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 #
5P01CA013106-42
Application #
8744325
Study Section
Special Emphasis Panel (ZCA1-RPRB-0 (O1))
Project Start
2013-01-01
Project End
2016-12-31
Budget Start
2013-01-01
Budget End
2013-12-31
Support Year
42
Fiscal Year
2013
Total Cost
$425,521
Indirect Cost
$199,494
Name
Cold Spring Harbor Laboratory
Department
Type
DUNS #
065968786
City
Cold Spring Harbor
State
NY
Country
United States
Zip Code
11724
Diermeier, Sarah D; Chang, Kung-Chi; Freier, Susan M et al. (2016) Mammary Tumor-Associated RNAs Impact Tumor Cell Proliferation, Invasion, and Migration. Cell Rep 17:261-74
O'Rourke, Kevin P; Dow, Lukas E; Lowe, Scott W (2016) Immunofluorescent Staining of Mouse Intestinal Stem Cells. Bio Protoc 6:
Anczuków, Olga; Krainer, Adrian R (2016) Splicing-factor alterations in cancers. RNA 22:1285-301
Tschaharganeh, Darjus F; Lowe, Scott W; Garippa, Ralph J et al. (2016) Using CRISPR/Cas to study gene function and model disease in vivo. FEBS J 283:3194-203
Hossain, Manzar; Stillman, Bruce (2016) Opposing roles for DNA replication initiator proteins ORC1 and CDC6 in control of Cyclin E gene transcription. Elife 5:
Arun, Gayatri; Diermeier, Sarah; Akerman, Martin et al. (2016) Differentiation of mammary tumors and reduction in metastasis upon Malat1 lncRNA loss. Genes Dev 30:34-51
Tschaharganeh, Darjus F; Xue, Wen; Calvisi, Diego F et al. (2016) p53-Dependent Nestin Regulation Links Tumor Suppression to Cellular Plasticity in Liver Cancer. Cell 165:1546-1547
O'Rourke, Kevin P; Ackerman, Sarah; Dow, Lukas E et al. (2016) Isolation, Culture, and Maintenance of Mouse Intestinal Stem Cells. Bio Protoc 6:
Tschaharganeh, Darjus F; Bosbach, Benedikt; Lowe, Scott W (2016) Coordinated Tumor Suppression by Chromosome 8p. Cancer Cell 29:617-9
Guo, Ya; Xu, Quan; Canzio, Daniele et al. (2015) CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function. Cell 162:900-10

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