Journal: Cancer Science

Article Title: Adoptive cell therapy using tumor‐infiltrating lymphocytes for melanoma refractory to immune‐checkpoint inhibitors

doi: 10.1111/cas.15009

Figure Lengend Snippet: Total mutation burden, transcriptome signature (ssGSEA score), and quantitative real‐time polymerase chain reaction analysis of pretreatment melanoma cells and expanded TILs. A, To evaluate their mutation status, exome sequencing was performed on the melanoma cells used for TIL manufacturing. The numbers of mutations and the mutated genes in each tumor are shown in the upper columns. Transcriptome signatures based on single‐sample gene set enrichment analysis (ssGSEA) of the tumor cells are shown in the lower columns. B, ssGSEA scores of gene sets related to tumor phenotype (based on microarray data) in the tumors of the three melanoma patients. The cut‐off score was set at 4,000. C, D, Quantitative RT‐PCR analysis of the expression levels of chemokines in the primary tumors (C) and of cytotoxic factors in the expanded TIL products (D). The results are fold‐changes in gene expression normalized to the endogenous reference gene; error bars are standard deviations

Article Snippet: Total RNA from isolated melanoma cells was subjected to microarray analysis using an Agilent SurePrint G3 Human GE v3 8x60K Microarray (DNA Chip Research Inc.).

Techniques: Mutagenesis, Real-time Polymerase Chain Reaction, Sequencing, Microarray, Quantitative RT-PCR, Expressing

Journal: PLoS ONE

Article Title: Adenomatous polyposis coli-binding protein end-binding 1 promotes hepatocellular carcinoma growth and metastasis

doi: 10.1371/journal.pone.0239462

Figure Lengend Snippet: (a and b) RNA microarray analysis to identify genes differentially expressed in the presence of EB1. Comparison of gene expression levels in EB1-KO HuH7 cells infected with control and EB1-expressing lentiviruses identified a number of genes upregulated by EB1 re-expression.

Article Snippet: After properly converting the extracted RNA to the cRNA labeled with Cy3 as recommended by the manufacturers, 0.6 μg of the cRNA was fragmented and hybridized at 65°C for 17 h to an Agilent SurePrint G3 Human GE v3 8x60K Microarray (Design ID: 072363) containing a total of 58,201 probes excluding control probes.

Techniques: Microarray, Expressing, Infection

Journal: Life

Article Title: NSD1 Mutations in Sotos Syndrome Induce Differential Expression of Long Noncoding RNAs, miR646 and Genes Controlling the G2/M Checkpoint

doi: 10.3390/life12070988

Figure Lengend Snippet: Real-time PCR validation of differentially expressed genes. ( a ) Quantitative expression measurements of five noncoding RNAs (i.e., lnc-C15orf57 , MIR646 , lnc-C2orf84-1 , Inc-C00665 and lnc-C20orf197-3 ) and ( b ) seven mRNAs (i.e., NOS3 , ZNF883 , CD19 , SFN , GSC , NDRG2 and SORBS1 ). The fold change represents the average difference in expression level of the respective genes between the SoS fibroblasts and the controls. The black bars depict the fold changes detected with the microarray, whereas the white bars show the average fold change with respect to the triplicate real-time PCR assessments. The fold changes indicating a downregulated expression are represented with negative values. The error bars represent the standard error of the mean. Significant levels were at p < 0.05. ( c ) Compared to healthy controls, five noncoding RNAs ( lin-C005, Inc-C20orf97 , MIR646HG , lnc-C15orf57 and Inc-C20orf84-1 ) and ( d ) seven mRNAs ( NOS3 , ZNF883 , CD19 , SFN , NDRG2 , SORBS1 and GSC ) were selected. The black bars depict healthy control (Ctr), and the white bars represent the Sotos syndrome patients (SoS pts). The results were consistent with the findings obtained from the microarray analysis. Data are presented as the mean ± standard deviation. * p < 0.05, ** p < 0.01.

Article Snippet: Briefly, cyanine-3-CTP-labeled cRNA was hybridized onto SurePrint G3 microarray chips (Design ID: G4851C), which contained 50,599 probes for 32,776 human mRNAs and 17,438 human lncRNAs; these were derived from authoritative databases, including RefSeq, Ensemble, GenBank and the Broad Institute.

Techniques: Real-time Polymerase Chain Reaction, Biomarker Discovery, Expressing, Microarray, Control, Standard Deviation

Journal: Frontiers in Immunology

Article Title: Identification of potential biomarkers and immune infiltration characteristics in recurrent implantation failure using bioinformatics analysis

doi: 10.3389/fimmu.2023.992765

Figure Lengend Snippet: Baseline Characteristics.

Article Snippet: Techniques , GPL16043 platform , Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 , GPL15789 platform , 10X Genomics Chromium platform.

Techniques: Microarray, Control