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

Public Health Relevance

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 .

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Program Projects (P01)
Project #
5P01CA013106-43
Application #
8744365
Study Section
Special Emphasis Panel (ZCA1-RPRB-0)
Project Start
Project End
Budget Start
2014-01-01
Budget End
2014-12-31
Support Year
43
Fiscal Year
2014
Total Cost
$402,866
Indirect Cost
$192,242
Name
Cold Spring Harbor Laboratory
Department
Type
DUNS #
065968786
City
Cold Spring Harbor
State
NY
Country
United States
Zip Code
11724
Chakraborty, A A; Scuoppo, C; Dey, S et al. (2015) A common functional consequence of tumor-derived mutations within c-MYC. Oncogene 34:2406-9
Mazurek, Anthony; Park, Youngkyu; Miething, Cornelius et al. (2014) Acquired dependence of acute myeloid leukemia on the DEAD-box RNA helicase DDX5. Cell Rep 7:1887-99
Huang, Chun-Hao; Lujambio, Amaia; Zuber, Johannes et al. (2014) CDK9-mediated transcription elongation is required for MYC addiction in hepatocellular carcinoma. Genes Dev 28:1800-14
Saborowski, Michael; Saborowski, Anna; Morris 4th, John P et al. (2014) A modular and flexible ESC-based mouse model of pancreatic cancer. Genes Dev 28:85-97
Fellmann, Christof; Lowe, Scott W (2014) Stable RNA interference rules for silencing. Nat Cell Biol 16:10-8
Jensen, Mads A; Wilkinson, John E; Krainer, Adrian R (2014) Splicing factor SRSF6 promotes hyperplasia of sensitized skin. Nat Struct Mol Biol 21:189-97
Weissmueller, Susann; Manchado, Eusebio; Saborowski, Michael et al. (2014) Mutant p53 drives pancreatic cancer metastasis through cell-autonomous PDGF receptor ? signaling. Cell 157:382-94
Bolden, Jessica E; Tasdemir, Nilgun; Dow, Lukas E et al. (2014) Inducible in vivo silencing of Brd4 identifies potential toxicities of sustained BET protein inhibition. Cell Rep 8:1919-29
Chen, Chong; Liu, Yu; Rappaport, Amy R et al. (2014) MLL3 is a haploinsufficient 7q tumor suppressor in acute myeloid leukemia. Cancer Cell 25:652-65
Das, Shipra; Krainer, Adrian R (2014) Emerging functions of SRSF1, splicing factor and oncoprotein, in RNA metabolism and cancer. Mol Cancer Res 12:1195-204

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