Journal: Journal of Medical Case Reports

Article Title: Chromosomal 16p microdeletion in Rubinstein-Taybi syndrome detected by oligonucleotide-based array comparative genomic hybridization: a case report

doi: 10.1186/1752-1947-6-30

Figure Lengend Snippet: Profile of the microarray analysis showing the deletion region as indicated in the highlighted area . A dye-swap experiment was performed to maximize the accuracy of detection of the deletion.

Article Snippet: Molecular karyotyping was performed using commercially available high resolution 244K 60-mer oligonucleotide microarray slide (Human Genome CGH Microarray 244A Kit, Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer's protocol.

Techniques: Microarray

Journal: Journal of Ayurveda and Integrative Medicine

Article Title: Genome-wide DNA methylation profiling after Ayurveda intervention to bronchial asthmatics identifies differential methylation in several transcription factors with immune process related function

doi: 10.1016/j.jaim.2023.100692

Figure Lengend Snippet: Characterization of treatment-associated DNA methylation (TADS) signatures by genomic distribution and enrichment analysis. (A) Among the 4820 differentially methylated probes, 2644 probes (55%; representing 1884 genes) were treatment unmethylated signatures (methylated in BT group and unmethylated in AT); and 2176 probes (45%; representing 1546 genes) were treatment-methylated signatures (unmethylated in BT and methylated in AT group). (B) Distribution of TADS in regions in relation to CpG islands. (C) Overall distribution of the TADS in genomic elements. (D) Distribution of the promoter probes in 4820 TADS around TSS and upstream region from the start of the gene. (E) Frequency of TADS in different genic regions categorized based on the sequence overlap and distance from TSS. (F) Frequency of treatment-unmethylated signatures and treatment-methylated signatures categorized according to absolute distance to the nearest TSS of gene.

Article Snippet: Equal concentrations of labeled cyanine3 and cyanine5 enriched for unmethylated and methylated DNA fragments respectively were co-hybridized onto the Agilent 244 K CpG island microarray chip (Agilent Technologies, USA) at 65 °C, and speed of the hybridization rotator was set to rotate at 18 rpm for 40 h. Slides were washed with wash buffer after hybridization, dried and scanned using G2505B DNA microarray scanner (Agilent Technology, USA) with Sure Scan High resolution technology (Methodology detailed in Supplementary Methods ).

Techniques: DNA Methylation Assay, Methylation, Sequencing

Journal: Neuro-Oncology

Article Title: Comparative analyses of gene copy number and mRNA expression in glioblastoma multiforme tumors and xenografts

doi: 10.1215/15228517-2008-113

Figure Lengend Snippet: Frequencies of genomic copy number gains and losses in glioblastoma multiforme (GBM) xenograft (GBMX) tumor lines and GBM clinical samples. (A) GBMX tumors (n = 21) analyzed on the Affymetrix Xba 50K SNP array platform. (B) GBM tumors (n = 82) analyzed on the Affymetrix Xba 50K SNP array platform.13 (C) GBM tumors (n = 56) analyzed on the BAC array platform.14 (D) GBM tumors (n = 221) analyzed on the Agilent 244K oligonucleotide array platform.2

Article Snippet: For analyses of GBM clinical specimens, segment mean thresholds of ±0.3 were used on data generated from SNP arrays, 13 and thresholds of ±0.1 were used on data generated from bacterial artificial chromosome (BAC) arrays 14 , 15 and Agilent 244K oligonucleotide arrays 2 (Agilent Technologies, Santa Clara, CA, USA).

Techniques: