microarray hybridisation  (Wageningen University and Research)

Journal: The botulinum journal

Article Title: Exploring genomic diversity in Clostridium botulinum using DNA microarrays

doi: 10.1504/tbj.2012.050195

Figure Lengend Snippet: Scheme used to select probes for the Group I subtyping microarray Notes: A total of 225 probes were selected. 146 probes corresponding to strain variable regions of the ATCC 3502 genome sequence were selected based on CGH analysis using Group I types A, B, and F test strains. In silico analysis was used to select the remaining probes representing genes not present in ATCC 3502, specific for either OkraB or LanglelandF strains, or other specific genes of interest.

Article Snippet: High density CGH microarrays Our laboratory developed a comparative genomic hybridisation (CGH) microarray featuring a total of 384,771 overlapping probes (~50–70 bp) representing the ATCC 3502 type A genome sequence in order to evaluate the level of genomic diversity among C. botulinum strains ( Raphael et al., 2008 ).

Techniques: Microarray, Sequencing, In Silico

Journal: The botulinum journal

Article Title: Exploring genomic diversity in Clostridium botulinum using DNA microarrays

doi: 10.1504/tbj.2012.050195

Figure Lengend Snippet: Matrix of correlation coefficients of the hybridisation results for bont/F5 encoding strains using the Group I subtyping microarray (see online version for colours)

Article Snippet: High density CGH microarrays Our laboratory developed a comparative genomic hybridisation (CGH) microarray featuring a total of 384,771 overlapping probes (~50–70 bp) representing the ATCC 3502 type A genome sequence in order to evaluate the level of genomic diversity among C. botulinum strains ( Raphael et al., 2008 ).

Techniques: Hybridization, Microarray

Journal: The botulinum journal

Article Title: Exploring genomic diversity in Clostridium botulinum using DNA microarrays

doi: 10.1504/tbj.2012.050195

Figure Lengend Snippet: Hybridisation of the Group II subtyping microarray by type E (n = 15), type B (n = 4) and type F (n = 3) C. botulinum strains Notes: Shown is the average % of probes hybridised (i.e., where log10 of the ratio of probe fluorescent compared to background ≥ 1.0) for each toxin serotype indicated. Error bars depict standard deviations.

Article Snippet: High density CGH microarrays Our laboratory developed a comparative genomic hybridisation (CGH) microarray featuring a total of 384,771 overlapping probes (~50–70 bp) representing the ATCC 3502 type A genome sequence in order to evaluate the level of genomic diversity among C. botulinum strains ( Raphael et al., 2008 ).

Techniques: Hybridization, Microarray

Journal: Cell Death & Disease

Article Title: FTO/IGF2BP2-mediated N6 methyladenosine modification in invasion and metastasis of thyroid carcinoma via CDH12

doi: 10.1038/s41419-024-07097-4

Figure Lengend Snippet: A M6A-mRNA epitranscriptomic microarray assay analysing the difference in m6A-related genes and mRNA levels between shFTO and control in CAL-62 cells ( n = 3 repetitions). B Overlapping of 1.5-fold m6A expression changes in CAL-62 cells with FTO knockdown and EMT-related functional genes. C Influences of shFTO or ( D ) FTO OE on the mRNA level of CDH12 in B-CPAP and CAL-62 cells ( n = 6 repetitions). E–F The influences of shFTO or FTO OE on the protein levels of CDH12 in B-CPAP and CAL-62 cells ( n = 3 repetitions). G Protein level of CDH12 in PTC and Nor tissues ( n = 7 paired). H The protein level of CDH12 in Nthy-ori 3-1, B-CPAP, CAL-62, and 8305 C cell lines ( n = 3 repetitions). I The mRNA level of CDH12 in PTC tissues and Nor tissues ( n = 40 paired). ( J ) Representative immunohistochemistry images of CDH12-positive cells in PTC and K ATC and Nor tissues (n = 5 paired). L MeRIP assay was performed to identify m6A antibody enrichment in CDH12 in CAL-62 cells ( n = 4 repetitions). M Variation in m6A modification enrichment of CDH12 after FTO knockdown in CAL-62 cells ( n = 4 repetitions). N Kaplan–Meier survival curves of disease-free survival based on CDH12. Bar=200 μm, * p < 0.05, ** p < 0.01, *** p < 0.001.

Article Snippet: Total RNA ( n = 3 repetitions) was prepared and microarray hybridisation was performed according to Arraystar’s standard protocols.

Techniques: Microarray, Control, Expressing, Knockdown, Functional Assay, Immunohistochemistry, Modification

Journal: PLoS ONE

Article Title: Detection of new pathways involved in the acceptance and the utilisation of a plant-based diet in isogenic lines of rainbow trout fry

doi: 10.1371/journal.pone.0201462

Figure Lengend Snippet: Fold changes obtained by microarray (fill) and by qPCR (hatched) when fed the M diet (dark grey) or the V diet (light grey) for genes involved in sensory perception (R23h versus A22h), immunity (R23h versus AB1h) and for amino acid metabolism (R23h versus A22h).

Article Snippet: Hybridisation was performed in a microarray hybridisation oven (Agilent) for 17h at 65°C.

Techniques: Microarray

Journal: PLoS ONE

Article Title: Detection of new pathways involved in the acceptance and the utilisation of a plant-based diet in isogenic lines of rainbow trout fry

doi: 10.1371/journal.pone.0201462

Figure Lengend Snippet: Correlation between gene expression patterns obtained through real-time PCR and microarray approaches.

Article Snippet: Hybridisation was performed in a microarray hybridisation oven (Agilent) for 17h at 65°C.

Techniques: Expressing, Real-time Polymerase Chain Reaction, Microarray