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Integrated Workflow for Genotyping, Transcriptomics, and Proteomics Data Analysis

Streamlined project workflow for combining genotyping, transcriptomics, and proteomics data in a single database using cell lines and patient samples. Collaboration opportunities available.

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Integrated Workflow for Genotyping, Transcriptomics, and Proteomics Data Analysis

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  1. Project workflow 1/4 RNAs RNAs Proteins Exon microarrays Mass Spectrometry Patient’s blood Lymphoblastoids culture Quality Control genotyping data expression data proteins data database

  2. Proteins workflow 2/4 EGEA Cell lines extraction Fraction 1 Fraction 2 aliquotation storage normalisation quality control sample transfer Identification aliquotation ClinProt Mass Spectrometry

  3. RNAs workflow 3/4 EGEA Cell lines extraction RNAs aliquotation quality control normalisation sample amplification / labelling ClinProt Mass Spectrometry

  4. Costs 4/4 RNA part cost estimation RNA extraction 4 000 Quality control 1 255 Exon microarrays 212 400 TOTAL 217 655 Protein part cost estimation Proteins extraction 3 160 Quality control 6 980 ClinProt Mass Spectrometry 5 860 TOTAL 16 000

  5. Arguments • Unique collection • Genotyping / transcriptomics / proteomics datas never integrated in a single database before • Cell culture almost finished at CEPH (Hélène Blanché) and CNG (Anne Boland) • Florence Demenais is interested in the analysis of the EGEA collection • Collaboration for proteomics analysis with Chris Holmes (Oxford) • Dixon publication in 2007 ‘Genome wide association study of global gene expression’ Solutions • Finance of the kits, consumables, etc… • Contract / Access to the lab…

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