The OHSU Massively Parallel Sequencing Shared Resource (MPSSR) was founded in 2009 with the mission of providing high quality, cost efficient short read sequencing services. The intent of the MPSSR is to offer state of the art sequencing for a variety of protocols - including genome resequencing, transcriptome analysis, miRNA analysis, and prometer analysis via ChIP-seq. The goal of the MPSSR is to help investigators examine the genetic profiles that underlie disease predisposition and to explore the fundamental operations of biological systems.
Role: Lab Manager, Massively Parallel Sequencing Shared Resource, Research Associate
Potter, Amiee, Ph.D.
Role: Research Associate
"The StepOne™ Real-Time PCR System is a 48-well, low-throughput Real-Time PCR instrument perfect for both first-time and experienced users. The StepOne™ Real-Time PCR System can be setup in a variety of configurations and comes ready to use, out of the box, with intuitive data analysis and instrument control software. Utilizing robust LED based 3-color optical recording, the StepOne™ Real-Time PCR System is designed to deliver precise, quantitative Real-Time PCR results for a variety of genomic research applications."
"The StepOnePlus™ Real-Time PCR System is a 96-well Real-Time PCR instrument perfect for both first-time and experienced users. The StepOnePlus™ Real-Time PCR System can be setup in a variety of configurations and comes ready to use, out of the box, with intuitive data analysis and instrument control software. Utilizing robust LED based 4-color optical recording, the StepOnePlus™ Real-Time PCR System is designed to deliver precise, quantitative Real-Time PCR results for a variety of genomic research applications."
Shared 64Tb of storage between analysis and storage servers.
Used for software and algorithm testing and pipeline development.
With 41Tb data storage.
"The cluster generation process on cBot has been significantly streamlined. Innovative features such as pre-packaged reagents, a single flow cell manifold, and integrated touch screen controls make the best next generation sequencing workflow even better.
cBot isothermally amplifies cDNA fragments that have been captured by complementary adapter oligonucleotides covalently bound to the surface of Illumina flow cells. Flow cells facilitate access of bound DNA to enzymes while ensuring high stability of surface-bound template and low non-specific binding of fluorescently-labeled nucleotides. Attached DNA fragments are extended and bridge amplified to create hundreds of millions of clusters, each of which contains ~1,000 identical copies of a single template molecule."
"The HiSeq 2000 sequencing system offers unprecedented output and a breakthrough user experience. Leveraging Illumina's proven and widely-adopted, reversible terminator-based sequencing by synthesis chemistry in combination with innovative engineering, HiSeq 2000 delivers the industry's highest sequencing output and fastest data generation rate. Human interaction design features and the easiest sequencing workflow set a new standard for simplicity and user experience."
A precursor for DNA re-sequencing.
Pares down sample to expressed.
Will also make sequence capture libraries.
"Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end)."
Illumina pipeline for data assembly. Convert raw image data into intensity scores, base calls, quality scored alignments, and additional formats for downstream analysis.
A quality control tool for high throughput sequence data.
"The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size."
Perform primary analysis for Illumina's sequencing instruments.
"SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that: is flexible enough to store all the alignment information generated by various alignment programs; is simple enough to be easily generated by alignment programs or converted from existing alignment formats; is compact in file size; allows most of operations on the alignment to work on a stream without loading the whole alignment into memory; allows the file to be indexed by genomic position to efficiently retrieve all reads aligning to a locus."
"SeqMonk is a program to enable the visualization and analysis of mapped sequence data. It was written for use with mapped next generation sequence data but can in theory be used for any dataset which can be expressed as a series of genomic positions. It's main features are:
- Import of mapped data from mapped data (BAM/SAM/bowtie/maq etc)
- Creation of data groups for visualisation and analysis
- Visualisation of mapped regions against an annotated genome.
- Flexible quantitation of the mapped data to allow comparisons between data sets
- Statistical analysis of data to find regions of interest
- Creation of reports containing data and genome annotation"