u133a oligonucleotide microarray  (Thermo Fisher)

Journal: Biology

Article Title: Genes Associated with the Immune System Affected by Ionizing Radiation and Estrogen in an Experimental Breast Cancer Model

doi: 10.3390/biology13121078

Figure Lengend Snippet: Profile of genes with differential expression acquired using an Affymetrix array (U133A) in an induced-radiation and -estrogen experimental breast cancer model, comparing genes such as ( A ) the TNF alpha-induced protein 6 gene ( TNFAIP6 ), ( B ) the interferon-related developmental regulator 1 gene ( IFRD1 ), ( C ) the Interferon-Induced Transmembrane protein 2 gene ( IFITM2 ), ( D ) the Interferon-Gamma Receptor 1 gene ( IFNGR1 ), ( E ) the Interferon Regulatory Factor 6 gene ( IRF6 ), and ( F ) the Nuclear Factor Interleukin 3-regulated gene ( NFIL3 ) in the following cell lines: MCF-10F/estrogen (Ct/E), Control/Alpha3 (Ct/A3), estrogen/Alpha5 (E/A5), Alpha3/Alpha5 (A3/A5), Alpha5/Tumor2 (A5/T2), and Alpha3/Tumor2 (A3/T2). The graphs were obtained from a gene expression cluster dendrogram repository from our laboratory for this article.

Article Snippet: The Affymetrix U133A oligonucleotide microarray (Affymetrix, Santa Clara, CA, USA), which comprises 14,500 genes, was used to assess gene expression in the breast cancer model, which included the cell lines Ct, E, A3, A5, and T2.

Techniques: Expressing, Control

Journal: Neurosurgical Review

Article Title: Glioblastoma invasion patterns from a clinical perspective—a systematic review

doi: 10.1007/s10143-024-02944-6

Figure Lengend Snippet: Overview of the outcomes of the 21 included studies: overall survival, progression free survival (PFS), author’s personal considerations

Article Snippet: Garcia et al., 2012 , Immunohistochemical analysis; Comparative genomic hybridisation; Affymetrix U133A oligonucleotide microarrays , VAV 1 weak expression (0–1%) = 27 patients → OS 12 months VAV 1 intensity (5 or > 5%) = 23 patients → OS 10 months , VAV 1 weak expression (0–1%) = 6 months VAV 1 intensity (5 or > 5%) = 5 months VAV1-positive cells were located around GBM-triggered vasculature (18%) and surrounding tumour mass (20%) , Mesenchymal subtype: 9 Classic subtype: 2 Proneural: 1 Cytoskeletal dynamics were found associated to VAV1 expression.

Techniques: Enzyme-linked Immunosorbent Assay, Immunohistochemical staining, Concentration Assay, Expressing, Hybridization, Staining, Migration, RNA Extraction, Microarray, Real-time Polymerase Chain Reaction, Immunofluorescence, Flow Cytometry, Activity Assay, Functional Assay, RNA Sequencing Assay, Methylation, Inhibition, Western Blot, Activation Assay, Extraction

Journal: International Journal of Molecular Sciences

Article Title: Tumor Biology Hides Novel Therapeutic Approaches to Diffuse Large B-Cell Lymphoma: A Narrative Review

doi: 10.3390/ijms252111384

Figure Lengend Snippet: Genetic and metabolic heterogeneity of DLBCL.

Article Snippet: , Monti et al., 2005. [ ] , , OxPhos , cluster signatures: NADH dehydrogenase complex, COX complex, ATP synthase (mitochondrial), ATP binding protein, ATP binding cassette subfamily, ATPase H+ transporter, TIMM, BFL-1/A1, MIHC, TNFA1P8, FAS, apoptosis-related protein 3, proteasome subunits, PTEN, etc. , , , , , three unsupervised clustering algorithms were used and compared: hierarchical clustering, self-organizing maps & model-based probabilistic clustering , GEPs by oligonucleotide microarrays (Affymetrix U133A & U133B) containing probe sets from 33,000 genes, FISH, morphologic analysis of TILs, IHC , DLBCL specimen from 176 patients , increased incidence of t(14;18) in OxPhos tumors; BCR/proliferation cluster had more abundant expression of cell-cycle regulatory genes, increased expression of DNA repair genes and p53, higher levels of many components of the BCR signaling cascade (CD19, Ig, CD79a, BLK, SYK, PLCγ2, MAP4K), additional B-cell–specific or essential TFs; the HR cluster was extensively studied: increased expression of T/NK cell receptor and activation pathway components, complement cascade members, macrophage/DC markers & inflammatory mediators; shared features of histologically defined T-cell/histiocyte-rich B-cell lymphoma, including fewer genetic abnormalities.

Techniques: Expressing, Microarray, Translocation Assay, Amplification, Selection, RNA Sequencing Assay, Activity Assay, DNA Sequencing, Mutagenesis, Activation Assay, Sequencing, Functional Assay, Binding Assay