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Next Generation Sequencing

Director:   Joseph R. Testa, PhD, FACMG
Manager:
Yinfei Tan, PhD
215-728-2898
P3009
Location & Phone: P3009
215-728-2898
Pricing &
Scheduling:
Contact Yinfei Tan for pricing and scheduling.

 

The NGS Unit provides Cancer Center members a platform for gene expression and massively parallel sequencing analysis solutions for cancer research. The NGS Unit currently operates an Illumina NextSeq 500 sequencer, and services offered include the following: RNA-seq; Exome-seq; ChIP-seq; CRISPR-seq; and 10X Genomics single cell sequencing. The GF also plans to purchase a NextSeq 2000, which was introduced in 2020 to fill the need between high capacity NovaSeq 6000 and the low-medium capacity NextSeq 500. The NextSeq 2000 provides 400 million or 1 billion single reads per run when using P2 or P3 reagents, respectively. In collaboration with the Biostatistics & Bioinformatics Facility (BBF), the NGS Unit helps PIs with data analysis and central storage. This Unit uses a centralized data management system, CaArray from the NCI, which has been established to ensure precise data archival, storage, and easy retrieval.

Two types of services are offered to PIs: full service and customer service. Full service includes sample preparation, library construction and deep sequencing process, as well as data analysis, all performed by the facility. The customer service helps investigators perform their own process using facility equipment and reagents under the guidance of the facility specialist.

Examples of NGS applications. RNA fusion analysis of a human T-cell leukemia sample, depicting a CDK6 / HOXA11-AS fusion gene (top left); heatmap of RNA-seq data depicting differential mRNA expression in parental mesothelioma cells versus cells following RIPK3 knockdown (top right); correlation analysis of of RNA-seq data from various mouse tissues (bottom left); and ChIP-seq analysis of Tcf7 binding of Fbwx7 promoter in mouse T-cell lymphoma (bottom middle).
This facility suppports Fox Chase Cancer Center's Cancer Center Support Grant (CCSG) from the National Cancer Institute.

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