1 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 ● Setting up and validation ● Core service: July

People Director –Prof Dave Berger Scientific Officers –Danie Theron ( ) –Nicky Olivier (2006-present) Statisticians –Loveness Dzikiti –Nanette Coetzer 3

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

Start-up Instrumentation Molecular Dynamics GenIII Spotter Genepix 4000B Scanner 532 nm / 635 nm

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

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

BIOPAD project ( ) Microarray Capacity Building project –UP, Inqaba Biotec, WITS Focus areas –Training Workshops Inqaba intern project –Standard Operating Procedures –External support for projects 8

Workshops - BIOPAD Lab training (2005 & 2006) 9 RegionAttendees ACGT22 Gauteng10 SA9

Workshops – Starter kit 10 RegionAttendees ACGT9 Gauteng4 SA3 Scaled down experiment (3 days)

Workshops ICTTD & Veterinary Science (2003) 11 RegionAttendees ACGT12 Gauteng3 SA3 Outside SA6

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

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

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

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

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 16

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

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

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 19

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

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 21

Costing 22 Region Spotting (per slide) Scanning (per slide) Data analysis ACGTR450 - R550Free RegionalR450 - R550R180Free ExternalR600 – R750R350R350/h

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 23

Projects by region 24 RegionPastCurrentFuture ACGT1748 Gauteng415 SA410 Africa102

Slides to date 25 Number Slides printed1970 Slides scanned2261

Student training DegreeNumber Hons3 MSc11 PhD17 Post-Doctoral6 Principal Investigators7 26

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

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 28

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 29

30 Thank you