Journal: Molecular Cancer Research

Article Title: Gut Microbiota–Mediated hsa_circ_0126925 Targets BCAA Metabolic Enzyme BCAT2 to Exacerbate Colorectal Cancer Progression

doi: 10.1158/1541-7786.MCR-24-0434

Figure Lengend Snippet: HFD-modulated gut microbiota regulates the expression of circRNAs. A, The circRNA expression profiles of intestinal tumors from CTL, HFD, and HFD+Abx AOM/DSS model mice were compared via high-throughput circRNA microarray sequencing. B, Mmu_circ_017841, mmu_circ_006689, mmu_circ_32011, circ_38945, mmu_circ_19191, mmu_circ_41893, and mmu_circ_45525, which appeared simultaneously in the upregulated circRNAs of the HFD vs. CTL and HFD+Abx groups. C–E , RT-qPCR was used to verify the differential expression of target mmu_circRNAs (mmu_circ_38945, mmu_circ_32011, mmu_circ_19191, and mmu_circ_45525) in groups of mice generated via three different modeling methods. F, Sanger sequencing results for circ_38945 and circ_0126925. G, Divergent and convergent primers were used to amplify circ_0126925, gDNA, and cDNA with or without RNase treatment before RT-qPCR. H, FISH analysis of the subcellular localization of circ_0126925. I, The proportions of cells in which circ_0126925 was expressed in the nucleus and cytoplasm. J and K, RT-qPCR and ISH were used to detect the expression of circ_0126925 in cancer and adjacent tissues. L, KM curve of the overall survival rate of patients with different expression levels of circ_0126925. In C–E , J , and K , unpaired and paired t tests were used for statistical analyses. In K , the differences between the KM curves were tested for significance by the log-rank test. *, P < 0.05; **, P < 0.01; ***, P < 0.001. ns indicates no significant difference between the two indicated groups.

Article Snippet: Then, the labeled circRNA was hybridized onto an Arraystar Mouse circRNA Array (8 × 15 K, Arraystar) and incubated in an Agilent Hybridization Incubator (Agilent) at 65°C for 17 hours.

Techniques: Expressing, High Throughput Screening Assay, Microarray, Sequencing, Quantitative RT-PCR, Quantitative Proteomics, Generated

Journal: BMC Genomics

Article Title: Identification of circRNAs expression profiles and functional networks in parotid gland of type 2 diabetes mouse

doi: 10.1186/s12864-024-10290-6

Figure Lengend Snippet: Differentially expressed circRNAs and mRNAs in PGs of db/db mice comparing to db/m mice. ( A ) Volcano plots presenting differences in the expression of circRNAs between db/db and db/m mice. ( B ) Volcano plots presenting differences in the expression of mRNAs between db/db and db/m mice. ( C ) Heat map of top 30 upregulated and downregulated circRNAs with raw intensity higher than 500. ( D ) Heat map of top 30 upregulated and downregulated mRNAs with raw intensity higher than 500. Values plotted on the x- and y-axes represent the averaged normalized signal values of each group (log2-scaled). CircRNA, circular RNA; PGs, parotid glands; mRNA, massage RNA

Article Snippet: The labelled cRNAs were hybridized onto the Arraystar Mouse circRNA Array (8 × 15 K; Arraystar).

Techniques: Expressing

Journal: BMC Genomics

Article Title: Identification of circRNAs expression profiles and functional networks in parotid gland of type 2 diabetes mouse

doi: 10.1186/s12864-024-10290-6

Figure Lengend Snippet: Validation of DE circRNAs and mRNAs by qRT-PCR. ( A ) Expression of 5 selected upregulated circRNAs in db/db mice and db/m mice. ( B ) Expression of 9 selected downregulated circRNAs in db/db mice and db/m mice. ( C ) Expression of 10 selected upregulated mRNAs in db/db mice and db/m mice. ( D ) Expression of 10 selected downregulated mRNAs in db/db mice and db/m mice. * P < 0.05 and ** P < 0.01, versus db/m mice, n = 4. DE, differently expressed; circRNA, circular RNA; mRNA, massage RNA

Article Snippet: The labelled cRNAs were hybridized onto the Arraystar Mouse circRNA Array (8 × 15 K; Arraystar).

Techniques: Quantitative RT-PCR, Expressing

Journal: BMC Genomics

Article Title: Identification of circRNAs expression profiles and functional networks in parotid gland of type 2 diabetes mouse

doi: 10.1186/s12864-024-10290-6

Figure Lengend Snippet: GO and KEGG pathway analysis based on CNC analysis of 7 selected circRNAs. ( A ) GO analysis of co-expressed mRNAs on cellular component (CC), biological process (BP), and molecular function (MF). ( B ) KEGG pathway analysis of co-expressed mRNAs of 7 selected circRNAs. GO, gene ontology; KEGG, kyoto encyclopedia of genes and genomes; CNC, coding–non-coding gene co-expression; mRNA, massage RNA; circRNA, circular RNA

Article Snippet: The labelled cRNAs were hybridized onto the Arraystar Mouse circRNA Array (8 × 15 K; Arraystar).

Techniques: Expressing

Journal: BMC Genomics

Article Title: Identification of circRNAs expression profiles and functional networks in parotid gland of type 2 diabetes mouse

doi: 10.1186/s12864-024-10290-6

Figure Lengend Snippet: Coding and non-coding co-expression network involving in PPAR signaling pathway, NF-kappa B signaling pathway, and cytokine-cytokine receptor interaction. Red nodes represent circRNAs; blue nodes represent mRNAs. Positive correlation is a solid line, negative correlation is a dashed line. PPAR, peroxisome proliferator-activated receptor; NF-kappa B, nuclear factor-kappa B; circRNA, circular RNA; mRNA, massage RNA

Article Snippet: The labelled cRNAs were hybridized onto the Arraystar Mouse circRNA Array (8 × 15 K; Arraystar).

Techniques: Expressing

Journal: BMC Genomics

Article Title: Identification of circRNAs expression profiles and functional networks in parotid gland of type 2 diabetes mouse

doi: 10.1186/s12864-024-10290-6

Figure Lengend Snippet: GO and KEGG pathway analysis based on ceRNA analysis of 7 selected circRNAs. ( A ) GO analysis of ceRNA function-related mRNAs on cellular component (CC), biological process (BP), and molecular function (MF). ( B ) KEGG pathway analysis of ceRNA function-related mRNAs. GO, gene ontology; KEGG, kyoto encyclopedia of genes and genomes; ceRNA, competing endogenous RNA; circRNA, circular RNA; mRNA, massage RNA

Article Snippet: The labelled cRNAs were hybridized onto the Arraystar Mouse circRNA Array (8 × 15 K; Arraystar).

Techniques:

Journal: BMC Genomics

Article Title: Identification of circRNAs expression profiles and functional networks in parotid gland of type 2 diabetes mouse

doi: 10.1186/s12864-024-10290-6

Figure Lengend Snippet: CircRNA-miRNA-mRNA network involving in the regulation of actin cytoskeleton, leukocyte trans-endothelial migration, and PPAR signaling pathways. Green node represents upregulated circRNAs; yellow nodes represent downregulated circRNAs; red nodes represent miRNAs; blue nodes represent mRNAs. Purple lines with T-shape arrow represent directed relationships; orange lines without arrow represent undirected relationships. CircRNA, circular RNA; miRNA, microRNA; mRNA, massage RNA; PPAR, peroxisome proliferator-activated receptor

Article Snippet: The labelled cRNAs were hybridized onto the Arraystar Mouse circRNA Array (8 × 15 K; Arraystar).

Techniques: Migration

Journal: BMC Genomics

Article Title: Identification of circRNAs expression profiles and functional networks in parotid gland of type 2 diabetes mouse

doi: 10.1186/s12864-024-10290-6

Figure Lengend Snippet: The DE circRNAs, miRNAs, and mRNAs involved in the regulation of actin cytoskeleton signaling pathway

Article Snippet: The labelled cRNAs were hybridized onto the Arraystar Mouse circRNA Array (8 × 15 K; Arraystar).

Techniques:

Journal: BMC Genomics

Article Title: Identification of circRNAs expression profiles and functional networks in parotid gland of type 2 diabetes mouse

doi: 10.1186/s12864-024-10290-6

Figure Lengend Snippet: Primers for validated circRNAs

Article Snippet: The labelled cRNAs were hybridized onto the Arraystar Mouse circRNA Array (8 × 15 K; Arraystar).

Techniques: