Winter 2019 Newsletter

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Flow cells
Pictured: Illumina NextSeq and NovaSeq flowcells and PacBio SMRT Cell.

FEATURED NEWS


next-gen

RNA-Seq | New low-cost option: $179/sample with 1-month turnaround

The UMGC launched a new Charter Service for RNA-Seq to provide a monthly shared 150 PE NovaSeq run that departs on the 1st business day of the month. The rate includes library prep and sequencing to 20 million reads/sample, but additional sequencing depth can be purchased. By batching RNA-Seq projects on an S2 or S4    flow cell, we are able to offer a competitive RNA-Seq rate with a guaranteed 1-month turnaround time. Find out more.

SERVICE NEWS & UPDATES


GBS icon

Genotyping-by-sequencing | 75 protocols developed for non-model species

As a licensed GBS service provider, we offer high-throughout, cost-effective NGS-based genotyping for UMN researchers. For species new to GBS, we minimize sequencing costs by developing species-specific protocols targeting the requested number of markers; we’ve developed GBS protocols for over 75 non-model species. If you think your research could benefit from genotyping on a genome-wide scale for SNP discovery, please reach out to gbs@umn.edu or see our website.

 

DIY geonoimics

DIY Genomics | Illumina MiSeq and NextSeq added to the DIY instruments

You asked, we listened. We’ve expanded our DIY sequencing instruments from just the Illumina iSeq (4 million reads output) to now include the MiSeq (16 million reads) and NextSeq 550 (120 or 360 million reads), giving clients with small to medium-sized sequencing projects an option to use our DIY service. As with all of our DIY instruments, training is required before instruments can be reserved. Contact Aaron Becker at next-gen@umn.edu for iSeq, MiSeq, or NextSeq training at our CCRB site.

 

gene expression

Gene Expression | UMGC named Olink Proteomics certified service provider

We are pleased to announce that the UMGC is now one of three labs in the U.S. certified by Olink Proteomics to offer their Proximity Extension Assay (PEA) technology for highly-multiplexed protein detection. Olink’s range of panels for biomarker discovery uses PEA technology to measure 92 biomarkers across 96 samples simultaneously using only 1 uL of serum, plasma, or almost any other type of biological sample. Contact Darrell Johnson for more info.

UPCOMING EVENTS


Spatial Genomics Interest Group | Ongoing 2020

Led by UMGC director, Dr. Kenny Beckman, UIC director Dr. Mark Sanders, and BLS Director Cole Drifka, the Spatial Genomics Interest Group (SGIG) provides a forum to connect UMN researchers from different disciplines with vendors of spatial genomic technologies and with three UMN core facilities (UMGC, UIC, BioNet) who are together coordinating the workflows for this multi-disciplinary field. Join SGIG to receive email updates on future meetings, pilot opportunities, and an invitation to join the group’s Slack discussion. Upcoming meeting:

NanoString DSP Technology
Thursday, January 16th
10:00 – 11:00, MRF 1-101

Join SGIG

UMGC NEWS & ANNOUNCEMENTS


Joan gabel

President Gabel visits the UMGC

Earlier this fall, we hosted the Board of Regents and President Joan Gabel, who learned about the University’s technology commercialization, highlighting our spin-off company CoreBiome and our collaborative efforts with MAISRC and MSI to release a chromosome-scale assembly of the zebra mussel genome. We were honored when President Gabel mentioned the UMGC in her inauguration speech the following week.

Welcome MiSeq #6

Our CCRB site is now home to a sixth MiSeq! To meet the need for quick, lower-output runs on single-lane flow cells paired with Illumina’s longest read length, the MiSeq has become a popular UMGC instrument for targeted sequencing of amplicons, including 16S rRNA, fungal ITS1/ITS2, eukaryotic 18S rRNA, and for the sequencing of small genomes.

Publication Acknowledgement

If your research leads to a publication, we would like to remind you that work performed and data generated by the UMGC should be formally listed in the Acknowledgements section and also included in presentations and posters. If substantial intellectual or experimental contribution was made by a UMGC scientist, a co-authorship should be considered. Please see the Association of Biomolecular Resource Facilities recommended guidelines on authorship or acknowledging contributions for core facilities.

FALL PUBLICATIONS


The UMGC develops novel genomic approaches through research and development in our Innovation Lab and also in collaboration with clients. Please see our website for our complete list of publications.

Influence of genetic polymorphism on transcriptional enhancer activity in the malaria vector Anopheles coluzzii

Nardini L, Holm I, Pain A, Bischoff E, Gohl DM, Zongo S, Guelbeogo W, Sagnon N, Vernick KD & Riehle MM. Scientific Reports. 2019 Oct 24. 9(1):15275.


Association between mitochondrial genetic variation and breast cancer risk: The Multiethnic Cohort

Li Y, Giorgi E, Beckman KB, Caberto C, Kazma R, Lum-Jones A, Haiman C, Marchand L, Stram D, Saxena R, Cheng I. PLos One. 2019 Oct 2. 14(10):e0222284.


Identification of Target Genes Mediated by Two-Component Regulators of Staphylococcus aureus Using RNA-Seq Technology

Lei T, Yang J, Becker AD, Ji Y. Methods Mol Biol. 2019 Sept 16. 2020, 2069:125-138.


Genome projects in invasion biology

McCartney MA, Mallez S, Gohl DM. Conservation Genetics. 2019 Sept 11. 20 (6):1201-1222.


Stress responses, M2 macrophages, and a distinct microbial signature in fatal intestinal acute graft-vesus-host disease

Holtan S, Shabaneh A, Betts B, Rashidi A, MacMillan M, Ustun C, Amin K, Vaughn B, Howard J, Khoruts A, Arora M, DeFor T, Johnson D, Blazar B, Weisdorf D, Wang J. JCI Insight. 2019 Aug 8. 4(17):e129762.