Journal: Cancer Research

Article Title: Molecular Inversion Probe Analysis of Gene Copy Alterations Reveals Distinct Categories of Colorectal Carcinoma

doi: 10.1158/0008-5472.can-06-0595

Figure Lengend Snippet: Figure 2. Heat map of cluster from significant gene copy alterations in colorectal cancer cell lines and carcinoma samples. Unsupervised hierarchical clustering was done on the data set of significant gene copy regions as determined by CLAC. The dendrogram from the clustering algorithm was used to generate a heat map, graphically depicting the relationship among the colorectal cancer cell lines. The heat map of the data uses a green (losses) versus red (gains) color scale. Each column represents an individual MIP arranged by chromosome and physical location in increasing order from left to right. A, each row represents a separate colorectal cancer cell line. The two topmost branches are designated as clusters 1 and 2. A subcluster branch representing MSI cell lines is labeled as 1a. B, each row represents a separate colorectal carcinoma sample. The two topmost clusters are labeled as clusters 1 and 2.

Article Snippet: Colorectal cancer cell lines (CACO2, COLO320, DLD1, HCT116, HCT15, LOVO, LS174T, LS180, NCIH508, NCIH747, RKO, SKCO1, SW1116, SW403, SW48, SW480, SW620, and SW837) were obtained from the American Type Culture Collection (Manassas, VA) and grown under the recommended conditions according to the manufacturer’s instructions.

Techniques: Labeling

Journal: Cancer Research

Article Title: Molecular Inversion Probe Analysis of Gene Copy Alterations Reveals Distinct Categories of Colorectal Carcinoma

doi: 10.1158/0008-5472.can-06-0595

Figure Lengend Snippet: Figure 3. Overall frequency of deletions and amplifications of clusters 1 and 2 classification of primary colorectal carcinomas. The gene copy frequency between cluster 1 and 2 is separately plotted. Y axis, overall frequency of gene copy changes for individual MIP; X axis, location of probe as arranged by chromosome and their nucleotide location.

Article Snippet: Colorectal cancer cell lines (CACO2, COLO320, DLD1, HCT116, HCT15, LOVO, LS174T, LS180, NCIH508, NCIH747, RKO, SKCO1, SW1116, SW403, SW48, SW480, SW620, and SW837) were obtained from the American Type Culture Collection (Manassas, VA) and grown under the recommended conditions according to the manufacturer’s instructions.

Techniques:

Journal: Turkish Journal of Biochemistry

Article Title: Resveratrol modulates miRNA machinery proteins in different types of colon cancer cells

doi: 10.1515/tjb-2023-0076

Figure Lengend Snippet: Figure 1: Dose–response curves and IC50 values of RSV COLO320 (A) and COLO741 (B) cells treated with different concentrations of RSV for 24 and 48 h, respectively.

Article Snippet: Cell lines and cell culture COLO320 (ATCC: CCL-220.1) and COLO741 (ECACC: 93052621) cell lines were used.

Techniques:

Journal: Turkish Journal of Biochemistry

Article Title: Resveratrol modulates miRNA machinery proteins in different types of colon cancer cells

doi: 10.1515/tjb-2023-0076

Figure Lengend Snippet: Figure 2: Immunoreactivity of CD-9 (A, B), CD-63 (C, D), Dicer (E, F), eIF2α (G, H), Ago2 (I, J), in control (A, C, E, G, I) and 25 μg/mL RSV-treated (B, D, F, H, J, L, N) COLO320 cells. Scale bars=20 μm.

Article Snippet: Cell lines and cell culture COLO320 (ATCC: CCL-220.1) and COLO741 (ECACC: 93052621) cell lines were used.

Techniques: Control

Journal: International Journal of Molecular Medicine

Article Title: Expression levels of hnRNP K and p21 WAF1/CIP1 are associated with resistance to radiochemotherapy independent of p53 pathway activation in rectal adenocarcinoma

doi: 10.3892/ijmm.2018.3898

Figure Lengend Snippet: Analysis of intracellular signaling pathways. (A) siRNA knockdown of hnRNP K was confirmed by western immunoblotting. (B) Increases in p53 Ser15-phosphorylation, PARP cleavage and CHK2 (Thr68) phosphorylation upon ionizing radiation in (a) Colo320 and (b) SW480 cells were neither affected by mock-siRNA nor by hnRNP K-siRNA transfection. hnRNP K, heterogeneous nuclear ribonucleoprotein K; PARP, poly (ADP-ribose) polymerase; siRNA, small interfering RNA; Con, control.

Article Snippet: The SW480 and Colo320 CRC cell lines were newly purchased from the Leibniz Institute DSMZ (Braunschweig, Germany).

Techniques: Protein-Protein interactions, Knockdown, Western Blot, Phospho-proteomics, Transfection, Small Interfering RNA, Control

Journal:

Article Title: Prediction of DNA single-strand conformation polymorphism: analysis by capillary electrophoresis and computerized DNA modeling

doi:

Figure Lengend Snippet: Human p53 exon 7 mutations

Article Snippet: The PCR products were screened for homogeneity by agarose gel electrophoresis and diluted 10-fold in H 2 O ( 2 ). table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Cell line a Type of mutation Position of mutation b Base pair change H 596 Point mutation 14 060 (245) G–T Colo 320 Point mutation 14 069 (248) C–T Namalwa Point mutation 14 070 (248) G–A Open in a separate window a American Type Culture Collection (Rockville, MD). b Nucleotide position with respect to GenBank Locus HSP53G, accession number 54156, amino acid position is in parenthesis.

Techniques: Mutagenesis

Journal:

Article Title: Prediction of DNA single-strand conformation polymorphism: analysis by capillary electrophoresis and computerized DNA modeling

doi:

Figure Lengend Snippet: CE of PCR samples. Electropherograms of exon 7 mutations found in the H 596, Colo 320 and Namalwa cell lines are shown in comparison to wild type. The PCR samples were separated by CE using the Perkin Elmer ABI PRISM™ Model 310 Genetic Analyzer. For each sample, the fluorescence signal is plotted as a function of migration time after sample loading. The fluorescence profiles for the mutant and wild type DNA strands are indicated by blue (sense) and green (antisense) lines. Separations were performed at 13 kV using the GENESCAN capillary and polymer system at an instrument setting of 35°C as described (see Materials and Methods).

Article Snippet: The PCR products were screened for homogeneity by agarose gel electrophoresis and diluted 10-fold in H 2 O ( 2 ). table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Cell line a Type of mutation Position of mutation b Base pair change H 596 Point mutation 14 060 (245) G–T Colo 320 Point mutation 14 069 (248) C–T Namalwa Point mutation 14 070 (248) G–A Open in a separate window a American Type Culture Collection (Rockville, MD). b Nucleotide position with respect to GenBank Locus HSP53G, accession number 54156, amino acid position is in parenthesis.

Techniques: Fluorescence, Migration, Mutagenesis

Journal:

Article Title: Prediction of DNA single-strand conformation polymorphism: analysis by capillary electrophoresis and computerized DNA modeling

doi:

Figure Lengend Snippet: Temperature dependence of CE-SSCP mobility shifts. A bar graph depiction of the change in CE migration time of Colo 320 (relative to wild type, WT). CE separations (as described above) were performed as a function of temperature and the resulting changes in migration times plotted relative to wild type. Open bars, sense strand; filled bars, antisense strand. Changes in migration times are plotted in scan units where 4.5 U = 1 s. Adapted from Atha et al. (1) with permission.

Article Snippet: The PCR products were screened for homogeneity by agarose gel electrophoresis and diluted 10-fold in H 2 O ( 2 ). table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Cell line a Type of mutation Position of mutation b Base pair change H 596 Point mutation 14 060 (245) G–T Colo 320 Point mutation 14 069 (248) C–T Namalwa Point mutation 14 070 (248) G–A Open in a separate window a American Type Culture Collection (Rockville, MD). b Nucleotide position with respect to GenBank Locus HSP53G, accession number 54156, amino acid position is in parenthesis.

Techniques: Migration

Journal:

Article Title: Prediction of DNA single-strand conformation polymorphism: analysis by capillary electrophoresis and computerized DNA modeling

doi:

Figure Lengend Snippet: Temperature dependence of CE-SSCP. Electropherogram of Colo 320 as a function of temperature. The sense and antisense DNA strands (SSDNA) are completely separated and undergo stepwise changes in conformation until the temperature reaches 50°C at which the SSCP effect ‘melts out’ and the complementary single stands are unresolved (see also fig.2) . The initial peaks, corresponding to the duplex and internal standard (DSDNA), are vertically aligned with respect to migration time. Measurements were performed using the Beckman PAC/E and the Perkin Elmer ABI GeneScan polymer and CE system as described (see Materials and Methods). Adapted from Atha et al. (1) with permission.

Article Snippet: The PCR products were screened for homogeneity by agarose gel electrophoresis and diluted 10-fold in H 2 O ( 2 ). table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Cell line a Type of mutation Position of mutation b Base pair change H 596 Point mutation 14 060 (245) G–T Colo 320 Point mutation 14 069 (248) C–T Namalwa Point mutation 14 070 (248) G–A Open in a separate window a American Type Culture Collection (Rockville, MD). b Nucleotide position with respect to GenBank Locus HSP53G, accession number 54156, amino acid position is in parenthesis.

Techniques: Migration

Journal:

Article Title: Prediction of DNA single-strand conformation polymorphism: analysis by capillary electrophoresis and computerized DNA modeling

doi:

Figure Lengend Snippet: 5′-Sorted stem trace of the wild type sense and Colo 320 sense solution spaces produced by an MFOLD 3.1 DPA, run with DNA energy rules (corresponding to an older version 2.3), with salt concentrations of 0.1 M Na+ and 0.0 M Mg2+. Presented solution spaces were calculated for a range of temperatures from 30 to 70°C in 5°C increments (with an exception for 37°C, instead of 35°C). Stems 1 and 2 are unique to MFOLD’s solution spaces. Stems 3, 3M, 4, 5 and 6 are the same as those predicted by RNAstructure 3.5. Melting of the structures can be seen as the increasing sparseness of the stem traces with increasing temperature.

Article Snippet: The PCR products were screened for homogeneity by agarose gel electrophoresis and diluted 10-fold in H 2 O ( 2 ). table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Cell line a Type of mutation Position of mutation b Base pair change H 596 Point mutation 14 060 (245) G–T Colo 320 Point mutation 14 069 (248) C–T Namalwa Point mutation 14 070 (248) G–A Open in a separate window a American Type Culture Collection (Rockville, MD). b Nucleotide position with respect to GenBank Locus HSP53G, accession number 54156, amino acid position is in parenthesis.

Techniques: Produced

Journal:

Article Title: Prediction of DNA single-strand conformation polymorphism: analysis by capillary electrophoresis and computerized DNA modeling

doi:

Figure Lengend Snippet: 5′-Sorted stem trace of the wild type antisense and Colo 320 antisense solution spaces produced by an MFOLD 3.1 DPA, run with DNA energy rules (corresponding to an older version 2.3), with salt concentrations of 0.1 M Na+ and 0.0 M Mg2+. Presented solution spaces were calculated for a range of temperatures from 30 to 70°C in 5°C increments (with an exception for 37°C, instead of 35°C). Stems 1 and 2 are unique to MFOLD’s solution spaces. Stems 3 (wild type, light green ), 3M (Colo 320, dark green), 4, 5 and 6 are the same as those predicted by RNAstructure 3.5. Melting of the structures can be seen as the increasing sparseness of the stem traces with increasing temperature.

Article Snippet: The PCR products were screened for homogeneity by agarose gel electrophoresis and diluted 10-fold in H 2 O ( 2 ). table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Cell line a Type of mutation Position of mutation b Base pair change H 596 Point mutation 14 060 (245) G–T Colo 320 Point mutation 14 069 (248) C–T Namalwa Point mutation 14 070 (248) G–A Open in a separate window a American Type Culture Collection (Rockville, MD). b Nucleotide position with respect to GenBank Locus HSP53G, accession number 54156, amino acid position is in parenthesis.

Techniques: Produced