1. 1 Sample Multiplexing 1-26-09

2. © 2007 Illumina, Inc. Illumina, Sentrix, Array of Arrays, BeadArray, DASL, Infinium, GoldenGate, BeadXpress, VeraCode, IntelliHyb, iSelect, Solexa and Making Sense Out of Life are registered trademarks or trademarks of Illumina Inc. © 2007 Illumina, Inc. Illumina, Sentrix, Array of Arrays, BeadArray, DASL, Infinium, GoldenGate, BeadXpress, VeraCode, IntelliHyb, iSelect, Solexa and Making Sense Out of Life are registered trademarks or trademarks of Illumina Inc. Key Features & Benefits 3-primer multiplexing method –Allows intensity resetting for each read –Greatly increases sample scalability while maintaining system specifications Compatible with either single or paired reads –Flexibility for various applications Same Cluster Generation workflow as standard SR / PE protocol –Processing of up to 96 samples simultaneously on the Cluster Station –Unlike ePCR technologies where a separate ePCR is needed per slide section Easily scalable to higher levels of multiplexing –Flexibility to go beyond the 12-plex Minimal changes to workflow –Uses same simplified workflow 6-base index design –Allows for one-base differences to be fully recoverable –Allows for error correction in the index reads

3. © 2007 Illumina, Inc. Illumina, Sentrix, Array of Arrays, BeadArray, DASL, Infinium, GoldenGate, BeadXpress, VeraCode, IntelliHyb, iSelect, Solexa and Making Sense Out of Life are registered trademarks or trademarks of Illumina Inc. © 2007 Illumina, Inc. Illumina, Sentrix, Array of Arrays, BeadArray, DASL, Infinium, GoldenGate, BeadXpress, VeraCode, IntelliHyb, iSelect, Solexa and Making Sense Out of Life are registered trademarks or trademarks of Illumina Inc. Applications Supported Enabled Applications: –Targeted resequencing –Small genome resequencing –Chip-Seq –mRNA Seq Applications not compatible: –DGE –small RNA

4. © 2007 Illumina, Inc. Illumina, Sentrix, Array of Arrays, BeadArray, DASL, Infinium, GoldenGate, BeadXpress, VeraCode, IntelliHyb, iSelect, Solexa and Making Sense Out of Life are registered trademarks or trademarks of Illumina Inc. © 2007 Illumina, Inc. Illumina, Sentrix, Array of Arrays, BeadArray, DASL, Infinium, GoldenGate, BeadXpress, VeraCode, IntelliHyb, iSelect, Solexa and Making Sense Out of Life are registered trademarks or trademarks of Illumina Inc. Components Required for: Single Read Multiplexing ProductQuantityCatalog Number Single Read Genomic Sample Prep Kit1FC-102-1001 Multiplexing Sample Preparation Oligonucleotide Kit1PE-400-1001 Single Read Cluster Gen Kit v2 (GAI or GAII)1 FC-103-2001 (GAI) or GD-203-2001 (GAII) Multiplexing Sequencing Primers and PhiX Control1PE-400-1002 36 Cycle SBS Sequencing Kit v31 FC-104-3002 18 Cycle SBS Sequencing Kit v31 FC-104-3001

5. © 2007 Illumina, Inc. Illumina, Sentrix, Array of Arrays, BeadArray, DASL, Infinium, GoldenGate, BeadXpress, VeraCode, IntelliHyb, iSelect, Solexa and Making Sense Out of Life are registered trademarks or trademarks of Illumina Inc. © 2007 Illumina, Inc. Illumina, Sentrix, Array of Arrays, BeadArray, DASL, Infinium, GoldenGate, BeadXpress, VeraCode, IntelliHyb, iSelect, Solexa and Making Sense Out of Life are registered trademarks or trademarks of Illumina Inc. Multiplexing with Cluster Generation Kits v2: Extra Steps Required Multiplexing with the Cluster Generation v2 Kits requires an extra protocol. This protocol is called “Multiplexing_Compatibility_CustomerLetter.pdf” and can be obtained from TechSupport or from your FAS. Illumina is currently developing Cluster Generation Kits for use with multiplexing applications.

6. © 2007 Illumina, Inc. Illumina, Sentrix, Array of Arrays, BeadArray, DASL, Infinium, GoldenGate, BeadXpress, VeraCode, IntelliHyb, iSelect, Solexa and Making Sense Out of Life are registered trademarks or trademarks of Illumina Inc. © 2007 Illumina, Inc. Illumina, Sentrix, Array of Arrays, BeadArray, DASL, Infinium, GoldenGate, BeadXpress, VeraCode, IntelliHyb, iSelect, Solexa and Making Sense Out of Life are registered trademarks or trademarks of Illumina Inc. Components Required for: Paired-End Multiplexing Product Quanti tyCatalog Number Paired-End Sample Prep Kit1PE-102-1001 Multiplexing Sample Preparation Oligonucleotide Kit1PE-400-1001 Paired-End Cluster Gen Kit v2 (GAI or GAII)1 PE-103-2001 (GAI) or PE-203-2001 (GAII) Multiplexing Sequencing Primers and PhiX Control1PE-400-1002 36 Cycle SBS Sequencing Kit v32 FC-104-3002 18 Cycle SBS Sequencing Kit v31 FC-104-3001

7. © 2007 Illumina, Inc. Illumina, Sentrix, Array of Arrays, BeadArray, DASL, Infinium, GoldenGate, BeadXpress, VeraCode, IntelliHyb, iSelect, Solexa and Making Sense Out of Life are registered trademarks or trademarks of Illumina Inc. © 2007 Illumina, Inc. Illumina, Sentrix, Array of Arrays, BeadArray, DASL, Infinium, GoldenGate, BeadXpress, VeraCode, IntelliHyb, iSelect, Solexa and Making Sense Out of Life are registered trademarks or trademarks of Illumina Inc. Components Required for: Single-Read mRNA-Seq Multiplexing ProductQuantityCatalog Number mRNA-Seq Sample Prep Kit1RS-100-0801 Multiplexing Sample Preparation Oligonucleotide Kit1PE-400-1001 Single Read Cluster Gen Kit v2 (GAI or GAII)1 FC-103-2001 (GAI) or GD-203-2001 (GAII) Multiplexing Sequencing Primers and PhiX Control1PE-400-1002 36 Cycle SBS Sequencing Kit v31 FC-104-3002 18 Cycle SBS Sequencing Kit v31 FC-104-3001

8. © 2007 Illumina, Inc. Illumina, Sentrix, Array of Arrays, BeadArray, DASL, Infinium, GoldenGate, BeadXpress, VeraCode, IntelliHyb, iSelect, Solexa and Making Sense Out of Life are registered trademarks or trademarks of Illumina Inc. © 2007 Illumina, Inc. Illumina, Sentrix, Array of Arrays, BeadArray, DASL, Infinium, GoldenGate, BeadXpress, VeraCode, IntelliHyb, iSelect, Solexa and Making Sense Out of Life are registered trademarks or trademarks of Illumina Inc. Components Required for: Paired-End mRNA-Seq Multiplexing * * Illumina does not currently support data analysis for Paired-End mRNA-Seq Multiplexing Product Quant ityCatalog Number mRNA-Seq Sample Prep Kit1RS-100-0801 Multiplexing Sample Preparation Oligonucleotide Kit1PE-400-1001 Paired-End Cluster Gen Kit v2 (GAI or GAII)1 PE-103-2001 (GAI) or PE-203-2001 (GAII) Multiplexing Sequencing Primers and PhiX Control1PE-400-1002 36 Cycle SBS Sequencing Kit or v32FC-104-3002 18 Cycle SBS Sequencing Kit or v31FC-104-3001