? GENOMICS CORE The Genomics Core will assist all three projects, through the standardization of protocols and sequencing platforms, thus resulting in shared expertise and economies of scale. This centralized resource will play a coordinating role for all aspects of genomic data production, including automated library preparation, sequencing, data storage and distribution. The Genomics Core will be led by Dr. Adriana Heguy, PhD, Professor of Pathology at the NYU School of Medicine and Director of the Genome Technology Center (GTC) at NYU Langone Health. She is an internationally known genomics scientist with >10 years running genomics facilities for cancer research. Her lab is a state-of-the-art fully equipped genomic facility staffed with expert personnel specializing in high volume Illumina deep sequencing and automated sample preparation for large numbers of samples and a variety of applications including RNA-Seq, ChIP-Seq, ATAC-Seq, bisulfite sequencing and chromatin conformation sequencing approaches. Dr. Heguy has worked extensively with Dr. Skok and Dr. Aifantis during the past 4 years, generating key data featured in numerous high impact publications.
The specific aims of the Genomics Core are: 1) to standardize all sample preparation and sequencing, and facilitate data sharing and storage among P01 projects and cores through high performance computing (HPC) resources; 2) to provide chromatin profiling library preps (ChIP-Seq and ATAC-Seq) and sequencing; 3) to perform chromatin conformation library preps (HiC, 4-C, 5-C, Capture HiC) and sequencing; 4) to provide exome sequencing and transcriptome profiling (RNA-Seq, scRNA-Seq) and 5) to perform whole genome and reduced representation bisulfite library preps and sequencing. The Genomics Core will extend beyond the current capabilities of the existing GTC, which is a shared resource partly supported by an NCI Cancer Center Support Grant. The Skok and Aifantis labs will assist the Genomics Core with the standardization of chromatin conformation library prep protocols, and the Melnick lab and Aifantis lab will work closely with the Core to standardize genome bisulfite sequencing protocols as well. The Genomics Core will coordinate sample workflow with the Pathology Core led by Dr. Giorgio Inghirami, which will supply human cells and nucleic acids for the projects, and after sequencing, with the Computational Core, led by Dr. Aristotelis Tsirigos, 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%.
? GENOMICS CORE The Genomics Core will assist all three projects, by processing all samples to generate genomic data. Genomic data in this application means information about the mutational status of the samples, the genes expressed in each sample, as well as the chromatin state of the cells, which regulates gene expression. Standardization, consistency of results and cost effectiveness will be provided by having all samples processed by one common lab with the required instrumentation and technical expertise. Genomic data generated by this Core will be used to advance our understanding of genomic and chromatin dysregulation in cancer.
