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: Cell

Article Title: Neuronal Small RNAs Control Behavior Transgenerationally

doi: 10.1016/j.cell.2019.04.029

Figure Lengend Snippet: Sorting of Neurons Followed by RNA Sequencing Allows the Characterization of Neuronal RDE-4-Dependent Small RNAs (A) Scheme depicting the production of RNA libraries specifically from neurons of C. elegans . Single-cell suspensions were produced out of wild type, rde-4 (−), and Psng-1::rde-4 strains that express Prab-3::rfp in neurons ( Kaletsky et al., 2016 , Stefanakis et al., 2015 ), followed by immediate fluorescence-activated cell sorting (FACS). Sorted RFP + neurons were collected for total RNA isolation. (B) Expression levels of NeuroSTGs in rescued Psng-1::rde-4 worms (y axis) compared to rde-4 ( ne299 ) mutants (x axis). Shown are the averaged expression values (log2 of rpm) of NeuroSTGs (see also ). Each dot represents a NeuroSTG. 46 NeuroSTGs (red) displayed differential expression between groups (analyzed with Deseq2, adjusted p value < 0.1). (C) x-fold enrichment or depletion values of upregulated NeuroSTGs (left) and downregulated NeuroSTGs (right) following neuronal RDE-4 rescue. See also Figure 1 E. For the clarity of display, complete depletion (linear enrichment = 0) appears with the smallest value in the scale. ns, p > 0.05; ∗∗∗∗ p < 10 −4 . (D) Changes in neuronal mRNA levels (y axis) in Psng-1::rde-4 compared to rde-4 (−) neurons, plotted against changes in their associated NeuroSTGs (x axis). Each dot represents the values for one gene, and the 46 genes with significant changes in their corresponding NeuroSTGs are shown (analyzed with Deseq2, adjusted p value < 0.1). Nine genes (red) exhibited also differential mRNA expression (analyzed with Deseq2, adjusted p value < 0.1). See also Figure S2 and .

Article Snippet: The microarray experiments were performed using Affymetrix GeneChip® C. elegans Genome Array oligonucleotide arrays (Thermofisher).

Techniques: RNA Sequencing, Produced, Fluorescence, FACS, Isolation, Expressing, Quantitative Proteomics

Journal: Cell

Article Title: Neuronal Small RNAs Control Behavior Transgenerationally

doi: 10.1016/j.cell.2019.04.029

Figure Lengend Snippet:

Article Snippet: The microarray experiments were performed using Affymetrix GeneChip® C. elegans Genome Array oligonucleotide arrays (Thermofisher).

Techniques: Recombinant, Multiplex Assay, DNA Purification, DNA Library Preparation, Saline, Suspension, Plasmid Preparation, Software

Journal: Biology

Article Title: Genes Related to Motility in an Ionizing Radiation and Estrogen Breast Cancer Model

doi: 10.3390/biology13110849

Figure Lengend Snippet: Relative expression of cell motility genes from Affymetrix array (U133A) in an experimental breast cancer model induced by radiation and estrogen. The analyzed genes were ( a ) ADAM12 , ( b ) CYR61 , ( c ) FLRT2 , ( d ) SLIT2 , ( e ) VNN1 , ( f ) MYLK , ( g ) MAP1B , and ( h ) TUBA1A in 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) cell lines. Red indicates a positive value and blue a negative one. The graphs were obtained from a cluster-dendrogram repository of gene expression from our laboratory for this article.

Article Snippet: The Affymetrix U133A oligonucleotide microarray experiment was conducted once and contained 14,500 genes.

Techniques: Expressing, Control

Journal: Molecular and Cellular Biology

Article Title: Role for E2F in Control of Both DNA Replication and Mitotic Functions as Revealed from DNA Microarray Analysis

doi: 10.1128/mcb.21.14.4684-4699.2001

Figure Lengend Snippet: FIG. 1. Analysis of cell cycle progression in MEFs. (A) MEF cells were synchronized either by serum starvation or by HU block and brought back to the cell cycle progression either by adding serum (left panel) or by adding the fresh medium containing serum without HU (right panel). Cells were harvested at the indicated time points, stained with propidium iodide, and processed for flow cytometry. Percentage of cells in S phase at each time point is plotted. (B) E2F DNA-binding activity in the samples described in panel A. Nuclear extracts prepared from the indicated samples were assayed for E2F DNA-binding activity by electrophoretic mobility shift assay as described in the text. The identity of the indicated E2F binding activities is based on relative gel mobility and identification with specific antibodies. (C) Cyclin E expression during the cell cycle progression. RNA was prepared from the indicated samples and analyzed by Northern blotting, using a cyclin E cDNA probe. An equal amount of mRNA was loaded in each lane. (D) Comparison of gene expression measurement by the Affymetrix GeneChip cyclin E array to that obtained by densitometric scanning of a Northern blot of the same RNA sample. The average difference values of cyclin E gene calculated by the Affymetrix GeneChip expression analysis algorithm were normalized across the two experiments and plotted (I). The intensity of the cyclin E bands in the Northern blot shown in panel C was measured by densitometric scanning. The values are normalized across each experiment and plotted (F).

Article Snippet: For these experiments, we have made use of Affymetrix GeneChip DNA microarrays that contain murine gene sequences and expressed sequence tags (ESTs) and then assayed the profile of gene expression following expression of E2F proteins in quiescent cells.

Techniques: Blocking Assay, Staining, Cytometry, Binding Assay, Activity Assay, Electrophoretic Mobility Shift Assay, Expressing, Northern Blot, Comparison, Gene Expression

Journal: Molecular and Cellular Biology

Article Title: Role for E2F in Control of Both DNA Replication and Mitotic Functions as Revealed from DNA Microarray Analysis

doi: 10.1128/mcb.21.14.4684-4699.2001

Figure Lengend Snippet: FIG. 2. Identification of patterns of gene expression following growth stimulation and during the mammalian cell cycle. Expression profile of individual genes in the serum stimulation and HU release experiments, clustered according to the methods described in the text. The expression level of each gene in the two experiments was displayed by a pseudo-color visualization matrix (6). In each experiment, a ver- tical column represents all of the clustered genes for a given time point. The intensity of expression, as determined from the average difference values calculated by GeneChip expression analysis (Affy- metrix), is depicted by the intensity of red color.

Article Snippet: For these experiments, we have made use of Affymetrix GeneChip DNA microarrays that contain murine gene sequences and expressed sequence tags (ESTs) and then assayed the profile of gene expression following expression of E2F proteins in quiescent cells.

Techniques: Gene Expression, Expressing