APPLIED GENOMICS,COMPUTATION
AND TRANSLATIONAL CORE
The AGCT Core generates genomic, transcriptomic, epigenomic & metagenomic information for basic and clinical research. We make complex technologies and methodologies available and interpretable to the research and clinical community.
As a Certified Service Provider, we specialize in 10x Genomics Single Cell Sequencing and Spatial Gene Expression Assays.
Events
BFG/AGCT Core Seminar Series
10.19.2021
Speaker: Jason H. Moore, PhD. FACMI
Title: Automated Genetic Analysis
Date: 10/26/2021
Time: 10:00AM-11:00AM
Location: Zoom
News
10X Genomics Spatial Biology Symposium
10x Genomics will be holding a Spatial Biology Symposium on Thursday 10/14/21 starting at 9AM. Jasmine Plummer, the Associate Director of the Applied Genomics Shared Resource, will be a panel discussion speaker during the Translational Research Session starting at 11:15AM. Hear how she used a multiomic approach to identify transcription factors whose networks resolve subcortical regions of the developing human brain which are not seen by scRNA-Seq, scATAC-Seq, spatial RNA-Seq or ChIP-Seq alone
New Equipment
The Singulator is a benchtop hands-off dissociator that provides both whole-cell and nuclei tissue dissociations. The S100 model comes with a chilling chamber for cold dissociation to decrease transcriptional stress response and dissociation bias for nuclei isolation. Protocols are quick and easy to use, with the ability to make small changes to suit the tissue of interest. Cells isolation take anywhere from 20-60min while nuclei only take 7min to process. The singulator is a new addition to our Sample Preparation workflow with high reproducibility and viability.
Featured Publications
JAMA.
January 2021
Emergence of a Novel SARS-CoV-2 Variant in Southern California. Zhang W.J, Plummer J.T, Vail E, et. al
A spike in COVID-19 has occurred in Southern California since October 2020. Analysis of SARS-CoV-2 in Southern California prior to October indicated most isolates originated from clade 20C that likely emerged from New York via Europe early in the pandemic.1 Since then, novel variants of SARS-CoV-2 including those seen in the UK (20I/501Y.V1/B.1.1.7), South Africa (20H/501Y.V2/B.1.351), and Brazil (P.1/20J/501Y.V3/B.1.1.248) have emerged, with the concern of increased infectivity and virulence.2,3 Thus, we analyzed variants of SARS-CoV-2 in Southern California to establish whether one of these known strains or a novel variant had emerged.
Science Advances.
June 2021
Mesenchymal growth hormone receptor deficiency leads to failure of alveolar progenitor cell function and severe pulmonary fibrosis. Xie T, Kulur V, Liu N, Deng N, Wang Y, et. al
Recent studies have identified impaired type 2 alveolar epithelial cell (ATII) renewal in idiopathic pulmonary fibrosis (IPF) human organoids and severe fibrosis when ATII is defective in mice. ATIIs function as progenitor cells and require supportive signals from the surrounding mesenchymal cells. The mechanisms by which mesenchymal cells promote ATII progenitor functions in lung fibrosis are incompletely understood. We identified growth hormone receptor (GHR) is mainly expressed in mesenchymal cells, and its expression is substantially decreased in IPF lungs. Higher levels of GHR expression correlated with better lung function in patients with IPF. Profibrotic mesenchymal cells retarded ATII growth and were associated with suppressed vesicular GHR expression. Vesicles enriched with Ghr promote ATII proliferation and diminished pulmonary fibrosis in mesenchymal Ghr-deficient mice. Our findings demonstrate a previously unidentified mesenchymal paracrine signaling coordinated by GHR that is capable of supporting ATII progenitor cell renewal and limiting the severity of lung fibrosis.
Latest Papers + Studies
Porritt RA, Zemmour D, Abe M, Lee Y, Meena Narayanan M, Teixeira de Carvalho T, Gomez AC, Martinon D, Santiskulvong C, Fishbein MC, Chen S, Crother TR, Shimada K, Arditi M, Noval Rivas M. NLRP3 Inflammasome Mediates Immune-Stromal Interactions in Vasculitis. Circ Res. 2021 Sep 14 PDF
Porritt RA, Paschold L, Rivas MN, Cheng MH, Yonker LM, Chandnani H, Lopez M, Simnica D, Schultheiß C, Santiskulvong C, Van Eyk J, McCormick JK, Fasano A, Bahar I, Binder M, Arditi M. HLA class I-associated expansion of TRBV11-2 T cells in multisystem inflammatory syndrome in children. .J Clin Invest. 2021 May 17 PDF
Xie T, Kulur V, Liu N, Deng N, Wang Y, Rowan SC, Yao C, Huang G, Liu X, Taghavifar F, Liang J, Hogaboam C, Stripp B, Chen P, Jiang D, Noble PW. Mesenchymal growth hormone receptor deficiency leads to failure of alveolar progenitor cell function and severe pulmonary fibrosis. Sci Adv. 2021 Jun 9. PDF
Lin YN, Mesquita T, Sanchez L, Chen YH, Liu W, Li C, Rogers R, Wang Y, Li X, Wu D, Zhang R, Ibrahim A, Marbán E, Cingolani E. Extracellular vesicles from immortalized cardiosphere-derived cells attenuate arrhythmogenic cardiomyopathy in desmoglein-2 mutant mice. Eur Heart J. 2021 Sep 14. PDF
Liu X, Rowan SC, Liang J, Yao C, Huang G, Deng N, Xie T, Wu D, Wang Y, Burman A, Parimon T, Borok Z, Chen P, Parks WC, Hogaboam CM, Weigt SS, Belperio J, Stripp BR, Noble PW, Jiang D. Categorization of lung mesenchymal cells in development and fibrosis. iScience. 2021 May 19. PDF
Shiao SL, Kershaw KM, Limon JJ, You S, Yoon J, Ko EY, Guarnerio J, Potdar AA, McGovern DPB, Bose S, Dar TB, Noe P, Lee J, Kubota Y, Maymi VI, Davis MJ, Henson RM, Choi RY, Yang W, Tang J, Gargus M, Prince AD, Zumsteg ZS, Underhill DM. Commensal bacteria and fungi differentially regulate tumor responses to radiation therapy. Cancer Cell. 2021 Sep 13. PDF
Wenjuan Zhang, PhD; Brian D. Davis, BSc; Stephanie S. Chen, BSc; Jorge M. Sincuir Martinez, BS; Jasmine T. Plummer, PhD; Eric Vail, MD. Emergence of a Novel SARS-CoV-2 Variant in Southern California. JAMA. January 2021 PDF
Li C, Peng Z, Wang Y, Lam G, Nissen N, Tang J, Yuan X, Lewis M, Greene MI, Pandol SJ, Wang Q. Epithelial cell transforming 2 is regulated by Yes-associated protein 1 and mediates pancreatic cancer progression and metastasis. Physiol Gastrointest Liver Physiol. 2021 Mar 1. PDF
Shaharuddin SH, Wang V, Santos RS, Gross A, Wang Y, Jawanda H, Zhang Y, Hasan W, Garcia G Jr, Arumugaswami V, Sareen D. Deleterious Effects of SARS-CoV-2 Infection on Human Pancreatic Cells.. Front Cell Infect Microbiol. 2021 Jun 23. PDF
Li C, Peng Z, Wang Y, Lam G, Nissen N, Tang J, Yuan X, Lewis M, Greene MI, Pandol SJ, Wang Q. Epithelial cell transforming 2 is regulated by Yes-associated protein 1 and mediates pancreatic cancer progression and metastasis. Am J Physiol Gastrointest Liver Physiol. 2021 Mar 1. PDF
Gonzalez TL, Eisman LE, Joshi NV, Flowers AE, Wu D, Wang Y, Santiskulvong C, Tang J, Buttle RA, Sauro E, Clark EL, DiPentino R, Jefferies CA, Chan JL, Lin Y, Zhu Y, Afshar Y, Tseng HR, Taylor K, Williams J 3rd, Pisarska MD. High-throughput miRNA sequencing of the human placenta: expression throughout gestation. Epigenomics. 2021 Jul PDF
Wenjuan Zhang, PhD; John Paul Govindavari, DO; Brian D. Davis, BSc; Stephanie S. Chen, BSc; Jong Taek Kim, MD; Jianbo Song, PhD; Jean Lopategui, MD; Jasmine T. Plummer, PhD; Eric Vail, MD. Analysis of Genomic Characteristics and Transmission Routes of Patients With Confirmed SARS-CoV-2 in Southern California During the Early Stage of the US COVID-19 Pandemic. JAMA Netw Open. 2020 PDF