human genome u133plus2 microarrays  (Thermo Fisher)

Journal: BMC Bioinformatics

Article Title: Evaluation of gene expression data generated from expired Affymetrix GeneChip ® microarrays using MAQC reference RNA samples

doi: 10.1186/1471-2105-11-S6-S10

Figure Lengend Snippet: The workflow of study design and data analysis New gene expression data were generated in 2009 with expired U133A microarrays and unexpired U133Plus2 microarrays using the same MAQC reference RNA samples and compared to the microarray and TaqMan ® gene expression data generated in 2005 by the MAQC project.

Article Snippet: Each of the two samples was processed in triplicate, starting from independent labeling reactions with a new aliquot of the reference sample from the same tube, a) on Affymetrix Human Genome U133A microarrays that were four years ago past the manufacturer’s expiration dates and b) on unexpired Human Genome U133Plus2 microarrays.

Techniques: Expressing, Generated, Microarray

Journal: BMC Bioinformatics

Article Title: Evaluation of gene expression data generated from expired Affymetrix GeneChip ® microarrays using MAQC reference RNA samples

doi: 10.1186/1471-2105-11-S6-S10

Figure Lengend Snippet: New data generated for this study with Affymetrix GeneChip ® microarrays

Article Snippet: Each of the two samples was processed in triplicate, starting from independent labeling reactions with a new aliquot of the reference sample from the same tube, a) on Affymetrix Human Genome U133A microarrays that were four years ago past the manufacturer’s expiration dates and b) on unexpired Human Genome U133Plus2 microarrays.

Techniques: Generated, Hybridization

Journal: BMC Bioinformatics

Article Title: Evaluation of gene expression data generated from expired Affymetrix GeneChip ® microarrays using MAQC reference RNA samples

doi: 10.1186/1471-2105-11-S6-S10

Figure Lengend Snippet: Comparisons of the log 2 fold changes detected in 2009 and in 2005 using the same type of U133Plus2 microarrays (a) all 8,550 common genes; (b) the 7,069 genes with p < 0.05 in either 2009 or 2005; and (c) the 5,880 genes with p < 0.05 in both 2009 and 2005. Fold changes were generated by comparing sample B to sample A, i.e ., B/A. The blue and green dots indicated the up- and down-regulated genes, respectively. The red dots were the genes with reverse regulation directionalities in 2009 and in 2005. Under the three scenarios (a, b, and c), the overlap of differentially expressed genes between 2009 and 2005 is 91.37%, 97.44%, and 99.78%, respectively, suggesting a high degree of stability of the two MAQC reference RNA samples.

Article Snippet: Each of the two samples was processed in triplicate, starting from independent labeling reactions with a new aliquot of the reference sample from the same tube, a) on Affymetrix Human Genome U133A microarrays that were four years ago past the manufacturer’s expiration dates and b) on unexpired Human Genome U133Plus2 microarrays.

Techniques: Generated

Journal: BMC Bioinformatics

Article Title: Evaluation of gene expression data generated from expired Affymetrix GeneChip ® microarrays using MAQC reference RNA samples

doi: 10.1186/1471-2105-11-S6-S10

Figure Lengend Snippet: Correlations of log 2 intensities generated in 2009 among the replicates of samples A and B (a) expired U133A microarrays and (b) unexpired U133Plus2 microarrays. Each scatterplot represents the comparison of log 2 intensities of 8,550 common genes from two hybridizations.

Article Snippet: Each of the two samples was processed in triplicate, starting from independent labeling reactions with a new aliquot of the reference sample from the same tube, a) on Affymetrix Human Genome U133A microarrays that were four years ago past the manufacturer’s expiration dates and b) on unexpired Human Genome U133Plus2 microarrays.

Techniques: Generated

Journal: BMC Bioinformatics

Article Title: Evaluation of gene expression data generated from expired Affymetrix GeneChip ® microarrays using MAQC reference RNA samples

doi: 10.1186/1471-2105-11-S6-S10

Figure Lengend Snippet: Comparisons of log 2 fold changes detected with expired U133A and unexpired U133Plus2 microarrays (a) all 8,550 common genes; (b) the 6,835 genes with p < 0.05 in either expired U133A microarrays (2009) or unexpired U133Plus2 microarrays (2009); and (c) the 5,120 genes with p < 0.05 in both expired U133A (2009) and unexpired U133Plus2 (2009) microarrays. Fold changes were generated by comparing sample B to sample A, i.e ., B/A. The blue and green dots indicated the up- and down-regulated genes, respectively. The red dots were the genes with reverse regulation directionalities. Under the three scenarios (a, b, and c), the overlap of differentially expressed genes between expired U133A (2009) and unexpired U133Plus2 (2009) microarrays is 89.94%, 96.99%, and 99.98%, respectively, indicating a high degree of consistency between differential gene expression data generated from expired U133A and unexpired U133Plus2 microarrays. Note that the fold changes measured with expired U133A microarrays exhibited some degree of compression ( i.e ., with smaller absolute values) when compared to those obtained with unexpired U133Plus2 microarrays.

Article Snippet: Each of the two samples was processed in triplicate, starting from independent labeling reactions with a new aliquot of the reference sample from the same tube, a) on Affymetrix Human Genome U133A microarrays that were four years ago past the manufacturer’s expiration dates and b) on unexpired Human Genome U133Plus2 microarrays.

Techniques: Generated, Expressing

Journal: BMC Bioinformatics

Article Title: Evaluation of gene expression data generated from expired Affymetrix GeneChip ® microarrays using MAQC reference RNA samples

doi: 10.1186/1471-2105-11-S6-S10

Figure Lengend Snippet: Distribution of the log 2 intensities of 8,550 common genes Sample A hybridized on expired U133A (a) and unexpired U133Plus2 (b) microarrays; Sample B hybridized on expired U133A (c) and unexpired U133Plus2 (d) microarrays. For each gene, the log 2 intensities of the three technical replicates were averaged. Based on microarray data generated in 2009.

Article Snippet: Each of the two samples was processed in triplicate, starting from independent labeling reactions with a new aliquot of the reference sample from the same tube, a) on Affymetrix Human Genome U133A microarrays that were four years ago past the manufacturer’s expiration dates and b) on unexpired Human Genome U133Plus2 microarrays.

Techniques: Microarray, Generated

Journal: BMC Bioinformatics

Article Title: Evaluation of gene expression data generated from expired Affymetrix GeneChip ® microarrays using MAQC reference RNA samples

doi: 10.1186/1471-2105-11-S6-S10

Figure Lengend Snippet: Percentage of Present calls based on 8,550 common genes There is a significant difference in the percentage of Present calls between unexpired U133Plus2 microarrays (73.6%) and expired U133A microarrays (64.5%). Based on microarray data generated in 2009.

Article Snippet: Each of the two samples was processed in triplicate, starting from independent labeling reactions with a new aliquot of the reference sample from the same tube, a) on Affymetrix Human Genome U133A microarrays that were four years ago past the manufacturer’s expiration dates and b) on unexpired Human Genome U133Plus2 microarrays.

Techniques: Microarray, Generated

Journal: BMC Bioinformatics

Article Title: Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees

doi: 10.1186/1471-2105-10-77

Figure Lengend Snippet: Classification of the 604,258 probes within the Affymetrix U133Plus2 microarray . The pie chart depicts the relative percentage of probes comprising each of the nine probe categories described in the Methods section.

Article Snippet: We developed an algorithm to rapidly map short sequence tags to complete genomes (Renaud and Wolfsberg, unpublished) and used it to determine how many times each probe in the Human Genome U133Plus2 microarray (Affymetrix) had an exact match in the human and chimpanzee genomes.

Techniques: Microarray

Journal: BMC Bioinformatics

Article Title: Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees

doi: 10.1186/1471-2105-10-77

Figure Lengend Snippet: Classification of the 54,675 probe sets within the Affymetrix U133Plus2 microarray . The composition of probe sets with respect to probe categories is depicted. The height of each bar represents the number of probe sets (Y-axis) that contain a least one probe in the indicated category (X-axis). The gray segment of each bar represents the number of probe sets where less than six probes of the indicated category are present. The black segment comprising each bar represents the number of probe sets where more than six probes of the indicated category are present.

Article Snippet: We developed an algorithm to rapidly map short sequence tags to complete genomes (Renaud and Wolfsberg, unpublished) and used it to determine how many times each probe in the Human Genome U133Plus2 microarray (Affymetrix) had an exact match in the human and chimpanzee genomes.

Techniques: Microarray

Journal: BMC Bioinformatics

Article Title: Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees

doi: 10.1186/1471-2105-10-77

Figure Lengend Snippet: Classification of probes in the Affymetrix U133Plus2 microarray

Article Snippet: We developed an algorithm to rapidly map short sequence tags to complete genomes (Renaud and Wolfsberg, unpublished) and used it to determine how many times each probe in the Human Genome U133Plus2 microarray (Affymetrix) had an exact match in the human and chimpanzee genomes.

Techniques: