1. Page 1 Mouse Genome CGH Microarray 44A

2. Page 2 Mouse Genome CGH Microarray Kit 44A Designed for CGH, Validated with samples of known aberrations Designed for genome-wide profiling of genomic aberrations on a single chip.  Genome-wide coverage with average resolution ~35kb  Based on UCSC Genome Browser mm5 (NCBI Build 33)  All probes and annotations mapped to mm6 (NCBI Build 34)  Probe selection biased toward genes (73% intragenic vs. 27% intergenic)  Optimized probe design for aCGH application  Similar probe design and validation process as used in Human CGH array  Include CGH eQC grid  Compatible with current Agilent microarray platform and CGH protocols Part number:G4414A List price:$3750/Kit with volume break Discount:EDU (20%) and VEU Standard catalog array packaging Only commercially available Mouse CGH Microarray !

3. Page 3 Mouse Genome CGH Microarray Kit 44A Designed for CGH, Validated with samples of known aberrations  Consisting of ~43,000 60-mer oligonucleotide probes on 1”x3” slide  Genome-wide coverage with average resolution ~35kb*  Content source: UCSC Genome Browser mm5 (NCBI Build 33)  All probes and annotations mapped to latest NCBI Build 34  Probe selection biased toward genes 1 probe per well-characterized gene 2 or more probes for each of ~1100 cancer genes Intragenic probes (73%); intergenic probes (27%)  Optimized probe design for CGH application  Ability to detect single copy and homozygous deletions as well as low and high level amplifications  Compatible with current Agilent microarray platform and protocols * Calculated by using the total size of the non-repeated genome divided by the total # of features

4. Page 4 Tiled candidate probes across non-repeat masked regions across the genome in 30 bp steps between cut sites for restriction enzymes (RsaI and AluI) – sourced from UCSC Genome Browser mm5 (NCBI Build 33) Performed homology search and retained highly specific probes Filtered homology-searched probe set on the same in silico parameters as used in designing Human CGH array Selected the best set of ~ 80,000 semifinal probes biasing toward genes & exons Performed empirical validation using normal M/F cell-line samples and outliers were eliminated Remove any probes that do not map to NCBI Build 34 Final probe set within a narrow Tm range Probe Design Methodology

5. Page 5 Genomic Coverage and Probe Distribution Total # of Features44,290 # of Biological Probes43,020 # of Unique Biological Probes42,404 # of Replicated Biological Probes308 x 3 Total # of Control probes1,270 ___________________________________________ Intragenic probes 31,552 (73%) Exonic probes 17,344 (55%) Intronic probes 14,208 (45%) Intergenic probes 11,468 (27%)

6. Page 6 Mouse CGH Array Processing Oligo aCGH v2.0 protocol (Supplement with following material changes) Mouse Cot-1 DNA (1.0mg/ml)Invitrogen p/n 18440-016 C57BL/6J Genomic DNA: MaleJackson Labs p/n 000664 C57BL/6J Genomic DNA: FemaleJackson Labs p/n 000664

7. Page 7 Mouse Genomic DNA Digested Phi29 amplified Un-cut Digested Un-cut Un-amplified

8. Page 8 Separation Histogram 3ug gDNA into Direct Labeling X probes autosome probes

9. Page 9 Ts65Dn Mouse Ts65Dn mice are trisomic for the genes carried in the small translocation chromosome, symbolized Ts(17 16 )65Dn, that are normally located on Chr16. Learn more from www.jax.orgwww.jax.org

10. Page 10 Ts(17 16 )65Dn Chromosome 16 Polarity=1Polarity=-1 Combined 3ug gDNA into Direct Labeling

11. Page 11 Ts(17 16 )65Dn Chromosome 16 Breakpoint T65Dn translocation breaks mouse Chr 16 just proximal to the amyloid precursor protein (App) gene and contains the HSA21-homologous genes from App to the telomere.

12. Page 12 Aberrations in Lymphoma Cell Line 1 (Combined dye-swaps; 10pt. Moving average) Collaboration Data from Lynda Chin, DFCI

13. Page 13 Aberrations in Lymphoma Cell Line 2 (Combined dye-swaps; 10pt. Moving average) Collaboration Data from Lynda Chin, DFCI