Core D provides cutting edge genomic and proteomic tools to the members of the Program. CSHL has made a very substantial institutional commitment during the last funding cycle to development of a large next-generation sequencing facility, and has considerable capacity provided by four HiSeq and twelve llx lllumina sequencers, along with sequencing machines from Pacific BioSciences and 454. Enabled by this Core D provides as extensive set of next-generation sequencing tools applications for Program Project members. This includes RNA-Seq ,Chip-Seq and innovative DNA methylome analysis tools. In addition. Core D will allow program members to perform copy-number variation (CfvIV) and single-nucleotide variation (SNV) and other mutational analysis with the next-generation sequencing tools. In addition the Core will aid investigators in de-convolution of multiplexed shRNA screens. Core D will also enable projects that utilize next-generation sequencing technologies for analyzing DNA or RNA at the single-cell level. Core D also performs real-time PCR analysis with TaqMan and microarray services. Core D employs a world leader in the field of proteomics. Dr. Darryl Pappin. Specific services include quantitative proteome profiling using SILAC or iTRAQ, analysis of the protein content of multiprotein complexes, and analysis of post-translational modifications. Core D also provides a dedicated computational scientist who will provide Program Project members with expert analysis of the high-throughput genomic and proteomic data generated by Core D. Custom tools will be developed for Program Project members where needed. Finally, Core D acquires human tumor samples and human cancer cell lines for Program Project members from available public sources including the Cooperative Human Tissue Network and isolates DNA, RNA, or protein as needed
Genomic and proteomic analyses are now standard practices for molecular biology. Core D is committed to keeping at the leading front of technology to continue its impact, for example, in the development of improved methods for single-cell analysis of gene expression and epigenetic and copy number variations, and in continuing to develop the technology for genomic and epigenomic profiling .
| Banito, Ana; Li, Xiang; Laporte, Aimée N et al. (2018) The SS18-SSX Oncoprotein Hijacks KDM2B-PRC1.1 to Drive Synovial Sarcoma. Cancer Cell 34:346-348 |
| Skucha, Anna; Ebner, Jessica; Schmöllerl, Johannes et al. (2018) MLL-fusion-driven leukemia requires SETD2 to safeguard genomic integrity. Nat Commun 9:1983 |
| Banito, Ana; Li, Xiang; Laporte, Aimée N et al. (2018) The SS18-SSX Oncoprotein Hijacks KDM2B-PRC1.1 to Drive Synovial Sarcoma. Cancer Cell 33:527-541.e8 |
| Lin, Kuan-Ting; Ma, Wai Kit; Scharner, Juergen et al. (2018) A human-specific switch of alternatively spliced AFMID isoforms contributes to TP53 mutations and tumor recurrence in hepatocellular carcinoma. Genome Res : |
| On, Kin Fan; Jaremko, Matt; Stillman, Bruce et al. (2018) A structural view of the initiators for chromosome replication. Curr Opin Struct Biol 53:131-139 |
| Knott, Simon R V; Wagenblast, Elvin; Khan, Showkhin et al. (2018) Asparagine bioavailability governs metastasis in a model of breast cancer. Nature 554:378-381 |
| Shamay, Yosi; Shah, Janki; I??k, Mehtap et al. (2018) Quantitative self-assembly prediction yields targeted nanomedicines. Nat Mater 17:361-368 |
| Tramentozzi, Elisa; Ferraro, Paola; Hossain, Manzar et al. (2018) The dNTP triphosphohydrolase activity of SAMHD1 persists during S-phase when the enzyme is phosphorylated at T592. Cell Cycle 17:1102-1114 |
| Arun, Gayatri; Diermeier, Sarah D; Spector, David L (2018) Therapeutic Targeting of Long Non-Coding RNAs in Cancer. Trends Mol Med 24:257-277 |
| Tarumoto, Yusuke; Lu, Bin; Somerville, Tim D D et al. (2018) LKB1, Salt-Inducible Kinases, and MEF2C Are Linked Dependencies in Acute Myeloid Leukemia. Mol Cell 69:1017-1027.e6 |
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