Massively Parallel Sequencing Shared Resource (MPSSR)

Massively Parallel Sequencing Shared Resource (MPSSR)
The OHSU Massively Parallel Sequencing Shared Resource functions as a full service genomics facility serving research scientists and clinicians with a full range of applications based upon massively parallel sequencing protocols.
OHSU begins modified operations on March 23rd, 2020. During modified operations, the research programs at OHSU are on hold to help ensure the health and safety of laboratory staff and the OHSU community. The only ongoing research will be coronavirus related. The MPSSR has been asked to remain open during the period of modified operations so that we can support coronavirus research. Our operations will be as follows:
  1. We will only accept samples for library preparation or sequencing for projects approved by the OHSU Covid-19 Research Task Force.
  2. Coronavirus researchers should still use the iLab application process to initiate work. Our forms will be modified to allow researchers to indicate that their work has been approved by the task force.
  3. We will continue to process any and all samples submitted to us before the end of the day on March 20, 2020.
  4. No samples will be processed on the MPSSR 10x Genomics Chromium system during modified operations.
  5. Ongoing operations assume that Oregon does not invoke a shelter in place order. Should that happen, we will consult with the Chief Research Officer and comply with the instructions provided to us.

About

The OHSU Massively Parallel Sequencing Shared Resource (MPSSR) was founded in 2009 to provide high quality, cost efficient short read sequencing services to help investigators examine the genetic profiles that underlie disease predisposition and to explore the fundamental operations of biological systems. In addition to sequencing services, the MPSSR offers a variety of library construction services - including genome resequencing with sequence capture and transcriptome analysis. Contact us about your proposed work to see how we can assist you.

We offer the following library preparation services: Illumina TruSeq standard and stranded RNA-seq, low input RNA-seq via Nugen Ovation and Clontech SMART-seq, single cell RNA-seq with the 10x Chromium system, miRNA libraries using the Clontech small RNA library kit, and DNA exome capture with the Illumina Nextera RapidCapture protocol. 

Following a multi-year pilot program supported by the OHSU Research Office, we now offer alignment services for “bulk” RNA-seq. We also provide alignment of all single cell RNA-seq data we generate as part of our single-cell processing protocol.

Funding for our initial Illumina GAIIx sequencer was provided by a generous grant from the M.J. Murdock Charitable Trust. Funding for our upgrade to the HiSeq 2000 was provided by OHSU. Funding for the HiSeq 2500 and the NextSeq 500 was provided by the M.J. Murdock Charitable Trust. Funding for the NovaSeq 6000 was provided by the M.J. Murdock Charitable Trust and OHSU.

The MPSSR receives support from the Knight Cancer Institute, the Portland Alcohol Research Center (PARC), and the Vaccine and Gene Therapy Institute.

MPSSR Core Informational Flyer

Quick links and quick information

Quick links

Major equipment

  • Illumina NovaSeq 6000
  • Illumina HiSeq 2500 Sequencer
  • Illumina NextSeq 500 Sequencer
  • Illumina cBot
  • 10x Genomics Chromium  Single Cell RNA-seq System
  • Covaris S220 sonicator
  • Separate servers for data collection and assembly, data distribution, and data alignment
  • LifeTechnology StepOne Real Time PCR System
  • LifeTechnology StepOnePlus Real Time PCR System
  • Agilent 2100 Bioanalyzer
  • Agilent 4200 TapeStation

Sequencing human samples

The sequence of DNA is a unique identifier that cannot be fully anonymous.  Because of this, all samples submitted to the MPSSR that have been derived from human subjects MUST be coded so that the MPSSR cannot directly identify the subject and MUST be accompanied by IRB approval.

Our NovaSeq 6000 is now up and running

Thanks to funding provided by the M.J. Murdock Charitable Trust and OHSU, we have added a NovaSeq 6000 as our primary sequencing instrument. Effective January 24th, 2020, the NovaSeq is operational and generating data for our clients. 

Contact us

The OHSU Massively Parallel Sequencing Shared Resource is located in room 5390 on the 5th floor of Richard Jones Hall on OHSU's Marquam Hill Campus in Portland, OR.

Primary contacts:

Robert Searles, Ph.D., Director
searlesr@ohsu.edu
Oregon Health and Science University
Richard Jones Hall 5327A
3181 SW Sam Jackson Park Road, Mail Code L581
Portland, OR   97239
Ph: 503-418-2736

Amy Carlos, Laboratory Manager
carlosa@ohsu.edu
Oregon Health & Science University
Richard Jones Hall 5381
3181 SW Sam Jackson Park Road, Mail Code L581
Portland, OR   97239
Ph. 503-418-9378

Attribution

MPSSR acknowledgement

When presenting and publishing results from projects processed by the Massively Parallel Sequencing Shared Resource, inclusion of the following statement is appreciated:

Short read sequencing assays were performed by the OHSU Massively Parallel Sequencing Shared Resource.

Contact the MPSSR director to report your publication for inclusion on our website.

External users

The MPSSR is again accepting samples from outside the Oregon university system. We have a new contract that needs to be reviewed and signed by both parties before work can begin. We can also provide the required OHSU tax identification information. Please note that we are not accepting samples that require us to bill foreign entities.