SRX026996 Whole genome re-sequencing of aneuploid yeast strain "Sample1" SRP003582 Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast Genomic libraries were prepared according to manufacturer’s recommendations, except sonication was used instead of nebulization. Briefly, 5 µg of genomic DNA was sonicated using a BiorupterTM UCD-200 and the overhangs resulting from fragmentation were converted in to blunt ends, using T4 DNA polymerase and E. coli DNA polymerase I Klenow fragment. Then, an adenine base was added to the 3’ end of the blunt phosphorylated DNA fragments using the polymerase activity of Klenow fragment (3’ to 5’ exo minus). Adapters with a single thymine base overhang at their 3’ end are then ligated to the ends of the DNA fragments. Products of the ligation reaction are purified and size-selected on a gel to obtain a size range of approximately 300bp. 18 cycles of PCR were done to enrich for fragments with Illumina adapters on both ends. The library was then purified and quantified using an Agilent Bioanalyzer. Cluster generation, and read sequencing was performed following manufacturer’s recommendation. Image analysis, base calling and genome alignment were performed using the Illumina Genome Analyzer pipeline. SRS115008 Sample1 Sample1 WGS GENOMIC PCR 0 Application Read Forward 1 1 Application Read Reverse 41 Illumina Genome Analyzer II SRX026999 Whole genome re-sequencing of aneuploid yeast strain "Sample3" SRP003582 Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast Genomic libraries were prepared according to manufacturer’s recommendations, except sonication was used instead of nebulization. Briefly, 5 µg of genomic DNA was sonicated using a BiorupterTM UCD-200 and the overhangs resulting from fragmentation were converted in to blunt ends, using T4 DNA polymerase and E. coli DNA polymerase I Klenow fragment. Then, an adenine base was added to the 3’ end of the blunt phosphorylated DNA fragments using the polymerase activity of Klenow fragment (3’ to 5’ exo minus). Adapters with a single thymine base overhang at their 3’ end are then ligated to the ends of the DNA fragments. Products of the ligation reaction are purified and size-selected on a gel to obtain a size range of approximately 300bp. 18 cycles of PCR were done to enrich for fragments with Illumina adapters on both ends. The library was then purified and quantified using an Agilent Bioanalyzer. Cluster generation, and read sequencing was performed following manufacturer’s recommendation. Image analysis, base calling and genome alignment were performed using the Illumina Genome Analyzer pipeline. SRS115009 Sample3 Sample3 WGS GENOMIC PCR 0 Application Read Forward 1 1 Application Read Reverse 41 Illumina Genome Analyzer II SRX027000 Whole genome re-sequencing of aneuploid yeast strain "Sample2626" SRP003582 Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast Genomic libraries were prepared according to manufacturer’s recommendations, except sonication was used instead of nebulization. Briefly, 5 µg of genomic DNA was sonicated using a BiorupterTM UCD-200 and the overhangs resulting from fragmentation were converted in to blunt ends, using T4 DNA polymerase and E. coli DNA polymerase I Klenow fragment. Then, an adenine base was added to the 3’ end of the blunt phosphorylated DNA fragments using the polymerase activity of Klenow fragment (3’ to 5’ exo minus). Adapters with a single thymine base overhang at their 3’ end are then ligated to the ends of the DNA fragments. Products of the ligation reaction are purified and size-selected on a gel to obtain a size range of approximately 300bp. 18 cycles of PCR were done to enrich for fragments with Illumina adapters on both ends. The library was then purified and quantified using an Agilent Bioanalyzer. Cluster generation, and read sequencing was performed following manufacturer’s recommendation. Image analysis, base calling and genome alignment were performed using the Illumina Genome Analyzer pipeline. SRS115007 Sample2626 Sample2626 WGS GENOMIC PCR 0 Application Read Forward 1 1 Application Read Reverse 41 Illumina Genome Analyzer II SRX027001 Whole genome re-sequencing of aneuploid yeast strain "Sample113" SRP003582 Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast Genomic libraries were prepared according to manufacturer’s recommendations, except sonication was used instead of nebulization. Briefly, 5 µg of genomic DNA was sonicated using a BiorupterTM UCD-200 and the overhangs resulting from fragmentation were converted in to blunt ends, using T4 DNA polymerase and E. coli DNA polymerase I Klenow fragment. Then, an adenine base was added to the 3’ end of the blunt phosphorylated DNA fragments using the polymerase activity of Klenow fragment (3’ to 5’ exo minus). Adapters with a single thymine base overhang at their 3’ end are then ligated to the ends of the DNA fragments. Products of the ligation reaction are purified and size-selected on a gel to obtain a size range of approximately 300bp. 18 cycles of PCR were done to enrich for fragments with Illumina adapters on both ends. The library was then purified and quantified using an Agilent Bioanalyzer. Cluster generation, and read sequencing was performed following manufacturer’s recommendation. Image analysis, base calling and genome alignment were performed using the Illumina Genome Analyzer pipeline. SRS115010 Sample113 Sample113 WGS GENOMIC PCR 0 Application Read Forward 1 1 Application Read Reverse 41 Illumina Genome Analyzer II SRX027002 Whole genome re-sequencing of aneuploid yeast strain "Sample120" SRP003582 Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast Genomic libraries were prepared according to manufacturer’s recommendations, except sonication was used instead of nebulization. Briefly, 5 µg of genomic DNA was sonicated using a BiorupterTM UCD-200 and the overhangs resulting from fragmentation were converted in to blunt ends, using T4 DNA polymerase and E. coli DNA polymerase I Klenow fragment. Then, an adenine base was added to the 3’ end of the blunt phosphorylated DNA fragments using the polymerase activity of Klenow fragment (3’ to 5’ exo minus). Adapters with a single thymine base overhang at their 3’ end are then ligated to the ends of the DNA fragments. Products of the ligation reaction are purified and size-selected on a gel to obtain a size range of approximately 300bp. 18 cycles of PCR were done to enrich for fragments with Illumina adapters on both ends. The library was then purified and quantified using an Agilent Bioanalyzer. Cluster generation, and read sequencing was performed following manufacturer’s recommendation. Image analysis, base calling and genome alignment were performed using the Illumina Genome Analyzer pipeline. SRS115011 Sample120 Sample120 WGS GENOMIC PCR 0 Application Read Forward 1 1 Application Read Reverse 41 Illumina Genome Analyzer II SRX027003 Whole genome re-sequencing of aneuploid yeast strain "Sample124" SRP003582 Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast Genomic libraries were prepared according to manufacturer’s recommendations, except sonication was used instead of nebulization. Briefly, 5 µg of genomic DNA was sonicated using a BiorupterTM UCD-200 and the overhangs resulting from fragmentation were converted in to blunt ends, using T4 DNA polymerase and E. coli DNA polymerase I Klenow fragment. Then, an adenine base was added to the 3’ end of the blunt phosphorylated DNA fragments using the polymerase activity of Klenow fragment (3’ to 5’ exo minus). Adapters with a single thymine base overhang at their 3’ end are then ligated to the ends of the DNA fragments. Products of the ligation reaction are purified and size-selected on a gel to obtain a size range of approximately 300bp. 18 cycles of PCR were done to enrich for fragments with Illumina adapters on both ends. The library was then purified and quantified using an Agilent Bioanalyzer. Cluster generation, and read sequencing was performed following manufacturer’s recommendation. Image analysis, base calling and genome alignment were performed using the Illumina Genome Analyzer pipeline. SRS115012 Sample124 Sample124 WGS GENOMIC PCR 0 Application Read Forward 1 1 Application Read Reverse 41 Illumina Genome Analyzer II