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ENCODE Strategy Task Group Plans and Timelines

This workshop aims to identify new and missing data and analyses in the ENCODE project. Participants will collaborate on various tasks related to DNA sequence variants, cell phenotyping, biology of K562 and GM12878 cells, and brainstorm new ideas for analysis projects. Timelines for each task are specified.

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ENCODE Strategy Task Group Plans and Timelines

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  1. ENCODE Strategy Task Group Plans and Timelines ENCODE Analysis Workshop Bethesda December 8-9, 2008

  2. Participants • Assigned Group • Ian Dunham • Jim Kent • Barbara Wold • Mike Snyder • Tom Gingeras • Eric Green • Rick Myers Additional Participants Yijun Ruan Elise Feingold Laura Dillon Kate Rosenbloom Piero Carninci Ross Hardison Mark Gerstein John Stamatoyannopoulos

  3. Help identify new/missing data and analyses (or “Add value to analysis projects”) • DNA sequence variants • Collaborate with 1000 Genomes Project (Rick Myers, Mark Gerstein) • Help Variation Group get GM12878 CGH data (from Evan Eichler) • Get someone to do CGH on K562 (Mike Snyder?) • Analyze control and ChIP reads from all groups for variants (Tim Reddy, Simon Xi) • Timelines: • Introduce Sequence Variant Group to 1000 Genomes: By Dec. 15 • Get CGH data from Evan Eichler: By Jan. 15 • CGH experiment on K562: By Jan. 30 • Analyze control reads for variants: By Jan. 20

  4. Help identify new/missing data and analyses (or “Add value to analysis projects”) • Cell Phenotyping • Define what experiments need to be done • Immunocytochemistry of known proteins • FACS for known proteins • FACS or cytogenetics for ploidy (i.e., genome-wide at whole chromosome level) • Find someone to do them (Scott Tenenbaum for proteins; ?? for cytogenetics ploidy experiment) • Timelines: • Identify lab to do the experiments (funding?): By Dec. 9 • Immunocytochemistry and/or FACS for proteins: By Mar. 15 • Cytogenetics: By Mar. 15

  5. Help identify new/missing data and analyses (or “Add value to analysis projects”) • Biology of K562 and GM12878 cells • Check our genomic data for known expression, TFs, etc. (Jim Kent, Ross Hardison, John Stam, Barbara Wold, Rick Myers) • Identify experts in erythroid/megakaryocyte and B cell biology (Rick Myers, Elise Feingold) • Timelines: • Check our genomic data: By Jan. 30 • Identify experts: By Jan. 15

  6. Our continuing tasks • Identify/discuss new ideas, new analyses, new experiments emanating from data analyses (and get these to each Task Group) • A bit like the AWG Coordinating Committee • Anyone can join • Timelines: • Establish a few times for calls: By Jan. 5 • Have some calls: By Mar. 30

  7. ABC • ABC • ABC • ABC • ABC • ABC • ABC • ABC • ABC

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