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A Decade of Microarrays ACGT Microarray Facility Nicky Olivier

A Decade of Microarrays ACGT Microarray Facility Nicky Olivier. In the beginning. Institutions involved: UP & CSIR – Shared start-up costs Physical location: Agriculture Building Special installation required Department Plant Science and FABI Equipment - June 2001

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A Decade of Microarrays ACGT Microarray Facility Nicky Olivier

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  1. A Decade of Microarrays ACGT Microarray Facility Nicky Olivier

  2. In the beginning • Institutions involved: • UP & CSIR – Shared start-up costs • Physical location: Agriculture Building • Special installation required • Department Plant Science and FABI • Equipment - June 2001 • Setting up and validation • Core service: July 2002

  3. People • Director • Prof Dave Berger • Scientific Officers • DanieTheron (2001-2006) • Nicky Olivier (2006-present) • Statisticians • LovenessDzikiti • Nanette Coetzer

  4. Advisors Prof Jane Morris (ACGT) Prof HenkHuismans (UP) • Equipment and hardware acquisitions • Approval of projects • Approval Annual Financial Statements • Future plans for Facility

  5. Start-up Instrumentation 2001 Molecular Dynamics GenIII Spotter Genepix4000B Scanner 532 nm / 635 nm

  6. Instrumentation 2008 • Agilent Hybridization oven and chambers Multiplexing slides 1x244K, 2x105K, 4x44K, 8x15K

  7. Instrumentation 2009 • Bio-Rad Automated Electrophoresis system Quantification of RNA quality/concentration RQI score for consistency

  8. BIOPAD project (2005-2007) • Microarray Capacity Building project • UP, InqabaBiotec, WITS • Focus areas • Training • Workshops • Inqaba intern project • Standard Operating Procedures • External support for projects

  9. Workshops - BIOPAD • Lab training (2005 & 2006)

  10. Workshops – Starter kit • Scaled down experiment (3 days)

  11. Workshops • ICTTD & Veterinary Science (2003)

  12. Workshops - Annual • Data analysis • Genetics & Bioinformatics Hons • Interested researchers/students • NBN • Data analysis for Bioinformatics students

  13. Services – Project planning • Experimental design • Statistical relevance • Choice of slides/platform • Oligonucleotide design

  14. Services – Sample QC • RNA/DNA isolation • Experion • RNA analyses – microarray, qPCR, RNAseq • DNA analyses – HTS • Evaluation of external Bioanalyzer results • Evaluation of RNA gels

  15. Services – Hybridization • Lab space and tech support • Hyb-up chambers in waterbath • cDNA, oligo, gDNA • Agilent hyb oven

  16. Services – Scanning • Spotted arrays – resolution 10 µm • Agilent arrays – resolution 5 µm • Single channel or dual channel scans • Data backup at Facility • Data capture assistance

  17. Services – Data analysis • Results file generation and QC • Data normalization • Statistical analysis + output • Downstream protocols • Annotation assistance • GEO/ArrayExpress submission assistance

  18. Software • Spotverify • Verification of differential gene expression • SSHscreen • SSH library quality evaluation • SSH-DB • Moderated database for sequences, BLAST • MADIBA • Annotation, biological function etc.

  19. Communication • Lectures to UP undergraduate students • Lectures to UP postgraduate students • Lectures to external undergraduate students • Lectures to external postgraduate students • Discussions and demos for visitors

  20. Operating philosophy • Non-profit • No hybridisation service offered • Student/Researcher training • Increase capacity in techniques • Make microarray technology accessible

  21. Costing model • Not full-cost • Scientific Officer salary from UP • Departmental responsibilities • Reagents at cost price • Data analysis with free software • Scripts given to researchers for further use

  22. Costing

  23. Financial Administration • Funds in UP cost point • Yearly financial statements to advisors • UP users: • Internal fund transfers • External users • Invoice issued by UP • Payments administered by UP Finance • Excess funds for instrument maintenance

  24. Projects by region

  25. Slides to date

  26. Student training

  27. Publications • 14 Publications in peer review journals • 1 Book chapter • 3 Hons reports • 8 MSc theses • 11 PhD theses

  28. Challenges / Opportunities • Spotter printing pins • Spotted arrays becoming obsolete • Scanner laser service • Scanner resolution • RNAseq • Agilent slides becoming more accessible • Partnership with supplier – greater awareness

  29. The Future • New Plant Science building • Dedicated labs • RNA isolation, Hybridization, Scanning • Equipment needed • High resolution Agilent scanner • 2 µm scanning resolution – high density • 1x1M, 2x400K, 4x180K, 8x60K

  30. Thank you

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