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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

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News

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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

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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.

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Latest Papers + Studies

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

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Contact Us

8723 Alden Dr. 
Steven Spielberg Building
Los Angeles, CA 90048

genomics@cshs.org

310-423-4066

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