Services

Ion Torrent Semiconductor Next Generation Sequencing

Ion Semiconductor Sequencing is a method of next-generation sequencing based on the detection of hydrogen ions that are released during the polymerization of DNA. This is a method of sequencing by synthesis, during which a complementary strand is built based on the sequence of a template strand.  This technology differs from other sequencing technologies in that no modified nucleotides or optics are used.  At present, supported applications for Ion Torrent semiconductor sequencing include: targeted DNA and RNA sequencing; exome sequencing; transcriptome sequencing; small RNA Sequencing; gene expression profiling; microbial or other small genome sequencing; as well as bacterial and viral typing.  In contrast to other sequencing platforms, Ion Torrent semiconductor sequencing has the advantages of quicker sequencing runs and reduced cost per sample.  Ion Torrent semiconductor sequencing is performed on either the Personal Genome Machine (PGM) or Proton instrument depending on desired read length and application.

Ion Torrent Certified Service Provider

The BU Microarray Resource is a Certified Service Provider for Ion AmpliSeq Transcriptome sequencing.  The Ion Torrent Certified Service Provider program is a global network of validated service providers that enable researchers in small and medium-sized laboratories to get high-quality transcriptome sequencing data generated on the Ion Proton instrument.  

Ion Torrent PGM Sequencing

The Ion Torrent Personal Genome Machine (PGM) is a small-scale, bench top instrument capable of processing samples for targeted DNA and RNA sequencing, small RNA sequencing, gene expression profiling, microbial genome sequencing, and bacterial and viral typing applications.  The PGM can provide three levels of sequence output according to three sequencing chip sizes: 314, 316, and 318.  The PGM can also provide sequence data in two read-lengths: 200bp and 400bp.  See below for detailed information about output by chip type.  For questions regarding PGM applications and choosing those best suited to your experimental needs, please contact the Microarray Resource.

Chip Type Sequencing Time Output [Mb] Output [Reads]
314 2.5 hrs 60 – 120 400-700K
316 3.0 hrs 300 – 600 2.0-3.5M
318 4.5 hrs 475 – 950 3.0-5.0M

The above data are provided for 200bp read-length applications and are dependent on the quality of input RNA and DNA, as well as final sequencing libraries.

Ion Torrent Proton Sequencing

The Ion Torrent Proton sequencer is a larger-scale instrument than the Personal Genome Machine, and is capable of processing samples for all applications supported by the PGM in addition to whole transcriptome and exome sequencing.  Currently, the Proton Instrument utilizes the P1 chip to provide 4-7 Gb of sequencing over 60-80M reads of approximately 150bp length in 4.5 hours, dependent on the quality of input RNA and DNA, as well as final sequencing libraries.  For questions regarding Proton applications and choosing those best suited to your experimental needs, please contact the Microarray Resource.

Affymetrix GeneChip® System for Gene Expression Analysis

The Affymetrix GeneChip system is a commercial microarray platform that allows whole genome gene expression analysis for a wide variety of experimental organisms (http://www.affymetrix.com/products/arrays/index.affx). This system has three major advantages over other array systems: it is easy to get rapid results; it has the capability to monitor the expression of every gene in the genome; and it is the most widely used commercial microarray platform.

Getting started with Affymetrix GeneChips is easy:

  • Set-up an appointment with members of the Microarray Resource to discuss your experiment. This is optional, but highly recommended.
  • Give us total RNA (See our recommendations). Standard processing is available starting with as little as 50 ng of total RNA. Exon arrays require 1 µg of total RNA.
  • Wait for us to process your samples
  • Standard analysis is included, or work with Microarray Resource to further analyze data

Affymetrix GeneChip® miRNA Array

The GeneChip® miRNA Array is a powerful and cost effective tool for studying the role of microRNAs (miRNAs). The array provides comprehensive miRNA coverage (Sanger miRNA database V20 content and additional human small nuclear RNAs (snoRNAs and scaRNAs)) with multiple organisms (Human, mouse, rat, canine, and monkey) on a single array. Input amounts: 0.13 – 3µg of total RNA or low molecular weight RNA enriched from 0.1-3 ug of total RNA (for new users we recommend to start with 1 ug of total RNA or LMW RNA enriched from 1 ug of total RNA).

Affymetrix GeneChip® Gene 1.0 ST & 2.0ST and Transcriptome 1.0 & 2.0 Array System for Human, Mouse and Rat

The Affymetrix GeneChip Gene 1.0 ST & 2.0ST and Transcriptome 1.0 & 2.0 Array Systems represents a new generation of array products and offer a number of important advantages: they are more cost-effective for gene expression profiling, and measure expression using probes that span the full length of the transcript (unlike previous Affymetrix arrays that used probes targeted to the 3’ end of the transcript).

Affymetrix GeneChip® System for Exon-level Gene Expression Analysis

The Affymetrix GeneChip Exon Array system provides, for the first time, exon-level expression profiling of the whole-genome on a single array. The arrays contain probes for over 1 million exon clusters within regions of the genome known or predicted to be transcribed. This new generation of GeneChip allows investigation of the expression of individual exons to analyze alternative splicing. Exon Array GeneChips are available for human, mouse, and rat.

Affymetrix GeneChip® System for Genotyping

The Affymetrix GeneChip system is a commercial microarray platform that allows high-throughput genotyping for human samples with as little as 250 ng of genomic DNA. The new Affymetrix® Genome-Wide Human SNP Array 6.0 contains more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation. The SNP Array 6.0 drives genetics forward by enabling a new study paradigm for researchers—a whole-genome approach to replication. This new approach increases the overall statistical genetic power to detect associations and eliminates other disadvantages tied to selecting a limited subset of markers in the replication phase.

Affymetrix GeneChip™ CustomSeq™ Resequencing Arrays

Affymetrix GeneChip CustomSeq Resequencing Arrays provides flexible custom arrays that are capable of determining up to 300 kb of unique, high-quality, double-stranded sequence. Flexible array formats of 50kb, 100kb, or 300kb are available. Sequences may cover a single contiguous region or multiple dispersed fragments, facilitating the analysis of whole genomes, multiple genes, and/or multiple organisms on a single array.

A Human Mitochondrial Resequencing array is available as a catalog product. The array interrogates the entire 16 kb of the mitochondrial genome.

Affymetrix GeneChip™ Whole Genome Tiling Arrays

The Affymetrix GeneChip Tiling Array Sets contain probes that cover virtually every base pair of the genome and are designed for identifying novel transcripts, mapping sites of protein/DNA interaction in chromatin immunoprecipitation (ChIP) experiments, and other experiments. Probes are tiled at 5-35 base pair resolution, depending on the organism, as measured from the central position of adjacent 25-mer oligos. Array sets are available for a variety of organisms in several different configurations. The probes for interrogating each chromosome are contained on a single array from the whole genome array set and each array is available separately.

Affymetrix GeneChip™ Legacy Arrays

Previous generations of all Affymetrix GeneChips are available for users seeking to add new data to existing gene-expression datasets. Please contact us for pricing.

Please contact the Microarray Resource for more information and to discuss all projects involving Affymetrix GeneChip exon, genotyping, resequencing, or tiling arrays.