmpliSeq™ technology, Ion TargetSeq™ kits (3 custom enrichment kits and 1 multiblocker kit).

Library solutions: Ion AmpliSeq™ Library Kits, Ion Xpress™ Plus Fragment Library Kit, Ion Total RNA-Seq Kit v2, Ion Library Equalizer™ Kit, and 384 barcodes supported by Torrent Suite™ Software.

Data analysis solutions: Torrent Suite Software processes signals, calls bases, aligns sequences, and performs basic variant calling as the primary analysis software for the Ion PGM™ Sequencer. Optimized data analysis workflows have been developed for targeted DNA sequencing, targeted RNA sequencing, microbial de novo sequencing, microbial typing research, and other research applications using third-party software solutions and freely downloadable plug-ins. Ion Reporter™ Software performs controlled analysis, annotation, and reporting of variants along with application-specific workflows to support single, trio, and paired tumor–normal analysis.

Ion PGM Sequencer specifications:

Working environment (for indoor use only) Temperature: 68–77°F (20–25°C) Humidity: 40–60%, noncondensing Altitude: <6,500ft. Gas supply Connection: 0.25 in. push-to-connect fitting Pressure: 35–45 psi Composition: nitrogen (grade 4.5, 99.995% or better). Other connections Ethernet: 1 GigE USB: 2x USB 2.0. Power Voltage: 100 V (min) to 240 V (max), Current: 9 A (max), Frequency: 50/60 Hz, Power draw: 200–300 W. Dimensions 24 x 20 x 21 in./61 x 51 x 53 cm (W x D x H). Weight Crated for shipment: 85 lb/39 kg, Free-standing: 65 lb/30kg.

Ion PGM Torrent Server specifications:

Product configuration: A single free-standing tower computer appliance, included with the purchase of the Ion PGM System. Includes Torrent Suite Software with all necessary software components to deliver signal processing, base calling, read alignment, and variant calling. Processor Dual 8-core 2.6 GHz CPUs, Memory 64 GB RAM, Storage (approx.) 18 TB, Operating System Ubuntu™. Dimensions (approx.) 9 x 28 x 43 in./22 x 71 x 17 cm (W x D x H). Weight (approx.) 121 lb/55 kg. Power Voltage: 100 V (min) to 240 V (max), Current: 12 A (max), Frequency: 50/60 Hz, Power draw: 1,100 W. Data formats Industry-standard FASTQ, SFF, BAM, and VCF format outputs.

Ion OneTouch 2 System:

The Ion OneTouch 2 System performs template amplification and enrichment as part of the manual workflow for the Ion PGM, Ion Proton, and Ion S5 and Ion S5 XL systems. It provides scalable template preparation for all Ion semiconductor chips. With its small footprint, the system fits easily on any bench top. Provides scalable template preparation for all Ion semiconductor sequencing chips. Supports up to 400 bases on the Ion S5™, Ion S5™ XL and Ion PGM Systems and up to 200 bases on the Ion Proton System. Supports multiplexed samples. Fits easily on any benchtop with its small instrument footprint. The Ion OneTouch 2 Instrument is scalable and supports all Ion semiconductor sequencing chips. This flexibility enables automated preparation and fast sequencing for maximum flexibility in project type and size. The Ion OneTouch 2 Instrument also supports processing of multiplexed libraries, reducing the time and cost of template preparation for both DNAand RNA-based applications.

Ion OneTouch 2 System specifications:

System: Ion OneTouch 2 System includes: Ion OneTouch 2 Instrument, Ion OneTouch ES. Dimensions and weight: Ion OneTouch 2 Instrument: (12 x 16 x 14 in., 23 lb.; 30 x 41 x 36 cm, 10.4 kg), Ion OneTouch ES: (9.5 x 12.5 x 11 in., 12 lb.; 24 x 32 x 28 cm, 5.4 kg). System run time: 5 hours total time for Ion PGM Sequencer template preparation—minutes of hands-on time. 8 hours total time for Ion Proton Sequencer template preparation—minutes of hands-on time .Throughput: Supports template preparation for all Ion semiconductor sequencing chips. Library types: Supports template preparation with a broad range of libraries used for various applications: Genomic DNA (fragment and mate-paired), Amplicon, RNA (cDNA). Operating environment Temperature: 15–25°C; humidity: 20–80%, noncondensing. Power requirements: 110/220 V (US/international). Multiplexing: Up to 384 barcoded libraries for DNA- or RNA-based applications.