The European Bioinformatics Institute Atlas of Gene Human Gene Expression Proposal - resources Alvis Brazma, Tom Freeman and Helen Parkinson

The European Bioinformatics Institute Existing EBI Resources for this project  Co-developers of MIAME annotation standard  ArrayExpress Database  MIAMExpress data submission tool  Data analysis tools, Expression Profiler  Interoperability within EBI databases  Expertise in data mining

The European Bioinformatics Institute Existing reference data  Lacking input in experimental design  Poorly annotated, lack of provenance on samples  Data not fully available, e.g. cel file for Affy data confidential, image data not available Novartis dataNovartis data  Experiments done without input of bioinformaticians until after completion

The European Bioinformatics Institute Human Tissue Source  Peterborough tissuebank,two tissue sources – donated, cadaveric  Tissues dissected and Snap frozen according to SOP’s by pathologists ( SOP’s available to us)  Time of death vs. time of dissection/freezing as low as 4 h  Full prior ethics approval for our project

The European Bioinformatics Institute Annotation  Full pathologists report using Minimum Pathology  Histology report for normal tissues  Patient history, anonymised GP records available if required  sex, age, clinical and drug history is supplied as recommended by the FDA regulations  tissue is quality controlled by cryostat sectioning, sections available for follow up

The European Bioinformatics Institute DataBasing  Using filemaker at present, upgrading to mySQL, developing new schema  Tab delimited file export possible for parsing into EBI databases  Free text annotation, needs cv/ontology development

The European Bioinformatics Institute Services  Collection of tissue to order  Collection organised guaranteed from same individual  Will prepare RNA if required to user specification  Cost recovery basis ~ £ 30/sample  Dissected brains if required/alternative Addenbrookes

The European Bioinformatics Institute Tissues available as standard  Adrenal  Aorta  Blood cells  Bladder  Bone marrow  Breast  Blood vessels(unspecified)  Cerebellum  Cerebral cortex  Colon  Duodenum  Eye (Retina, Cornea and lens)  Fallopian tube  Ileum Kidney (Glomerulus, tubule)  Liver  Lung  Lymph node  Ovary  Pancreas  Peripheral nerve  Pituitary  Prostate  Placenta  Parathyroid  Spinal cord  Skin  Spleen  Salivary gland  Striated muscle  Stomach (body and antrum)  Testis  Thyroid  Tonsil  Ureter  Uterine cervix  Uterine endometrium

The European Bioinformatics Institute Availability of tissues  If samples come from cadavers for organ donation some tissues are missing  Cadaver availability  Imposing our own restrictions on collection will limit which cadavers can be used, implication for timelines

The European Bioinformatics Institute Future possibilities..  Disease matched vs. normal tissues for follow ups  Repeat samples for QC  Tissue arrays from same individuals  Imaging capability, plus pathologist annotation for all tissues  Tissue sections for immunohistochemistry  Interoperability with tissuebank databases