Journal: PLoS ONE

Article Title: Adenomatous polyposis coli-binding protein end-binding 1 promotes hepatocellular carcinoma growth and metastasis

doi: 10.1371/journal.pone.0239462

Figure Lengend Snippet: (a and b) RNA microarray analysis to identify genes differentially expressed in the presence of EB1. Comparison of gene expression levels in EB1-KO HuH7 cells infected with control and EB1-expressing lentiviruses identified a number of genes upregulated by EB1 re-expression.

Article Snippet: After properly converting the extracted RNA to the cRNA labeled with Cy3 as recommended by the manufacturers, 0.6 μg of the cRNA was fragmented and hybridized at 65°C for 17 h to an Agilent SurePrint G3 Human GE v3 8x60K Microarray (Design ID: 072363) containing a total of 58,201 probes excluding control probes.

Techniques: Microarray, Expressing, Infection

Journal: Journal of Cellular and Molecular Medicine

Article Title: Signature of circular RNAs in peripheral blood mononuclear cells from patients with active tuberculosis

doi: 10.1111/jcmm.14093

Figure Lengend Snippet: Hierarchical cluster analysis of circRNA expression in PBMCs from active TB group compared with control group. Expression of the dysregulated circRNAs with FC ＞ 3 and FDR adjusted P value <0.05 was depicted in the hierarchical clustering. The red and green represented an increased and a decreased expression of circRNAs, respectively. Cluster analysis indicated that circRNAs expression pattern was altered in PBMCs from active TB patients. PBMC: peripheral blood mononuclear cells; FC: fold change; FDR: false discovery rate; PTC: active TB group; PCR: control group

Article Snippet: Subsequently, the qualified labelled circRNA samples with the yield ＞1.65 μg and the specific activity ＞9.0 pmol Cy3/μg cRNA were hybridized onto Arraystar Human circRNA Arrays containing 13 617 probes (V2, Arraystar Inc.) and the microarray slides were then incubated for 17 hours at 65°C in an Agilent Hybridization Oven (Agilent Technologies, Inc., Santa Clara, CA, USA).

Techniques: Expressing

Journal: Journal of Cellular and Molecular Medicine

Article Title: Signature of circular RNAs in peripheral blood mononuclear cells from patients with active tuberculosis

doi: 10.1111/jcmm.14093

Figure Lengend Snippet: RT‐qPCR analysis of selected circRNAs and miRNAs. (A) Confirmation of the expression of candidate differentially expressed circRNAs . hsa_circRNA_103017, hsa_circRNA_059914 and hsa_circRNA_101128 were enhanced, while hsa_circRNA_062400 was reduced in the active TB patient group (n = 31) vs healthy patient group (n = 30). (B) Prediction of possible miRNA targets of hsa_circRNA_101128. hsa‐let‐7a and hsa‐let‐7f were decreased in the case group (n = 31) compared with the controls (n = 30). (C) Expression level of hsa_circRNA_101128 was negatively correlated with that of let‐7a ( r = −0.56, P ＜ 0.05) . GAPDH and U6 were applied as reference genes of circRNAs and miRNAs, respectively. Data were analysed with the 2 - Δ Δ C t method. Student's t test was utilized for statistical analysis. * P < 0.05 vs controls

Article Snippet: Subsequently, the qualified labelled circRNA samples with the yield ＞1.65 μg and the specific activity ＞9.0 pmol Cy3/μg cRNA were hybridized onto Arraystar Human circRNA Arrays containing 13 617 probes (V2, Arraystar Inc.) and the microarray slides were then incubated for 17 hours at 65°C in an Agilent Hybridization Oven (Agilent Technologies, Inc., Santa Clara, CA, USA).

Techniques: Quantitative RT-PCR, Expressing

Journal: Journal of Cellular and Molecular Medicine

Article Title: Signature of circular RNAs in peripheral blood mononuclear cells from patients with active tuberculosis

doi: 10.1111/jcmm.14093

Figure Lengend Snippet: ROC analysis of differentially expressed circRNAs between patients with active TB and healthy patients. hsa_circRNA_103017, hsa_circRNA_059914 and hsa_circRNA_101128 showed good distinguishing efficiency with AUC values of 0.870 (95% CI, 0.779‐0.961), 0.821 (95% CI, 0.714‐0.928) and 0.817 (95% CI, 0.712‐0.922), respectively. However, hsa_circRNA_062400 exhibited poor ability to discriminate active TB patients from healthy controls. ROC, Receiver operating characteristic

Article Snippet: Subsequently, the qualified labelled circRNA samples with the yield ＞1.65 μg and the specific activity ＞9.0 pmol Cy3/μg cRNA were hybridized onto Arraystar Human circRNA Arrays containing 13 617 probes (V2, Arraystar Inc.) and the microarray slides were then incubated for 17 hours at 65°C in an Agilent Hybridization Oven (Agilent Technologies, Inc., Santa Clara, CA, USA).

Techniques:

Journal: Journal of Cellular and Molecular Medicine

Article Title: Signature of circular RNAs in peripheral blood mononuclear cells from patients with active tuberculosis

doi: 10.1111/jcmm.14093

Figure Lengend Snippet: Dysregulated circRNAs verified by RT‐qPCR and MREs

Article Snippet: Subsequently, the qualified labelled circRNA samples with the yield ＞1.65 μg and the specific activity ＞9.0 pmol Cy3/μg cRNA were hybridized onto Arraystar Human circRNA Arrays containing 13 617 probes (V2, Arraystar Inc.) and the microarray slides were then incubated for 17 hours at 65°C in an Agilent Hybridization Oven (Agilent Technologies, Inc., Santa Clara, CA, USA).

Techniques:

Journal: Journal of Cellular and Molecular Medicine

Article Title: Signature of circular RNAs in peripheral blood mononuclear cells from patients with active tuberculosis

doi: 10.1111/jcmm.14093

Figure Lengend Snippet: Detailed presentation of interactions between hsa_circRNA_101128 and its five potential miRNA targets. The 2D structure displayed the MRE sequence, pairing of miRNA target nucleotides and seed type. The “local AU” showed upstream and downstream of the seed sequence, black and red bars represented G/C and low accessibility as well as A/U and high accessibility of the seed, respectively, and bar height stands for the extent of accessibility. The position column showed the most likely relative MRE position on the linearized circRNA sequence. MRE, microRNA response elements

Article Snippet: Subsequently, the qualified labelled circRNA samples with the yield ＞1.65 μg and the specific activity ＞9.0 pmol Cy3/μg cRNA were hybridized onto Arraystar Human circRNA Arrays containing 13 617 probes (V2, Arraystar Inc.) and the microarray slides were then incubated for 17 hours at 65°C in an Agilent Hybridization Oven (Agilent Technologies, Inc., Santa Clara, CA, USA).

Techniques: Sequencing