Journal: PLoS ONE

Article Title: Acetate Supplementation Induces Growth Arrest of NG2/PDGFRα-Positive Oligodendroglioma-Derived Tumor-Initiating Cells

doi: 10.1371/journal.pone.0080714

Figure Lengend Snippet: A) PCR of OG33 and OG35 cells (grade II and grade III, respectively, primary oligodendroglioma-derived cells that exhibit self-renewal and tumorigenicity) maintained as floating spheres in stem cell medium for 4 days. A grade III oligodendroglioma tumor (Oligo tumor) and proneural (PN) GBM GSCs served as controls. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used as a loading control. OG cells expressed the OPC marker PDGFRα and Notch1, but lacked the neural stem cell markers CD133, SOX2, and Olig2. In contrast, they abundantly expressed the mesenchymal markers CD44, BCL2A1, Wilms Tumor 1 (WT1). B) Principal component analysis (PCA) of SNP raw intensity data from GeneChip® Human Mapping 250K Nsp Arrays. OG cells share similar gene amplifications/deletions to the established HOG oligodendroglioma cell line. Furthermore, the OG cells were more similar to mesenchymal GBM GSCs (GBM12, GBM9, and GBM34) than proneural GSCs (GBM44, GBM8, and GBM2). The Hs683 cell line, which was derived from a GBM tumor but shares features of oligodendroglioma tumors, failed to cluster with either tumor type. C) Immunocytochemistry after 3 days growth in stem cell medium (adherent on PLL) or differentiation medium revealed that the OG cells express a transition mesenchymal profile. In stem cell medium, cells expressed OPC markers (NG2 and PDGFRα), although less abundantly than Oli-Neu OPCs. In contrast, they abundantly expressed the mesenchymal markers CD44 and glutathione S-transferase π (GSTπ). In differentiation medium, OG33 and OG35 cells expressed lower levels of CNPase than Oli-Neu cells, and, unlike Oli-Neu cells, the OG cells failed to express myelin basic protein (MBP), a well-accepted marker of mature oligodendrocytes. Oli-Neu and PN GBM GSCs served as controls. Scale bar = 100 µm.

Article Snippet: Samples were hybridized to the Affymetrix 250K Nsp Array for 16 hours at 49°C followed by a double streptavidin-phycoerytherin staining and scanned on a GS3000-7G scanner.

Techniques: Derivative Assay, Marker, Wilms Tumor Assay, Immunocytochemistry

Journal: Nucleic Acids Research

Article Title: Targeted resequencing of candidate genes using selector probes

doi: 10.1093/nar/gkq1005

Figure Lengend Snippet: ( a ) Mutation detection and CNV analysis of a lung cancer patient sample with matched control. Upper panel: for each position in the targeted region the number of bases called in the patient-matched normal tissue is subtracted from the number of bases called in the tumor-derived DNA, and then divided with the sum of called bases for that position in the two samples. The exons of the 28 genes are lined up after each other and genes are demarked by alternating background color. Middle panel: the inferred gene copy-number variation in the corresponding genomic loci illustrated by log2 ratios (pink line) derived from SNP array data (Affymetrix Gene Chip Mapping 250K arrays). Middle panel: the log2 ratio (pink line) of the copy-number analysis done on an Affymetrix micro array. Lower panel: the allelic ratio between the major and minor allele at each position is compared between the two samples by subtraction ( b ). A correlation plot between the Affymetrix Gene Chip log2 tumor/normal signal ratio and the log2 tumor/normal sequencing read depth ratio. ( c ) Detection of a single base pair deletion in the TP53 gene. Forward (brown) and reverse (blue) reads are aligned to a 15-bp region of the TP53 gene. Deleted bases are indicated by dashed lines. Alignment visualized in Integrative Genomic Viewer (IGV ver.1.4.2). ( d ) Detection of the same mutation in the FFPE sample from the same tumor.

Article Snippet: SNP-array experiments were performed according to the standard protocols for Affymetrix GeneChip® Mapping NspI-250K arrays (Gene Chip Mapping 500K Assay Manual (P/N 701930 Rev2.), Affymetrix Inc., Santa Clara, CA, USA) and the arrays were scanned using the GeneChip® Scanner 3000 7G.

Techniques: Mutagenesis, Derivative Assay, Microarray, Sequencing

Journal: European Journal of Human Genetics

Article Title: Meta-analysis of genome-wide association for migraine in six population-based European cohorts

doi: 10.1038/ejhg.2011.48

Figure Lengend Snippet: Sample descriptives

Article Snippet: Platform , Illumina 370CNV , Illumina HumanHap300 HumanHap370 Affymetrix 250K Nsp array , Perlegen/ Affymetrix 600K , Perlegen/Affymetrix 600K , Illumina Human660W-Quad BeadChip , Illumina Infinium II HumanHap550 version 3.0.

Techniques: Software