Genomics Core

GENOMICS CORE: SUMMARY The Genomics Core will provide centralized expertise and instrumentation for all three projects, specifically library preparation, short-read and long-read sequencing, as well as data storage and distribution. This centralization of resources will result in economies of scale as well as standardization of protocol and sequencing platforms. The Genomics Core will be led by Dr. Adriana Heguy, PhD, Professor of Pathology at the NYU Grossman School of Medicine and Director of the Genome Technology Center (GTC) at NYU Langone Health. She is an internationally known genomics scientist with >16 years running genomics facilities for cancer research. Her lab is a state-of-the-art genomic facility specializing in library preparation for short-read and long- read sequencing for numerous applications of transcriptomics, genomics and epigenomics research, including RNA-Seq and scRNA-Seq, multiple chromatin conformation sequencing modalities such as Hi-C and Hi-ChIP, ChIP-Seq/Cut&Tag, ATAC-Seq, and whole genome sequencing, as well as many others. Key instrumentation includes 3 NovaSeq 6000, 1 NextSeq 2000, and the newest PromethION 24, and 4 liquid handlers from Tecan, Beckman and Hamilton for high throughput automated RNA-Seq, scRNASeq and other library prep modalities. Dr. Heguy has worked extensively with Drs. Skok, Aifantis and Melnick during the past 4 years of the P01, generating key data featured in numerous high impact publications. The specific aims of the Genomics Core are: 1) to provide chromatin profiling and conformation library preparation (ChIP-Seq/Cut&Tag and ATAC-Seq, scATAC-Seq, Hi-C, Hi-ChIP, 4-C, Capture Hi-C) and sequencing; 2) to provide transcriptome profiling (RNA- Seq, scRNA-Seq, Perturb-Seq); 3) to perform long-read Pore-C and Nano-NOME-Seq; and 4) to facilitate data management, sharing and storage among all projects and the Computational Core, through high performance computing (HPC) resources. The Genomics Core will extend beyond the current capabilities of GTC, which is a shared resource partly supported by an NCI Cancer Center Support Grant. The Skok, Aifantis and Melnick labs will assist the Genomics Core with the standardization of long-read chromatin conformation library prep protocols, specifically Nano-NOMe-Seq, Pore C and Perturb-Seq. The Genomics Core will coordinate sample workflow with the Pathology Core, and after sequencing, with the Computational Core, with which the GTC is already seamlessly integrated. There will be two half FTEs dedicated to the generation of data for these three projects, and Dr. Heguy’s effort at 10%.