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JUMP TO TOPIC (newest posts are at the top):
SERVICE & INSTRUMENT NEWS
- HiSeq 4000 service is ending on June 1st (posted 5/20/21)
- Illumina NovaSeq now available! (posted 4/15/21)
- GC3F is now a Certified Service Prover (CSP) for Sequel II services! (posted 3/15/21)
EVENTS
- PacBio Global Virtual User Meeting: Upcoming meeting on Tuesday, Nov. 9 (posted 11/2/21)
- PacBio Journal Club: Upcoming meeting on Wednesday, June 9 (posted 5/19/21)
- UO's Single Cell Groupie: Upcoming meeting on Friday, May 21 (posted 5/17/21)
- PacBio CSP Virtual Launch Party: Tuesday, April 27, 2021 (posted 4/21/21)
- UO's Single Cell Groupie: Upcoming meeting on Friday, May 16 (posted 4/12/21)
- 10x Visium Spatial Transcriptomics Grant Program: through April 16, 2021 (posted 3/24/21)
- UO's Single Cell Groupie: Upcoming meeting on Friday, March 19 (posted 3/18/21)
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ALL POSTS IN CHRONOLOGICAL ORDER BELOW!
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PacBio Global Virtual User Meeting 2021:
Tuesday, November 9, 2021 @ 8am-2pm PST (Americas region)
Featuring GC3F's own Research Assistant Maggie Weitzman
on the Sample Prep Expert Panel at 11:30am PST!
Highly accurate long-read sequencing, or HiFi sequencing, is being used around the world to inspire discoveries in human biomedical research, plant and animal sciences, and microbiology and infectious disease. This year, the Global Virtual User Meeting will showcase research using PacBio powered technology from whole genome sequencing for de novo assembly to comprehensive variant detection to RNA sequencing and more!
Register now for a 24-hour virtual journey (with 3 sessions for each global region) to join fellow researchers and hear from experts to learn how HiFi sequencing is expanding knowledge of genomes and inspiring advancements in science. On the agenda page, simply filter by the region of your choice, or this agenda link is pre-filtered for the Americas session (8am-2pm PST).
Hope to see you there!
If you want to get started on your own PacBio project, contact GC3F at genomics@uoregon.edu to discuss project details, and then it's as easy as creating an iLab account to submit your samples!
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Notice: HiSeq 4000 Service ending on June 1st
After a years of very productive use, our HiSeq 4000 will be going offline at the end of May. We will make sure that all existing submissions are either loaded on HiSeq runs before then, or sequenced on our new NovaSeq 6000. If you absolutely must have HiSeq data (additional replicates for a long running project, etc.), please contact us and we will do our best to accomodate your request.
Please note that all of the NovaSeq run modes now provide a lower cost per GB of data than the HiSeq 4000. This includes NovaSeq SP lanes, which are roughly equivalent in output to HiSeq 4000 lanes. In addition, the NovaSeq has proven to be fully compatible with every library type we have tried (including RAD-seq), so we are confident that making the switch to the new platform will benefit all of our existing HiSeq users!
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Upcoming PacBio Journal Club:
Wednesday, June 9, 2021 @ 10am
Join PacBio for their quarterly SMRT Science Journal Club, which provides researchers a platform to showcase their publications involving PacBio HiFi data.
Plus don't miss the breakout sessions where authors will be available for Q&A, meet and greet, and further discussion.
SMRT Science Journal Club:
Date: Wednesday, June 9, 2021
Time: 10:00 - 11:00 a.m. PDT
Featured Publications:
A Spatially Resolved Brain Region and Cell Type-Specific Isoform Atlas of the Postnatal Mouse Brain
Anoushka Joglekar, Weill Cornell Medicine
AAV-Genome Population Sequencing of Vectors Packaging CRISPR Components Reveals Design-Influenced Heterogeneity
Phillip Tai PhD, University of Massachusetts Medical School
Hope to see you there!
If you want to get started on your own PacBio project, contact GC3F at genomics@uoregon.edu to discuss project details, and then it's as easy as creating an iLab account to submit your samples!
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Upcoming meeting for UO's Single Cell (SC) Groupie:
Friday, May 21, 2021 @ 11am
UO's Single Cell (SC) Groupie is a platform for selected speakers and UO scienstists to present their own SC work for feedback, prepare for a conference talk, facilitate a journal club of a relevant SC manuscript, or use the time as a brainstorming session for their next SC experiment. The SC Groupie also regularly features seminar topics from 10x Genomics staff scientists!
The next SC Groupie meeting is Friday, May 21, 2021 @ 11am. Please contact SC Groupie organizer Michelle Massaquoi (msconce@uoregon.edu) to request the Zoom link and password.
Dr. John Postlethwait from the University of Oregon's Institute of Neuroscience will be presenting:
An adult three dimensional gene expression atlas for zebrafish
If you want to get started on your own 10x Genomics Single Cell project, contact GC3F at genomics@uoregon.edu to discuss project details, and then it's as easy as creating an iLab account to submit your samples!
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Join us on Tuesday, April 27, 2021 to celebrate GC3F getting certified as a PacBio Certified Service Provider (CSP) at our Virtual Launch Party!
Our CSP Launch Party event, on Tuesday, April 27, 2021 at 2:30pm PDT, will feature talks from highlighted scientists who have used GC3F's PacBio services to advance their research, as well as talks from PacBio staff scientists to provide updates on the latest SMRT Sequencing applications and capabilities.
Following the scheduled talks, we'll also be holding a social hour for you to meet PacBio & GC3F scientists and discuss ideas for your future projects! The list of speakers and topics is below, and you can also download a PDF of the event flyer here.
Attendance to this virtual event is FREE! REGISTERE HERE to reserve your seat. We look forward to seeing you there!
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Illumina NovaSeq now available in GC3F!
Thanks to a generous award from the Murdock Charitable Trust, GC3F is now offering Illumina sequencing services on a NovaSeq 6000 sequencer. The NovaSeq will be taking the place of our workhorse HiSeq 4000, and offerings the following advantages over the older platform:
- Multiple output modes from 400M up to 2500M read pairs per lane
- Lower cost per Gbp than HiSeq 4000, even in the lowest NovaSeq output mode (SP)
- Lowest cost per Gbp of any available sequencing platform in high output (S4) mode
- Fewer lanes per flowcell = less lead time waiting for lane submissions from other users needed to launch runs
- Full compatibility with all Illumina library types
Log in to iLab to submit a sample to run on the NovaSeq!
Pricing info for single-lane NovaSeq sequencing
Run Type |
Internal Rate |
External Rate |
Run Configurations |
Read Pairs per lane** |
| S4 300 Cycle | $4500 | $5625 | PE 2x150 | 2-2.5 billion+ |
| S4 35 Cycle | $3300 | $4163 | SR 53*, PE 2x32* | 2-2.5 billion+ |
| S1 300 Cycle | $3300 | $4163 | PE 2x150 | 650-800 million+ |
| S1 100 Cycle | $2490 | $3113 | SR 118*, PE 2x59* 10X scRNA | 650-800 million+ |
| SP 500 Cycle | $2700 | $3375 | PE 2x250 | 325-400 million+ |
| SP 300 Cycle | $1980 | $2475 | PE 2x150 | 325-400 million+ |
| SP 100 Cycle | $1440 | $1800 | SR 118*, PE 2x59* 10X scRNA | 325-400 million+ |
*All NovaSeq kits contain sufficient reagent to sequence an additional 38nt beyond the specified cycle number. These can be used for 10X cell barcodes, long dual index reads, or extended read length for the library inserts
**These are the official Illumina output specs and are conservative. Real world performance will often exceed these read numbers
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Upcoming meeting for UO's Single Cell (SC) Groupie:
Friday, April 16, 2021 @ 11am
UO's Single Cell (SC) Groupie is a platform for selected speakers and UO scienstists to present their own SC work for feedback, prepare for a conference talk, facilitate a journal club of a relevant SC manuscript, or use the time as a brainstorming session for their next SC experiment. The SC Groupie also regularly features seminar topics from 10x Genomics staff scientists!
The next SC Groupie meeting is Friday, April 16, 2021 at 11AM. Please contact SC Groupie organizer Michelle Massaquoi (msconce@uoregon.edu) to request the Zoom link and password.
Dr. Sonya MacParland from the Toronto General Hospital Research Institute and the University of Toronto wil be presenting:
Behind the Mask: Uncovering the Secrets of the Liver with Single Cell Resolution.
Dr. MacParland is an award-winning UHN scientist who has mapped thousands of cells within the human liver, including distinct macrophage populations. She is interested in understanding the liver as a unique immunological organ, where immune dysregulation of the liver is involed in many diseases.
If you want to get started on your own 10x Genomics Single Cell project, contact GC3F at genomics@uoregon.edu to discuss project details, and then it's as easy as creating an iLab account to submit your samples!
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10x Genomics Visium Spatial Transcriptomics Grant Program:
Submit your abstract by Friday, May 14, 2021
UO's GC3F (Genomics & Cell Characterization Core Facility)
is pleased to announce our collaboration with 10x Genomics and
UO's HGeM (Histology & Genetic Modification Core Facility) to sponsor a 10x Visium Spatial Transcriptomics Grant Program!
The selected winner will receive consultation, tissue sectioning and staining by HGeM, imaging and library prep with standard library QC by GC3F, and Illumina sequencing by GC3F for up to 4 samples for a pilot project using the 10x Visium application -- all at no cost!
Uncover the “Where” for every “What” when you map the location of gene expression in tissue
The relationship between cells and their relative locations within a tissue sample can be critical to understanding disease pathology. Visium is a groundbreaking spatial transcriptomics technology that allows scientists to measure all the gene activity in a tissue section and map where the activity is occurring. Already, this technology is leading to new discoveries that will prove instrumental in helping scientists gain a better understanding of biological processes and disease, but we want to hear from you. Share your ideas on how impactful and useful this technology will be in excelling your scientific research.
To submit an abstract for consideration on this grant program, please visit the UO & Visium Core Lab Grant Program Submission Page. 10x is accepting applications through Friday, May 14th, 2021.
Abstracts should include a description of your pilot experiment and overall project goals. Applicants must hold primary research positions at University of Oregon and must be planning to support a broader research aim for which they need pilot data.
Check the links below for more info on 10x Visium technology:
- Visium Spatial Transcriptomics product page
- Visium Spatial Transcriptomics high-level protocol overview
- Visium document resources - Tissue prep, user guide and protocol planners
- Visium webinars
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Upcoming meeting for UO's Single Cell (SC) Groupie:
Friday, March 19, 2021 @ 11am
Here at OU, there is a lot of excitement about 10x Single Cell Transcriptomics technology. The Single Cell (SC) Groupie was created as a platform for our many SC-interested scientists and labs to meet on a semi-regular basis, where selected speakers have the option to present their own SC work for feedback, prepare for a conference talk, facilitate a journal club of a relevant SC manuscript, or use the time as a brainstorming session for their next SC experiment. The SC Groupie also regularly features seminar topics from 10x Genomics staff scientists!
The next SC Groupie meeting is this Friday, March 19, 2021 at 11AM. Please contact SC Groupie organizer Michelle Massaquoi (msconce@uoregon.edu) to request the Zoom link.
Mea Songco and Gabrielle Coffing from the Niell Lab will be presenting:
Molecular organization of the octopus visual system using a single cell RNA-sequencing approach
We at GC3F have had the pleasure of working on numerous genomics projects with the octopus researchers at UO using 10x Genomics Single Cell technology, as well as with Iso-Seq and HiFi genomic sequencing using PacBio SMRT technology. We are excited to hear about some of their research findings at this meeting!
If you want to get started on your own 10x Genomics Single Cell project, contact GC3F at genomics@uoregon.edu to discuss project details, and then it's as easy as creating an iLab account to submit your samples!
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GC3F IS NOW A CERTIFIED SERVICE PROVIDER (CSP)
FOR PACBIO SEQUEL II SERVICES !!!
Here at GC3F, we continue to expand our capabilities in long-read PacBio Single Molecule, Real-Time (SMRT) sequencing for generating high-quality genome assemblies, comprehensive transcriptome analyses, structural variant analyses, and epigenetic information.
As a proven provider of PacBio services since 2017, and now a Certified Service Provider starting in 2021, we offer the Sequel II System for affordable, high-throughput studies of microbes, plants, animals, and humans.
PacBio SMRT technology consistently produces some of the longest average read lengths available in the industry. These long read lengths combined with high consensus accuracy (up to 99.99% = Q40 -- or better!), uniform coverage, and simultaneous epigenetic detection means that SMRT Sequencing delivers valuable insights that previously have been unavailable to the scientific community.
GC3F has achieved the PacBio Certified Service Provider status by undergoing a rigorous validation and training process. The certification shows that our lab can deliver the highest-quality services for SMRT Sequencing platforms.
Contact us at genomics@uoregon.edu to get started on your next SMRT Sequencing project, and create your iLab account to submit your samples today!
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NEW POLICY ON DATA RETENTION
We have had an increasing number of requests for the retrieval of old sequencing data from our archive. While we are always happy to help whenever we can, a couple of issues have arisen surrounding this:
1) Our sequence data archive should not be relied upon as a secure storage location. Old data is written to single, non-redundant drives, and the probability of hardware failure is significant. We have elected not to include the cost of long-term secure data storage in our sequencing rates.
2) Locating and re-posting old sequence data for download takes a significant amount of time, and there is a cost associated with that.
For these reasons, we are enacting the following policy:
Your data will be available at the indicated URL for 30 days from the date it was originally published. Please back up your data on at least two separate hard drives, preferably in multiple geographic locations (e.g. work and home). We recommend doing this immediately.
If you have lost your data after the 30 days have passed, we maintain a cold storage system as a last hope to retrieve your data. This cold storage system is a minimal effort, and is *not* designed for the longevity of your data (i.e. single hard drive storage, likely to fail).
If you have experienced a data loss event, please submit a Data Retrieval request through our iLab site under the "Request Services" tab.
Each lane or cell of data incurs a $100 fee upon successful retrieval. GC3F makes no guarantee on the timeliness of a data retrieval attempt. GC3F is not responsible and does not provide any warranty for data that have been published more than 30 days prior.
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FAQs ON GC3F's OPERATIONAL STATUS DURING COVID-19 PANDEMIC
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Are GC3F operations back to normal for the most part? YES!
Thanks for your patience while we experienced some processing delays as our staff was pulled from our normal GC3F duties to establish and operate the new COVID-19 testing facility on campus. New staff have now been hired for the COVID-19 lab, which means GC3F staff are back in the core and things are (mostly) back to normal here! We are currently accepting all types of service requests and sample prep projects, from both internal and external researchers.
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Can I access the GC3F to use the instrumentation? YES!
Please read and carefully adhere to our PPE, disinfection, & social distancing rules HERE (hard copies are also posted up around the core). We are strictly enforcing these rules! Please also remember to sign up on the iLab calendar if your instrument requires it.
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What do GC3F turnaround times look like these days?
If you are awaiting completion of a current service request, thanks for your patience while we ramp back up in the core and work hard to clear the queue backlogs. Rest assured that we are continuing to process your requests as quickly as we can. Also, remember that you can check the status of your requests and view your "place in line" any time by viewing the Sample Prep QUEUE, Illumina Sequencing QUEUE, or PacBio Sequencing QUEUE linked at the top of the <<< LEFT PANEL MENU <<< of this website.
If you are submitting a new service request, please expect some minor delays as we clear the backlogs and begin to return to normal processing times. If you have a time-sensitive service request, please contact us to coordinate your project and to get a better estimate of turnaround time. As always, we will do our best to help you meet pressing deadlines for critical projects.
Also, please continue to refer to this statement about turnaround times that is posted around our website:
We do our best to give an accurate estimate of turnaround time when service requests are submitted. These estimates are not guarantees and occasionally change due to unforeseen circumstances (instrument maintenance/repairs, staff sick leave, etc.). Please let us know if you have a hard deadline on project completion when you submit your service request and we will take measures to ensure that we either meet that deadline or inform you ASAP if circumstances beyond our control will cause us to miss it. Thanks!
We sincerely appreciate your patience and understanding during these extraordinary times! Please contact us if you have any questions or concerns.
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GC3F ACCESS DURING COVID-19 PANDEMIC
We are currently operating according to policies described in our approved Stage 1 Recovery Plan.
A summary of these policies is posted up around the core, as well as HERE.