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Update on StemBase, the database of the Stem Cell Genomics Project

Update on StemBase, the database of the Stem Cell Genomics Project. Miguel Andrade, OHRI, Ottawa. Stem Cell Genomics Project. StemBase. DVD release Oct 2005. Stem Cell Genomics Project. StemBase. DVD release Oct 2005. The Stem Cell Genomics Project.

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Update on StemBase, the database of the Stem Cell Genomics Project

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  1. Update on StemBase, the database of the Stem Cell Genomics Project Miguel Andrade, OHRI, Ottawa

  2. Stem Cell Genomics Project StemBase DVD release Oct 2005

  3. Stem Cell Genomics Project StemBase DVD release Oct 2005

  4. The Stem Cell Genomics Project • Objective: acquire a complete understanding of the genetic factors that: • specify stem cell identity and function; and • regulate commitment and differentiation • Rationale: • Stem cells play an essential role in the human body as they provide the starting material for every organ and tissue • Knowledge of regulatory genes acting in and on stem cells is necessary to exploit their full therapeutic potential

  5. STEM CELL NETWORK +20 GROUPS samples OGIC – GENOMICS PLATFORM Pearl Campbell data Bioinformatics Group data StemBase PUBLIC Yauk CL, Berndt ML, Williams A, Douglas GR. 2004. Comprehensive comparison of six microarray technologies. Nucleic Acids Research. 32(15): p. e124

  6. Data sharing model Submitter 4 Months each sample 1 Sample 12 months entire StemBase 2 Data 4 Approve release? Data production NO 5 Embargo or remove YES 3 Data Bioinformatics analysis Working StemBase 5 Publish data Published StemBase 6 Publicize data Network investigators Public StemBase

  7. Jane Aubin Mickie Bhatia John Dick Connie Eaves Jaques Galipeau Alain Garnier Marina Gertsenstein May Griffith John Hassell Norman Iscove Michael McBurney Rod McInnes Kelly McNagny Lynn Megeney James Piret Derrick Rancourt Janet Rossant Lawrence Rosenberg Michael Rudnicki Luc Sabourin Guy Savageau Ruth Slack Jacques P. Tremblay Valerie Wallace T. Michael Underhill Sue Varmuza Samuel Weiss Juan Carlos Zuniga-Pflucker Peter Zandstra SCN Sample Contributors

  8. Data collection 191 samples 1/4 Human 3/4 Mouse … Rat

  9. Stem Cell Genomics Project StemBase DVD release 1 Oct 2005

  10. StemBase Database of gene expression data in mouse and human stem cells Study genes important for stem cell function Affymetrix DNA microarray data. 185 samples. Serial Analysis of Gene Expression. 6 samples. Perez-Iratxeta, C., G. Palidwor, C.J. Porter, N.A. Sanche, M.R. Huska, B.P. Suomela, E.M. Muro, P. Krzyzanowski, E. Hughes, P.A. Campbell, M.A. Rudnicki and M.A. Andrade. 2005. Study of stem cell function using microarray experiments. FEBS Letters.579, 1795-1801.

  11. Usage (1 Nov 2005) 258 non SCN accounts 3,000 logins First commercial license

  12. Public web server http://www.scgp.ca:8080/StemBase/

  13. Data submission to GEO

  14. Data submission to GEO Required by some journals Largest gene expression data repository StemBase: High quality data Focused on stem cells More functionality GEO as a traffic catch

  15. Mouse / MOE430 R1 D4A V6.5 Embyoid bodies C2D C2A C2E J1 Embyoid bodies D4E Cancer R1 serum6999 D4D Myoblasts Embyoid bodies Cancer R1 serum64 Cancer Neurospheres Retinal primary Dim2 Mammospheres Retinal first passage Mammospheres undifferenciated Dermis Osteoblasts Neural Adipose Muscle Bone marrow Bone marrow Bone marrow Myospheres Bone marrow Dim1 Carolina Perez-Iratxeta

  16. Human / HGU133 Cord blood Bone marrow M-O7e Smad7 Cord blood M-O7e Dim2 Peripheral M-O7e I6 Fetal Cord blood Peripheral Bone marrow Kidney Hela Hela I6 Retinal primary Myoblasts Myoblasts differentiated Retinal first passage Dim1 Carolina Perez-Iratxeta

  17. ES EB Analysis of genes correlated with Oct4 self-renewal totipotency lineage commitment Oct4 Hypothesis: Analysis of genes correlated with Oct4 in stem cells will allow the identification of genes that are important for stem cell identity and lineage commitment Pearl Campbell

  18. Haematopioetic Neurospheres Osteoblasts Embryonic Cancer C2C12 Paul Krzyzanowski

  19. Time Series Time series analysis: differentiation three types of mESC (R1, J1, V6.5) into embryoid bodies 11 time points: 0hr, 6hr, 12hr, 18hr, 24hr, 36hr, 48h, 4day, 7day, 9day and 14day Hailesellasse et al. 2005. Search for genes important in mouse embryonic stem cell differentiation. Submitted.

  20. 6h<0h 12h<0h 12h>0h 6h>0h

  21. from down-regulated genes / signaling related c. Socs3 b. 1190003J15Rik a. Fblim1 TR_THY SOCS box d. Epha5 (Eph receptor A5) e. Pim3 f. Tagln Calponin repeat SAM 2 g. Herc1 WD40 RCC1 HECTc RCC1 SPRY i. Mras j. Rtn4 h. Spry4 l. D930005D10Rik h. Anxa3 Annexin repeats from down-regulated genes / nucleotide binding Zn finger domains Zn finger domains o. Sfrs5 m. Klf4 n. Egr1 RRM_1 from up-regulated genes q. Rbm5 p. Rbm14 RRM_1 RRM_1 G-patch zf-RanBP s. Khsrp r. Zfp54 Zn finger domains

  22. 1190003J15Rik Signal transduction (GO:0007165) Fblim1 Spry4 Mras Anxa3 Morphogenesis (GO:000653) D930005D10Rik Protein amino acid phosphorylation (GO:0006468) Zinc ion binding (GO:0043167) Rtn4 Tagln Socs3 Egr1 Epha5 Herc1 Zfp54 DNA binding Rbm14 Pim3 Klf4 Protein modification (GO:0006464) Rbm5 Nucleic acid binding (GO:0003676) Sfrs5 Khsrp RNA binding

  23. Future Integration of proteomics data New analysis features External datasets: More stem cell data Cancer sets (e.g. NCI) Normal tissue

  24. Stem Cell Genomics Project StemBase DVD release Oct 2005

  25. DVD release Oct 2005 Raw microarray data in StemBase as of 23 Oct 2005 154 samples 426 replicates 4 DVDs Lily Jin / Gareth Palidwor

  26. Ottawa Genome Centre Michael Rudnicki (director) William Read (project manager) Proteomics Lawrence Puente Lynn Megeney Genomics Core Facility Pearl Campbell Stem Cell Network Norman Iscove (U of T) Tim Hughes (U of T)

  27. Bioinformatics Enrique Muro Gareth Palidwor Carolina Perez-Iratxeta Neal Sanche (03-04) Lily Jin (-Sept05) Kagnew Hailesellasse (-Aug05) Miguel Andrade Christopher Porter Paul Krzyzanowski Andrew Kysyk

  28. Thanks! http://www.scgp.ca:8080/StemBase http://www.ottawagenomecenter.ca

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