Journal: Frontiers in Pharmacology

Article Title: Pharmacogenomic Characterization and Isobologram Analysis of the Combination of Ascorbic Acid and Curcumin—Two Main Metabolites of Curcuma longa —in Cancer Cells

doi: 10.3389/fphar.2017.00038

Figure Lengend Snippet: Meta-data of genes shown in the cluster analysis of whose mRNA expression correlated with log 10 IC 50 -values of vitamin C in the NCI tumor cell line panel .

Article Snippet: We correlated the IC 50 -values expressed on induction by curcumin and AA of 60 tumor cell lines by COMPARE analysis of microarray-based transcriptome-wide mRNA expression levels of these cell lines (Scherf et al., ).

Techniques: Expressing, Virus, Transduction, Activity Assay, Binding Assay, Coagulation, Phospho-proteomics, Residue, Sequencing, Membrane, Activation Assay, Control, Ubiquitin Proteomics

Journal: Frontiers in Pharmacology

Article Title: Pharmacogenomic Characterization and Isobologram Analysis of the Combination of Ascorbic Acid and Curcumin—Two Main Metabolites of Curcuma longa —in Cancer Cells

doi: 10.3389/fphar.2017.00038

Figure Lengend Snippet: Dendrograms and cluster image map of curcumin obtained by hierarchical cluster analysis of mRNA expression of 40 genes in the NCI cell line panel as analyzed by the Novartis microarray platform . The dendrogram on the left shows the clustering of cell lines and the dendrogram on the top shows the clustering of genes. The cluster image map shows each single mRNA expression value obtained by microarray analysis. The expression values have been normalized and color-coded.

Article Snippet: We correlated the IC 50 -values expressed on induction by curcumin and AA of 60 tumor cell lines by COMPARE analysis of microarray-based transcriptome-wide mRNA expression levels of these cell lines (Scherf et al., ).

Techniques: Expressing, Microarray

Journal: Frontiers in Pharmacology

Article Title: Pharmacogenomic Characterization and Isobologram Analysis of the Combination of Ascorbic Acid and Curcumin—Two Main Metabolites of Curcuma longa —in Cancer Cells

doi: 10.3389/fphar.2017.00038

Figure Lengend Snippet: Dendrograms and cluster image map of vitamin C obtained by hierarchical cluster analysis of mRNA expression of 40 genes in the NCI cell line panel as analyzed by the Novartis microarray platform . The dendrogram on the left shows the clustering of cell lines and the dendrogram on the top shows the clustering of genes. The cluster image map shows each single mRNA expression value obtained by microarray analysis. The expression values have been normalized and color-coded.

Article Snippet: We correlated the IC 50 -values expressed on induction by curcumin and AA of 60 tumor cell lines by COMPARE analysis of microarray-based transcriptome-wide mRNA expression levels of these cell lines (Scherf et al., ).

Techniques: Expressing, Microarray

Journal: Genes & Diseases

Article Title: Recent advances in elucidating the genetics of common variable immunodeficiency

doi: 10.1016/j.gendis.2019.10.002

Figure Lengend Snippet: Advantages and limitations of different genomic, transcriptomic and proteomics based platforms in Common variable immunodeficiency disease. ELISA, Enzyme-linked immunosorbent assay; SNP, Single nucleotide polymorphism.

Article Snippet: The major breakthrough in the sequencing technology, came with 13-years long, Human Genome Project (HGP) which was completed in 2003. , With the transition of sequencing technology to development of next generation sequencing based technology (Illumina, Roche 454, Ion Torrent/PGM sequencing, Oxford Nanopore) for rapid amplification of larger stretch of human genome, the sequencing platforms allowed for sequencing with 30× coverage or more.

Techniques: Enzyme-linked Immunosorbent Assay, Genome Wide, Biomarker Discovery, Sequencing, Electrophoresis, Next-Generation Sequencing, Amplification, High Throughput Screening Assay, Gene Expression, Generated, Microarray, Hybridization, Sample Prep, Transcriptome Wide Gene Expression, DNA Methylation Assay, Methylation, Quantitative Proteomics, Fourier Transform Infrared Spectroscopy, Spectroscopy

Journal: BMC Genomics

Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays

doi: 10.1186/1471-2164-10-497

Figure Lengend Snippet: Schematic of the HaloCHIP-chip microarray experiment design . HaloCHIP DNA (10-50 ng) obtained for both the experimental HaloTag-CREB and untransfected control sample was purified and amplified to a concentration of 1-10 μg using the whole genome amplification (WGA) method (Sigma) . The HaloTag-CREB amplified sample was labelled with Cy5 (green) and the untransfected control sample with Cy3 (red), then hybridized to a custom DNA oligo microarray manufactured by Roche NimbleGen. The oligo array was designed to cover on average a 1.8 kb region of 27,661 human promoter regions that contain 33,255 TSS predicted by SwitchGear Genomics. To obtain coverage of each promoter, an average of fourteen 50mer single stranded DNA probes, shown in purple, per promoter were used, with an average spacing of 131 bp per probe.

Article Snippet: A custom DNA oligo microarray was designed based upon promoter regions defined by SwitchGear Genomics genome-wide set of predicted transcription start sites (Figure ) [ - ].

Techniques: Microarray, Control, Purification, Amplification, Concentration Assay, Whole Genome Amplification

Journal: Handbook of Clinical Neurology

Article Title: Laboratory diagnosis of viral infection

doi: 10.1016/B978-0-444-53488-0.00005-5

Figure Lengend Snippet: Common molecular methods

Article Snippet: PCR or RT-PCR , DNA or RNA , Taq DNA polymerase, plus reverse transcriptase for RNA viruses , DNA , Gel electrophoresis, hybridization, real-time methods (e.g. TaqMan probes, SYBR green), fluorescent microspheres, microarray, melting curves, electrochemical , HIV, HCV, HBV, CMV viral load tests, enterovirus, respiratory viruses, HSV 1, 2, published protocols available for most viruses , Roche COBAS, Abbott m2000, Cepheid Gene Xpert, Roche LightCycler, Cepheid Smartcycler, Applied Biosystems, Luminex xTAG, GenMark eSensor, Biofire FilmArray, Nanosphere Verigene, Focus Simplexa , Several integrated platforms available ; most widely used for “home brew” assays; highly multiplexed assays can detect over 20 viruses in a single reaction .

Techniques: Amplification, DNA Gel Electrophoresis, Hybridization, SYBR Green Assay, Microarray, Luminex, Activity Assay, Kinetic Assay, Fluorescence

Journal: Cells

Article Title: Novel Approaches for Identifying the Molecular Background of Schizophrenia

doi: 10.3390/cells9010246

Figure Lengend Snippet: Results of recent schizophrenia genome-wide association studies (GWASs) and basic methods for identification of schizophrenia genes. ( A ) Manhattan plot for recent schizophrenia GWAS meta-analysis . Many GWAS regions cover several genes. However, some of them are located in intergenic DNA. Two representative GWAS regions are zoomed in: significantly associated polymorphisms are depicted as vertical bars. ( B ) Statistical fine-mapping of genetic associations. Each polymorphism’s probability to be causal is assessed in this type of analysis. Additional epigenetic information can improve prediction accuracy. Idealized fine-mapping of GWAS region is depicted. Only one of 10 genome-wide significant polymorphisms (highlighted in dashed rectangle) appears to be credible causal variant. ( C ) Trans-ethnic GWAS. Trans-ethnic study including human populations of three different ancestries is represented. Picture shows one of 10 variants from an idealized GWAS region as consistently (non-heterogeneously) associated with the phenotype. It is assumed that such variants are likely to be causal. ( D ) Study of highly penetrant mutations with brain-related phenotypes. Genes, identified using three different approaches of this class as being schizophrenia genes, are represented. Whole-exome sequencing (WES) studies indicated that rare mutations in SLC6A1 cause schizophrenia . This strongly suggests that expression of SLC6A1 is regulated by schizophrenia-associated common variants as one of GWAS regions is located in close vicinity to this gene (200 kb upstream). Rare Mendelian syndrome with psychiatric symptoms confirms role of TCF4 in schizophrenia development. Various disruptive mutations in this gene lead to dominant autosomal Pitt-Hopkins syndrome, characterized in particular by epilepsy and mental retardation . Finally, phenotypes of model animals with deliberately knocked-out genes identified ZNF536 as being one of the schizophrenia genes. ZNF536 double-knockout zebrafish line shows behavioural and neuroanatomical (decreased forebrain volume) changes . ( E ) Description of transcriptional effects of common variation in human neuronal cells. Converging lines of evidence obtained using these methods indicate that FOXG1 is likely to be regulated by a schizophrenia causal variant. Study of spatial chromatin organization in human fetal brain revealed that one of the schizophrenia GWAS regions interacts with the promoter of FOXG1 located 750 kb from it . Subsequent study showed that FOXG1 -interacting SNP rs1191551 is close to one of the fetal brain ATAC-seq peaks . Functional test (luciferase assay) demonstrated enhancer activity of genomic fragment, harbouring rs1191551. Furthermore, this activity was dependent on genotype. The role of this region in regulation of FOXG1 was additionally confirmed by CRISPR-Cas9 deletion of 500 bp surrounding rs1191551 in neural progenitor cells, with the latter leading to a significant decrease in expression of FOXG1 but not any other nearby gene.

Article Snippet: Episome-based functional reporter assays (luciferase assay and STARR-seq) , A potential enhancer sequence is inserted in specially-designed episome, harbouring reporter genes. Transfection of the construct into cells with subsequent measurement of reporter gene expression levels allows assessment of enhancer activity for a tested sequence in a given cell type. The luciferase test was designed for low-throughput testing of enhancer sequences (one at a time), whereas the STARR-seq allows testing of thousands of genomic sites in one experiment. , The luciferase assay is used to confirm regulatory activity of schizophrenia-associated genomic sites predicted to be enhancers in brain cells. Often, such predictions are based on the results of the aforementioned epigenomic methods: ChIP-seq, chromatin accessibility assays or high-throughput proximity ligation assays. Besides that, the influence of alternative alleles of schizophrenia-associated SNPs on activity of enhancers, in which given polymorphic sites reside, can be measured with the luciferase assay. STARR-seq can potentially be used to probe all genomic sites on their enhancer activity in a given brain cell type. Localisation of schizophrenia-associated variants inside STARR-seq confirmed brain enhancers can be considered strong evidence of causality. , [ , ] .

Techniques: GWAS, Genome Wide, Variant Assay, Sequencing, Expressing, Double Knockout, Functional Assay, Luciferase, Activity Assay, CRISPR

Journal: Cells

Article Title: Novel Approaches for Identifying the Molecular Background of Schizophrenia

doi: 10.3390/cells9010246

Figure Lengend Snippet: Approaches most commonly used in schizophrenia post-GWAS studies.

Article Snippet: Episome-based functional reporter assays (luciferase assay and STARR-seq) , A potential enhancer sequence is inserted in specially-designed episome, harbouring reporter genes. Transfection of the construct into cells with subsequent measurement of reporter gene expression levels allows assessment of enhancer activity for a tested sequence in a given cell type. The luciferase test was designed for low-throughput testing of enhancer sequences (one at a time), whereas the STARR-seq allows testing of thousands of genomic sites in one experiment. , The luciferase assay is used to confirm regulatory activity of schizophrenia-associated genomic sites predicted to be enhancers in brain cells. Often, such predictions are based on the results of the aforementioned epigenomic methods: ChIP-seq, chromatin accessibility assays or high-throughput proximity ligation assays. Besides that, the influence of alternative alleles of schizophrenia-associated SNPs on activity of enhancers, in which given polymorphic sites reside, can be measured with the luciferase assay. STARR-seq can potentially be used to probe all genomic sites on their enhancer activity in a given brain cell type. Localisation of schizophrenia-associated variants inside STARR-seq confirmed brain enhancers can be considered strong evidence of causality. , [ , ] .

Techniques: Next-Generation Sequencing, Reverse Transcription, Activity Assay, Comparison, Expressing, Quantitative Proteomics, Genome Wide, Chromatin Immunoprecipitation, Incubation, Purification, Sequencing, Functional Assay, Luciferase, Amplification, Ligation, Variant Assay, Transfection, Construct, Gene Expression, CRISPR, In Situ, Knock-Out, Blocking Assay, Microarray, Extraction, Derivative Assay