Our goal is to generate genomic, transcriptomic, epigenomic & metagenomic information for basic and clinical research. Our mission is to make complex technologies and methodologies available and interpretable to the research community.
BFG/AGCT Core Seminar Series
Speakers: Anja Bastian, PhD-10x Genomics
Jason Kim-10x Genomics
Jasmine Plummer, PhD-AGCT Core
Title: Envision new dimensions: Spatially map and quantify the whole transcriptome in the tissue context with Visium Spatial Solutions
Summary: Assessing gene expression with morphological context is critical in our understanding of biology and the progression of disease. Historically, it has been challenging to spatially interrogate complex heterogeneous tissues in a high-throughput manner, especially without previously generated assumptions about the genes being expressed. With Visium Spatial Solutions researchers can now map the whole transcriptome with morphological context.
Join us for this seminar to learn how Visium Spatial Solutions from 10x Genomics give you a comprehensive understanding of the relationships between cellular function, phenotype, relationships, and location in intact tissue sections. Discover novel insights into normal development, disease pathology, and clinical translational research.
10x Genomics and AGCT Core
Visium Spatial Gene Expression Grant Program
10x Genomics and the AGCT Core are pleased to announce a Visium Spatial Gene Expression grant program for innovative investigators at CSMC! This award covers 10x Genomics' kits for a pilot project of up to 2 tissue sections using Visium Spatial Gene Expression Solution, which provides whole transcriptome gene expression information within the context of the tissue (Core fees and sequencing costs are not included.) Submit abstracts by September 28, 2020. Open to Cedars-Sinai investigators only.
Mission Bio Tapestri at AGCT Core
The AGCT Core is on of the first genomics cores in Los Angeles to have the Tapestri from Mission Bio. The Mission Bio Tapestri platform is the first and only single cell multi-omics platform capable of detecting SNVs, CNVs, and protein changes simultaneously from the same cell. The Tapestri platform can be used to detect rare subclones (down to 0.1%), identify true mutation co-occurance in clonal populations, resolve zygosity, and reconstruct phylogenetic lineages. Compatible with fresh or frozen cells or tissue, as well methanol-fixed cells. Capture from 5,000-10,000 cells. Pre-designed targeted panels for hematologic and solid tumors available. Custom panels can be designed using the Tapestri Designer.
10x Genomics Chromium Connect at AGCT CORE
The AGCT Core, a 10x Genomics Certified Service Provider, is the first genomics core in Los Angeles to have the Chromium Connect from 10x Genomics. The Chromium Connect automates 10x Genomics’ scRNA-Seq assay, going from single cells to sequencing-ready libraries with minimal sample handling using an integrated and validated solution. Reduce errors from manual pipetting and minimize technical variation to generate consistent and reproducible single cell gene expression results across experiments, users, and sites. Run up to 8 samples in parallel and capture from 500-10,000 cells per sample.
Miltenyi Biotec Instruments for Single Cell Sample Preparation
Sample preparation for single cell assays is critical for successful cell captures and for high quality data. The AGCT Core has a suite of Miltenyi Biotec instruments to prepare high quality single cell suspensions. The gentleMACS Octo Dissociator with Heaters offers standardized tissue dissociation into single cells. The autoMACS Pro Separator, in combination with MACS MicroBeads, provides automated cell isolation of virtually any cell type. The MASCQuant Tyto Sorter sorts labelled cells without high pressure or decompression, resulting in higher viability compared to conventional droplet sorting procedures. The MACSQuant Analyzer 16 Flow Cytometer fully automates cell staining and data acquisition.
Miltenyi MACSQuant Tyto Sorter
Sample preparation for single cell assays is critical The AGCT Core, a 10x Genomics Certified Service Provider, is the first genomics core in Los Angeles to have the Chromium Connect from 10x Genomics. The Chromium Connect automates 10x Genomics’ scRNA-Seq assay, going from single cells to sequencing-ready libraries with minimal sample handling using an integrated and validated solution. Reduce errors from manual pipetting and minimize technical variation to generate consistent and reproducible single cell gene expression results across experiments, users, and sites. Run up to 8 samples in parallel and capture from 500-10,000 cells per sample.
Latest Papers + Studies
Noushmehr H, Monteiro A, Pharoah P, Pasaniuc B, Gayther SA. A transcriptome-wide association study of high-grade serous epithelial ovarian cancer identifies new susceptibility genes and splice variants. Nature Genetics. May 2019 PDF
Skalski JH, Limon-Tello JJ, Sharma P, Gargus MD, Ngyuen C, Tang J, Coelho AL, Hogaboam CM, Crother TR, Underhill DM. Expansion of commensal fungus Wallemia mellicola in the gastrointestinal mycobiota enhances the severity of allergic airway disease in mice. PLOS Pathogens. 2018 PDF
Rajamani U, Gross AR, Hjelm BE, Sequeira A, Vawter MP, Tang J, Gangalapudi V, Wang Y, Andres AM, Gottlieb RA, Sareen D.Super-Obese Patient-Derived iPSC Hypothalamic Neurons Exhibit Obesogenic Signatures and Hormone Responses. Cell Stem Cell. 2018 PDF
Ljubimova JY, Braubach O, Patil R, Chiechi A, Tang J, Galstyan A, Shatalova ES, Kleinman MT, Black KL, Holler E. Coarse particulate matter (PM2.5-10) in Los Angeles Basin air induces expression of inflammation and cancer biomarkers in rat brains. Sci Rep. 2018 PDF
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