human genome cgh microarray 244a kit  (Agilent technologies)

Journal: PLoS ONE

Article Title: In Vitro Analysis of Integrated Global High-Resolution DNA Methylation Profiling with Genomic Imbalance and Gene Expression in Osteosarcoma

doi: 10.1371/journal.pone.0002834

Figure Lengend Snippet: (A) Schematic workflow of microarray data analysis and integration. Individual microarrays in replicates (grey boxes), are imported, background corrected, and significantly enriched or depleted regions are detected and assigned to specific genes for DNA methylation, genomic imbalance, and gene expression. All data were analyzed, and integrated using Partek Genomic Suite (PGS) software, and network analysis was performed using Ingenuity Pathway Analysis (IPA). IN – input DNA, IP – immunoprecipitated DNA Cy3 and Cy5 – replicate experiment dye flip for a-CGH labeling, 1 and 2 – individual expression replicates, cor. – background normalized/corrected arrays, HMM – Hidden Markov Model algorithm, gen. seg. – genomic segmentation algorithm, ANOVA – analysis of variance algorithm. (B) Chromosome view of epigenetic, genetic, and expression changes at chromosome 7 in U2OS cells. A PGS generated visualization of the significant regions of genes with significant changes in expression (lane 1 profile), DNA methylation (lane 2 profile), genomic segmentation algorithm results (lane 3 heat map), and the corresponding a-CGH profile (lane 4 profile). The genomic segmentation scale and a-CGH profile values are in log 2 , while DNA methylation and gene expression y-axis scale represents average fold change to osteoblast levels, and size of each bar is proportional to the fold change (green – decrease, red – increase).

Article Snippet: The Agilent Human Genome CGH microarray 44k and 244A (Agilent Technologies, Inc., Palo Alto, USA) were used for the MG63 and U2OS array-CGH experiments, respectively.

Techniques: Microarray, DNA Methylation Assay, Expressing, Software, Immunoprecipitation, Labeling, Generated

Journal: BMC Research Notes

Article Title: Evaluation of high-resolution microarray platforms for genomic profiling of bone tumours

doi: 10.1186/1756-0500-3-223

Figure Lengend Snippet: Microarray platform characteristics

Article Snippet: The Agilent Human Genome CGH 244A microarray contains approximately 236,000 in situ synthesized 60-mer oligonucleotides spanning coding and non-coding regions.

Techniques: Microarray, Genome Wide

Journal: BMC Research Notes

Article Title: Evaluation of high-resolution microarray platforms for genomic profiling of bone tumours

doi: 10.1186/1756-0500-3-223

Figure Lengend Snippet: Reproducibility of replicate hybridisations and signal response to copy number

Article Snippet: The Agilent Human Genome CGH 244A microarray contains approximately 236,000 in situ synthesized 60-mer oligonucleotides spanning coding and non-coding regions.

Techniques: Genome Wide

Journal: BMC Research Notes

Article Title: Evaluation of high-resolution microarray platforms for genomic profiling of bone tumours

doi: 10.1186/1756-0500-3-223

Figure Lengend Snippet: Plot of measured log 2 ratios compared to theoretical values for specific chromosomes or chromosomal regions . Plot of average measured log 2 ratios compared to theoretical values for six specific chromosomes or chromosomal regions; the CDKN2A locus in 9p21.3, 9p21.3-p21.2, chromosome 2, chromosome 8, 1q (all in TC-32) and the MDM2 locus in 12q15 (in OSA) (representing 0, 1, 2, 3, 4 and >10 copies, respectively) for all microarray platforms and replicates. The slope and regression coefficient (R 2 ) for the regression line based on four of the regions, representing 1, 2, 3 and 4 copies, are given.

Article Snippet: The Agilent Human Genome CGH 244A microarray contains approximately 236,000 in situ synthesized 60-mer oligonucleotides spanning coding and non-coding regions.

Techniques: Microarray

Journal: BMC Research Notes

Article Title: Evaluation of high-resolution microarray platforms for genomic profiling of bone tumours

doi: 10.1186/1756-0500-3-223

Figure Lengend Snippet: Distribution of log 2 ratios for specific chromosomes or chromosomal regions . Distribution of log 2 ratios of all probes within six specific chromosomes or chromosomal regions; the CDKN2A locus in 9p21.3, 9p21.3-p21.2, chromosome 2, chromosome 8, 1q (all in TC-32) and the MDM2 locus in 12q15 (in OSA) (representing 0, 1, 2, 3, 4 and >10 copies, respectively) for all microarray platforms for A) normalized data and B) normalized data that have been smoothed using Gaussian smoothing with a window size of 50 kb and standard deviation of 10 kb. Smoothing was not possible for the small regions representing 0 and >10 copies (the CDKN2A and MDM2 loci) due to insufficient number of probes.

Article Snippet: The Agilent Human Genome CGH 244A microarray contains approximately 236,000 in situ synthesized 60-mer oligonucleotides spanning coding and non-coding regions.

Techniques: Microarray, Standard Deviation

Journal: BMC Research Notes

Article Title: Evaluation of high-resolution microarray platforms for genomic profiling of bone tumours

doi: 10.1186/1756-0500-3-223

Figure Lengend Snippet: Detection of copy number of specific regions

Article Snippet: The Agilent Human Genome CGH 244A microarray contains approximately 236,000 in situ synthesized 60-mer oligonucleotides spanning coding and non-coding regions.

Techniques: Genome Wide

Journal: BMC Research Notes

Article Title: Evaluation of high-resolution microarray platforms for genomic profiling of bone tumours

doi: 10.1186/1756-0500-3-223

Figure Lengend Snippet: Detection of copy number aberrations

Article Snippet: The Agilent Human Genome CGH 244A microarray contains approximately 236,000 in situ synthesized 60-mer oligonucleotides spanning coding and non-coding regions.

Techniques: Genome Wide

Journal: PLoS ONE

Article Title: Copy Number Variants in Patients with Severe Oligozoospermia and Sertoli-Cell-Only Syndrome

doi: 10.1371/journal.pone.0019426

Figure Lengend Snippet: Workflow with different arrays (244A, 400K), number of subjects and categorisation of CNVs.

Article Snippet: Genomic DNA was extracted from peripheral blood by standard methods and analysed at first by the commercially available Human Genome CGH Microarray Kits 244A (Agilent Technologies, Santa Clara, California, USA).

Techniques: