Journal: BMC Cancer

Article Title: Aberrant septin 9 DNA methylation in colorectal cancer is restricted to a single CpG island

doi: 10.1186/1471-2407-13-398

Figure Lengend Snippet: Genomic organization of SEPT9. The UCSC genome browser ( http://genome.ucsc.edu ) was used to display the location and genomic organization of SEPT9 on chromosome 17q25. (A) Genomic region covering approximately 300 kb: the eight amplicons (IDs given in red letters and within brackets) are shown after aligning their sequences using BLAST; CpG islands are shown in the track above the amplicons and gene transcripts are shown in the tracks below the amplicons. CGIs were numbered for easier reference within this manuscript. The UCSC display of transcripts is annotated with the combined IDs from Ensembl and NCBI/gene map for easier cross platform identification. (B) Detail of approximately 6 kb showing a higher resolution of the locations of the closely neighboring amplicons 4 to 7.

Article Snippet: Sections were then incubated with the primary antibody against Septin-9 (polyclonal AB cat.# PAB4799, Abnova, Germany) in 1:50 dilution for 60 minutes at 37°C, washed again in PBS, and detected with Alexa Fluor 546 dye in 1:100 dilution after 30 minutes of incubating at 37°C.

Techniques:

Journal: BMC Cancer

Article Title: Aberrant septin 9 DNA methylation in colorectal cancer is restricted to a single CpG island

doi: 10.1186/1471-2407-13-398

Figure Lengend Snippet: Bisulfite DNA sequencing results for SEPT9 amplicons. Each column displays results from one amplicon and each row displays results for one cell type. Within each of the rectangular boxes, the columns correspond to single CpGs and the three rows correspond to three patients. As all amplicons are drawn to the same scale the location of the amplicons is illustrated at the bottom with arrows pointing to the genomic map (compare to Figure ). Color coding: yellow = unmethylated (0%), green = partially methylated (50%), blue = fully methylated (100%), and lighter or darker green/blue colors provide methylation levels below or above 50%. White areas = no sequencing data available. Abbreviations: str = stromal cells, epi = epithelial cells, Norm = normal colon tissue, NAT1 = normal adjacent tissue (1 cm away from tumor), NAT2 = normal adjacent tissue (> 10 cm from tumor), Adeno = adenoma tissue, pat = patient no.: only the last number of the patient ID in Additional file : Table S1 is shown here.

Article Snippet: Sections were then incubated with the primary antibody against Septin-9 (polyclonal AB cat.# PAB4799, Abnova, Germany) in 1:50 dilution for 60 minutes at 37°C, washed again in PBS, and detected with Alexa Fluor 546 dye in 1:100 dilution after 30 minutes of incubating at 37°C.

Techniques: DNA Sequencing, Amplification, Methylation, Sequencing

Journal: BMC Cancer

Article Title: Aberrant septin 9 DNA methylation in colorectal cancer is restricted to a single CpG island

doi: 10.1186/1471-2407-13-398

Figure Lengend Snippet: Box plot diagrams of SEPT9 methylation. Results from amplicons 4 and 5 in different LCM tissue specimens. Data are shown separately for stromal (str) and epithelial (epi) cells and for the three patients in each group. Red = epithelial cells, blue = stromal cells. The horizontal bar within boxes shows the median, dots within the boxes the means, the lower and upper boundaries of boxes show the 25th and 75th percentiles, the whiskers are determined by the 5th and 95th percentiles.

Article Snippet: Sections were then incubated with the primary antibody against Septin-9 (polyclonal AB cat.# PAB4799, Abnova, Germany) in 1:50 dilution for 60 minutes at 37°C, washed again in PBS, and detected with Alexa Fluor 546 dye in 1:100 dilution after 30 minutes of incubating at 37°C.

Techniques: Methylation

Journal: BMC Cancer

Article Title: Aberrant septin 9 DNA methylation in colorectal cancer is restricted to a single CpG island

doi: 10.1186/1471-2407-13-398

Figure Lengend Snippet: Histopathology and Septin-9 immunohistochemistry. The images for H&E staining and IHC were obtained from adjacent sections and are from the same blocks used for LCM sampling. H&E staining in the left panel shows overall tissue morphology. The three IHC images per patient are from one slide: Hoechst staining (blue) marks nuclei, AlexaFluor 546 (red) shows Septin-9 protein; the right panel shows the combination of Hoechst and AlexaFluor 546. For better visualization of the Hoechst staining, these images were obtained with intensified brightness for the blue channel. Normal sections are from BSM0451; NAT1, NAT2, and tumor are from BSM0456, and adenoma is from BSM0457. All images are at 20x magnifications; the scale bars correspond to 100 μm.

Article Snippet: Sections were then incubated with the primary antibody against Septin-9 (polyclonal AB cat.# PAB4799, Abnova, Germany) in 1:50 dilution for 60 minutes at 37°C, washed again in PBS, and detected with Alexa Fluor 546 dye in 1:100 dilution after 30 minutes of incubating at 37°C.

Techniques: Histopathology, Immunohistochemistry, Staining, Sampling

Journal: BMC Cancer

Article Title: Aberrant septin 9 DNA methylation in colorectal cancer is restricted to a single CpG island

doi: 10.1186/1471-2407-13-398

Figure Lengend Snippet: Quantification of immunohistochemistry results. Expression of Septin-9 protein in stromal (blue boxes) and epithelial (red boxes) cells. The Y axis displays arbitrary units for the normalized fluorescence signals (ratio AlexaFluor 546 to Hoechst) in IHC slides. Each box plot contains multiple scanned slide sections from three patients.

Article Snippet: Sections were then incubated with the primary antibody against Septin-9 (polyclonal AB cat.# PAB4799, Abnova, Germany) in 1:50 dilution for 60 minutes at 37°C, washed again in PBS, and detected with Alexa Fluor 546 dye in 1:100 dilution after 30 minutes of incubating at 37°C.

Techniques: Immunohistochemistry, Expressing, Fluorescence