Comprehensive genomics services for research scientists and clinicians
As of January 1, 2024, the Integrated Genomics Laboratory is one shared resource comprising the former Massively Parallel Sequencing Shared Resource, the Gene Profiling Shared Resource, and the DNA Services Core. Please be aware that the reorganization is an ongoing process, particularly regarding our iLab integration.
IGL services include RNA and DNA isolation, sequencing library preparation, and sequencing, along with custom real-time PCR, a portal for oligonucleotide ordering, and cell line authentication.
The Integrated Genomics Lab is located on the 5th floor of Richard Jones Hall on OHSU's Marquam Hill campus.
Integrated Genomics Laboratory Staff
Publication Highlights
High-throughput robust single-cell DNA methylation profiling with sciMETv2 | Nature Communications
RNA-Seq of human whole blood: Evaluation of globin RNA depletion on Ribo-Zero library method
RNA-seq from archival FFPE breast cancer samples: molecular pathway fidelity and novel discovery
Validation of MicroRNA Biomarkers for Alzheimer’s Disease in Human Cerebrospinal Fluid
Mission
Facilitate research at OHSU by providing technologies, services, and expertise for genome-wide and targeted RNA and DNA analysis offered through a coordinated pipeline of services which can be accessed at whatever point researcher requires.
IGL Updates
- For those who missed our prior announcement, we have added a NextSeq 2000. This provides a number of lower capacity flow cells compared to our NovaSeq 6000.
- Flow cell prices have dropped. All prices have changed, with notable changes for the S2 and S4 flow cells on the NovaSeq 6000 and for the P1 and P2 flow cells on the NextSeq 2000.
- Due to the lower prices on the S2 flow cells, we are able to change our shared flow cell protocol so that we can shift from the S4 flow cells to the S2 flow cells as needed. This means that sequencing turnaround times on the shared flow cells should decline substantially.
- We have recently added a 10x Genomics Chromium iX for single-cell processing. This is in addition to our original Chromium Controller. Chromium iX GEM-X reagents are less expensive than NextGEM reagents and we are lowering our processing fee to make single-cell work more affordable for our users.
Events
Check back soon for future events!
Past Events
October 15th, 2024: Intro to the IGL Nanostring Counter
Discover the Nanostring Counter! Join the Integrated Genomics Laboratory (iGL) and Nanostring Technologies for a seminar on this versatile instrument for gene profiling and more. Learn how this shared resource can benefit your research and how to access it through the IGL Core.
Our expert speakers will include:
- Bailey Longoni from Nanostring Technologies
- Steve Kurtz, PhD, OHSU researcher and Counter user
- Jinah Kim, PhD, Core Scientist and instrument trainer in the IGL
Key topics covered:
- Counter technology and applications
- OHSU research utilizing Counter technology
- Training opportunities
- How to access the instrument and related resources through the IGL Core
When: 1-2 PM, October 15th
Where: OHSU Marquam Hill Campus, Richard Jones Hall, Room 4340
Link to Seminar Slides: /sites/default/files/2024-11/OHSU%20nCounter%20Seminar%2010152024.pdf
Link to WebEx Recording: https://echo360.org/media/8cfb3e10-afe6-4962-9f17-0b499587a03e/public
June 5, 2024: High Throughput Single-Cell RNA and Methylation Analysis
Join us at the OHSU Knight Cancer Research Building on June 5 for an insightful Lunch and Learn on Scale Bio's parallelized barcoding single-cell technology. This event is for anyone looking to better understand our RNA & Methylation applications. Our goal is to inspire and educate researchers on how these methodologies can help optimize your experiments and show you how they are being integrated at OHSU.
Presenters will be Melanie Masuda, Director, Market Development at Scale Bio, Itallia Pacentine, Computational Biologist II, from the OHSU Braun Lab and Robert Searles, Director at OHSU Integrated Genomics Laboratory.
- Time: Event is 11-12 PST, with a lunch hour from 12-1 pm.
- Location: Knight Cancer Research Building is 2720 S Moody Ave. Portland, OR 97201
- please come to the front door of address listed, and somebody will let you in.
- Parking: Any external folks attending will need to find street parking for this event on Meade Street, this is city pay-to-park spots, or they may pay to park at the RLSB underground parking garage next door to the KCRB. Entry to this parking is also on Meade Street.
April 25, 2024: OHSU Epigenetics Symposium
The OHSU Epigenetics Symposium, organized by the KCVI Epigenetics Consortium, will feature keynote addresses by Dr. Marisa Bartolomei (University of Pennsylvania) and Dr. Joe Ecker (UC San Diego). The program also includes presentations from researchers focused on epigenetics and a poster session featuring graduate students, postdocs, and research staff. A reception will be held at the conclusion of the event.
- Details here
- Please, register using the link on the flyer or here: https://lp.constantcontactpages.com/ev/reg/7n3hr8f
April 24, 2024: Biostatistics Shared Resource Virtual Seminar
The OHSU Knight Cancer Institute’s Biostatistics Shared Resource (BSR) and the Oregon National Primate Research Center’s (ONPRC) Bioinformatics and Biostatistics Core (BBC) are hosting a seminar to share their advice for bulk and single cell RNA-seq projects. Topics covered include experimental design considerations, general analysis pipeline, and how investigators should interpret the delivered results.
- Questions should be directed to BSR-Admin@ohsu.edu
- Please, find the WebEx link in the flyer /sites/default/files/2024-04/BSR_Monthly%20series_April.pdf
January 29, 2024: Sample size considerations for “omics” data
"Omics" studies often involve hundreds of outcome measures, rendering traditional power analysis insufficient. This talk tackles this challenge by exploring how strategic choices in sample size and analysis methods can navigate data complexity and maximize the chance of uncovering meaningful discoveries. Basic power analysis knowledge is recommended.
Presented by Jack Wiedrick, M.S. M.A. of the Biostatistics, Epidemiology, and Research Design (BERD) Program
May 17, 2023: PacBio Discoveries Roadshow
September 20, 2023: Single-cell RNAsequencing: From START to FINISH
Are you thinking about performing a single-cell RNA Sequencing experiment? This symposium on Wednesday September 20th, from 9:00 AM to 4:00 PM, will feature sessions on multiple aspects of a single-cell RNA sequencing experiment including experimental design, experiment day, and bioinformatic analysis. Single-cell RNA sequencing product vendors will present on topics that include selecting the best single-cell RNA sequencing experimental approach for your experimental question, tips on sample preparation, and bioinformatic solutions. Finally, multiple investigators from OHSU will share about their successes with single-cell RNA sequencing.
May 24th, 2022: Portland Multiomics Discovery Symposium
Symposium to learn how Chromium single cell and Visium spatial solutions from 10x Genomics can help you push the boundaries of your research.
- Sponsored by 10x Genomics and hosted by OHSU Knight Cancer Institute.
- See 10x Genomics presentation here
June 2, 2022: Symposium on Approaches on Single-Cell Analysis
October 25, 2022: IGL Single Cell and Spatial Transcriptomic Workshop
Information and technical planning support for single cell and spatial transcriptomics studies at OHSU.
OHSU Speakers: Aude Chiot, PhD & Jonathan Nelson, PhD
Wednesday, May 19th, 2021: NanoString nCounter® Webinar
Overview of nCounter® technology, panels, customization options, and services available through the Gene Profiling Shared Resource. See this webinar and more in the Assays of Interest section on the GPSR website.
December 2nd, 2021 OCTRI Research Forum: Power and Sample Size 101
See the recording of this research forum
Please see the Winter 2022 Integrated Genomics Laboratory Newsletter for updates on new equipment, core operations, and more!