the european bioinformatics institute atlas of gene human gene expression proposal - resources alvis...
TRANSCRIPT
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 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
source @ 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