Applied Genomics, Computation & Translational Core (Cedars-Sinai)

The Applied Genomics, Computation & Translational Core (AGCT Core) at Cedars-Sinai is a fully equipped, automated, high-throughput genomics facility offering the latest in next generation sequencing technologies, including single cell genomics, spatial transcriptomics, and bulk cell genomics. We generate and interpret single cell omics, genomics, transcriptomics, epigenomics, and metagenomics information for basic and clinical research. As a 10x Genomic Certified Service Provider, the AGCT Core specializes in single cell omics applications, including scRNA-Seq, scATAC-Seq, scV(D)J immune profiling, and scMultiome. We offer sample preparation for such assays, from fresh or frozen tissue, cryopreserved cells, fresh-frozen tissue blocks, and FFPE tissue blocks. The AGCT Core also specializes in Visium spatial transcriptomics for fresh-frozen or for FFPE tissue. Cryostat and microtome sectioning services are also available. Single cell DNA sequencing via the Mission Bio Tapestri system is also offered by the AGCT Core. The AGCT Core also offers bulk cell mRNA-Seq and total RNA-Seq for all sample types, including low-input or degraded RNA. miRNA-Seq is also available.  Our genomics offerings include whole genome and whole exome sequencing.  Our epigenomics services include ATAC-Seq and whole genome bisulfite sequencing.  For metagenomics, we offer amplicon sequencing of the V1-V2 region or all regions (V1-V9) of the 16S rRNA gene.  We also offer ITS amplicon sequencing for mycobiome studies. Sequencing-only services are also available.

We offer complete laboratory and bioinformatics analysis pipelines to accommodate standard needs, as well as work actively in collaborations to offer more sophisticated or custom solutions on most omics-wide investigations. We have set up solid pipelines associated with each sequencing service for primary data processing, including read alignment, quality control, and expression quantification (bulk & single-cell RNA-seq), variant calling (WGS/WES) or peak calling (bulk and single-cell ATAC-seq/CUT&TAG/ChIP-seq). We provide analysis for the latest in spatial transcriptomics technologies include 10x Genomics Visium for both fresh frozen and FFPE samples, as well as the GeoMx Digital Spatial Profiler. Our pipelines fully support analysis of multiomic data include 10x Genomics’ multiome and CITE-seq, and we have extensive experience analyzing data from various cell hashing techniques. We have also developed packages for in-depth, customized computational analyses driven by specific biological questions defined by investigators. Furthermore, we provide support on interpretation and presentation of results, generating extensive reports with publication-ready images, and drafting of bioinformatics and statistical methodology for manuscripts. We provide lifelong data curation and cloud storage for collaborators. 

Please visit the AGCT Core’s website for a complete list of available services, instrumentation, and detailed information about data processing and analyses.

Last updated
September 27, 2023