Benaroya Research Institute
Vivian Gersuk
1201 9th Ave
Seattle, WA 98101
https://www.benaroyaresearch.org/our-research/core-labs/genomics-core
RRID: RRID:SCR_026658
1.) Doni Jayavelu N, Benson B, Dela Cruz PC, Powell WT, Rich LM, Vanderwall ER, Gates CR, Nagel AJ, White MP, Samanas NB, Whitfield K, Hallstrand TS, Ziegler SF, Altman MC, Debley JS (2025 Dec 22). Bronchial epithelial transcriptome reveals dysregulated interferon and inflammatory responses to rhinovirus in exacerbation-prone pediatric asthma. JCI insight, 10(24), . . PMCID: 12890530.
2.) Nutt WS, Kluesner MG, Bingham E, Gad E, Miller D, Zepeda V, Snyder AJ, Marsh SA, Liudahl SM, Hoffman M, LeBlanc L, Volfbeyn ME, Garrison SM, Sarvothama M, Barry KC, Headley MB, Marcondes M, Srivastava S (2025 Dec 15). NKTR-255, a polymer-conjugated IL-15, synergizes with CAR-T cell therapy to activate endogenous anti-tumor immunity and improve tumor control bioRxiv, (), 2025.12.11.693768. . PMCID: 12746013.
3.) dela Cruz PC, Benson B, Jayavelu ND, Powell WT, Rich LM, Vanderwall ER, Gates CR, White MP, Samanas NB, Whitfield K, Hallstrand TS, Ziegler SF, Deutsch GH, Altman MC, Debley JS (2025 Dec 8). IL-13 Modulates Antiviral Effector and Proinflammatory Pathways in Rhinovirus-Infected Pediatric Bronchial Epithelium bioRxiv, (), 2025.12.06.692776. . PMCID: 12713584.
4.) DeBerg HA, Fahning ML, Varkhande SR, Schlenker JD, Schmitt WP, Gupta A, Singh A, Gratz IK, Carlin JS, Campbell DJ, Morawski PA (2025 Nov). T Cells Promote Distinct Transcriptional Programs of Cutaneous Inflammatory Disease in Keratinocytes and Dermal Fibroblasts. The Journal of investigative dermatology, 145(11), 2811-2827.e8. . PMCID: 12353163.
5.) Jayavelu ND, Benson B, dela Cruz PC, Powell WT, Rich LM, Vanderwall ER, Gates CR, Nagel AJ, White MP, Samanas NB, Whitfield K, Hallstrand TS, Ziegler SF, Altman MC, Debley JS (2025 Oct 19). Transcriptomic Profiling of Bronchial Epithelium Reveals Dysregulated Interferon and Inflammatory Responses to Rhinovirus in Exacerbation-Prone Pediatric Asthma bioRxiv, (), 2025.10.19.683298. . PMCID: 12633054.
6.) Avanessian SC, van den Bijgaart RJ, Chew NW, Supper VM, Tang TT, Zhang Y, Zhao YQ, Abe K, Gauthier J, Barry KC (2025 Oct 13). IL-2/IL-15 signaling induces NK cell production of FLT3LG augmenting anti-PD-1 immunotherapy Cancer immunology research, (), 10.1158/2326-6066.CIR-24-1259. . PMCID: 12582536.
The Genomics Core provides resources to BRI and external investigators for genomics analysis, from sample processing through data generation, as well as basic bioinformatics analysis, provided by our Bioinformatics Core Team. Currently available technologies focus on Illumina RNA and DNA sequencing. RNA-seq can be performed from a variety of sample types, including purified total RNA, cell populations (including low input samples of 50-1000 cells), or single cells (either plate-sorted rare populations or high-throughput 10x single-cell analyses). DNA-seq pipelines can also be performed, including bulk CUT&Tag/CUT&RUN, and ATAC-seq and single cell ATACseq and multiome capture. Custom prepared libraries can also be submitted for sequencing.
The Core laboratory houses three Illumina sequencers, two NextSeq2000 instruments and a Miseq, plus a 10x Chromium X and a 10x CytAssist. The Chromium X is able to run GEM-X assays on fresh cells and Flex assays on fixed cells. The CytAssist works to perform spatial profiling using Visium HD technology.
Additional equipment includes a ThermoFisher Kingfisher Flex, for extracting nucleic acid from a variety of sample types using magnetic bead technology with a throughput of up to 96 samples. Two Qiagen QIAcube Connect instruments automate extraction of nucleic acid using spin column technology. Ancillary equipment for sample processing includes a Formulatrix Mantis Liquid Handler, an Agilent TapeStation 4200 (to measure RNA/DNA integrity and size), and a Tecan NanoQuant (for high throughput sample quantitation).
