Journal: Cancer Cell International

Article Title: Dysregulation of pseudouridylation in small RNAs contributes to papillary thyroid carcinoma metastasis

doi: 10.1186/s12935-024-03482-3

Figure Lengend Snippet: Effects of PUS7 on miRNA, pre-miRNA and tsRNA ψ modification. A . Clinical index of 9 paired PTCs and paracancerousous tissues. B . Workflow of Arraystar Human Pseudouridine (ψ) small RNA modification microarray analysis. C . PCA plot comparing the PTC group and the paracancer group. D . The number of miRNAs, pre-miRNAs, and tsRNAs identified in PTCs and paracancerous tissues (Left), and the number of differentially modified miRNAs, pre-miRNAs, and tsRNAs found in PTCs (Right). E-F . Volcano plot ( E ) and heatmap ( F ) of diff-modified miRNAs, pre-miRNAs, and tsRNAs. G . The top two differentially modified pre-miRNAs. H . MeRIP-qPCR validation of ψ modification of pre-miR-8082 and pre-miR-152. Data are presented as mean ± SD. ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001

Article Snippet: B . Workflow of Arraystar Human Pseudouridine (ψ) small RNA modification microarray analysis.

Techniques: Modification, RNA modification, Microarray, Biomarker Discovery

Journal: bioRxiv

Article Title: Cannabinoids shift the basal ganglia miRNA m 6 A methylation profile towards an anti-inflammatory phenotype in SIV-infected Rhesus macaques

doi: 10.1101/2024.10.11.614514

Figure Lengend Snippet: A) Percent mature and star miRNAs with m 6 A methylation marks. B-D) m 6 A methylation patterns in each treatment group. E-G) Heatmap of m6A methylation profile versus miRNA abundance.

Article Snippet: We have completed the Arraystar Human N6-methyladenosine (m6A) small RNA modification microarray analysis of the samples you submitted.

Techniques: Methylation

Journal: bioRxiv

Article Title: Cannabinoids shift the basal ganglia miRNA m 6 A methylation profile towards an anti-inflammatory phenotype in SIV-infected Rhesus macaques

doi: 10.1101/2024.10.11.614514

Figure Lengend Snippet: A) Neuroinflammation network molecules associated with the with miRNAs with m6A hypomethylation (left) or hypermethylation (right).

Article Snippet: We have completed the Arraystar Human N6-methyladenosine (m6A) small RNA modification microarray analysis of the samples you submitted.

Techniques:

Journal: Oncotarget

Article Title: Identification of novel genetic regulations associated with airway epithelial homeostasis using next-generation sequencing data and bioinformatics approaches

doi: 10.18632/oncotarget.19752

Figure Lengend Snippet: Gene expressions of the (A) upregulated and (B) downregulated genes shown in Table were analyzed using GSE43696 microarray data from the GEO database. The results showed that gene expressions of both MEF2C and MDGA1 were significantly downregulated in patients with either mild-moderate or severe asthma compared to normal controls. n.s. means no significance, * represents p-value < 0.05, ** represents p-value < 0.01, and *** represents p-value < 0.001. (Probe information of GSE43696 array from GEO database: FGF2-#1, A_23_P218918; FGF2-#2, A_24_P931472; TP53I11, A_23_P368028; MDGA1, A_23_P310460; MEF2C, A_23_P320739; IRAK3, A_23_P162300; LOX, A_23_P122216; NEURL1-#1, A_23_P138492; TFPI-#1, A_23_P156826; TFPI-#2, A_23_P330070; TFPI-#3, A_23_P17095; NAIP, A_23_P110473.)

Article Snippet: Samples were applied to Welgene Biotechnology Company (Welgene, Taipei, Taiwan) for RNA preparation and microarray analysis.

Techniques: Microarray

Journal: Oncotarget

Article Title: Identification of novel genetic regulations associated with airway epithelial homeostasis using next-generation sequencing data and bioinformatics approaches

doi: 10.18632/oncotarget.19752

Figure Lengend Snippet: Gene expressions of the 13 upregulated genes shown in Table were analyzed using GSE43696 microarray data from the GEO database. None of these 13 genes were significantly upregulated in patients with asthma. n.s. means no significance, * represents p-value < 0.05, ** represents p-value < 0.01, and *** represents p-value < 0.001. (Probe information of GSE43696 array from GEO database: OCLN, A_23_P92672; CLDN1, A_23_P57784; NLGN4X-#1, A_23_P364592; XYLT1, A_24_P787897; FGFR3, A_23_P500501; COL5A1-#1, A_23_P158593; COL5A1-#2, A_23_P83818; MMP9, A_23_P40174; SCIN, A_23_P157136; CACNA1A-#1, A_24_P130559; RGS2, A_23_P114947; LMO2, A_23_P53126; UTY, A_23_P329835; EPB41L3, A_23_P4536.)

Article Snippet: Samples were applied to Welgene Biotechnology Company (Welgene, Taipei, Taiwan) for RNA preparation and microarray analysis.

Techniques: Microarray

Journal: Oncotarget

Article Title: Identification of novel genetic regulations associated with airway epithelial homeostasis using next-generation sequencing data and bioinformatics approaches

doi: 10.18632/oncotarget.19752

Figure Lengend Snippet: Gene expressions of the 40 downregulated genes shown in Table were analyzed using GSE43696 microarray data from the GEO database. The results showed that KCNJ2 expression was significantly downregulated in patients with severe asthma. n.s. means no significance, * represents p-value < 0.05, ** represents p-value < 0.01, and *** represents p-value < 0.001. (Probe information of GSE43696 array from GEO database: KCNJ2, A_23_P329261; FN1, A_24_P334130; FOS, A_23_P106194; PTGER1, A_23_P4808; RAC2, A_ 23_P218770 ; FZD2, A_23_P141362; GLI2, A_23_P209246; RAC3-#1, A_23_P125001; RASGRP2-#1, A_23_P64058; EGLN3-#1, A_23_P360379; FGF13, A_23_P217319; HHIP, A_23_P167129; MMP1, A_23_P1691; CHRM4-#1, A_23_P104845; MYLK, A_23_P143817; HLA-DQB1, A_23_P8108; NTNG1-#1, A_23_P201547; NTNG1-#12, A_24_P359671; CNTN1, A_23_P390700; ITGB2, A_23_P329573; ITGA4, A_23_P56505; HLA-F-#1, A_23_P145264; HLA-F-#2, A_23_P145264; HS3ST3A1, A_23_P66525; HS3ST2, A_23_P118158; HS3ST3B1-#1, A_23_P77918; LAMA1, A_32_P313405; COL4A2, A_23_P205031; COL1A2, A_24_P277934; COL6A1, A_32_P32254; DUSP10, A_24_P182494; KCNMB4, A_23_P64792; ATP1A4, A_23_P160177; ATP1A1, A_23_P1072; ADRA2C, A_23_P256158; FLI1, A_24_P355649; NGFR, A_23_P389897; MMP3, A_23_P161698; TLR4, A_24_P69538; KCNJ12, A_24_P339429; ITGA4, A_23_P56505; HTR1F-#1, A_23_P166674; PTPRB, A_23_P53390.)

Article Snippet: Samples were applied to Welgene Biotechnology Company (Welgene, Taipei, Taiwan) for RNA preparation and microarray analysis.

Techniques: Microarray, Expressing

Journal: Oncotarget

Article Title: Identification of novel genetic regulations associated with airway epithelial homeostasis using next-generation sequencing data and bioinformatics approaches

doi: 10.18632/oncotarget.19752

Figure Lengend Snippet: Functional analysis of 504 differentially expressed genes discovered from the GE microarray data was performed by functional annotation (Biological Processes) in DAVID database. The results showed that these genes were involved in cell adhesion (26 genes), keratinization (9 genes), keratinocyte differentiation (11 genes), proteolysis (30 genes), collagen catabolic process (12 genes), extracellular matrix organization (20 genes), and peptide cross-linking (12 genes). The selected criteria were EASE = 0.1, p-value < 0.05, and fold enrichment > 1.3.

Article Snippet: Samples were applied to Welgene Biotechnology Company (Welgene, Taipei, Taiwan) for RNA preparation and microarray analysis.

Techniques: Functional Assay, Microarray

Journal: The Journal of Clinical Endocrinology and Metabolism

Article Title: Unique Gene Expression Profile Associated with an Early-Onset Multiple Endocrine Neoplasia (MEN1)-Associated Pituitary Adenoma

doi: 10.1210/jc.2011-1127

Figure Lengend Snippet: Microarray signal values and relative expression measured by real-time PCR for the genes FOS, GNAS, GADD45A, AKAP9, and NTS. Dotted lines indicate the expression of the corresponding genes in normal pituitaries. A, Studies performed in the MEN1-associated pituitary tumor, showing concordance with the expression pattern observed in microarray analysis, for all genes evaluated. B, Results from the sporadic pituitary adenoma. Except for GADD45A, the pattern of gene expression observed in microarray was confirmed by real-time PCR.

Article Snippet: Normal pituitary RNA for amplification and microarray analysis was obtained commercially (BD Biosciences Clontech, Palo Alto, CA) and comprised a pool of poly A + RNA from 88 male/female (sudden death) Caucasians, ages 16–88 yr. Total tumor RNA (5 μg) and poly A + selected (0.2 μg) RNA from pooled normal pituitaries were subject to linear RNA amplification using commercial reagents (MessageAMP aRNA Kit; Ambion, Austin, TX) in a single round of amplification.

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

Journal: Biology Open

Article Title: Sucrose non-fermenting related kinase enzyme is essential for cardiac metabolism

doi: 10.1242/bio.20149811

Figure Lengend Snippet: (A) Gene ontology (GO) terms for biological processes that over represented in SNRK WT and SNRK KO microarray data sets. Fold change analysis obtained by TaqMan qPCR analysis from mRNA isolated from E17.5 (B) and Neonate (C) SNRK WT and KO hearts (n = 3 for each genotype) and (D) SNRK knockdown in hESC-derived CMs infected with empty vector shRNA control (Control) lentivirus and SNRK shRNA lentivirus (shSNRK) (n = 3 from three independent cardiomyocyte infections). The results are the mean of the fold change ± SEM. * p-value <0.05, # 0.05< p-value <0.10.

Article Snippet: E17.5 heart tissues were isolated from WT (n = 3), and KO (n = 3) embryos and sent to Arraystar Inc, Rockville MD for RNA isolation and microarray analysis.

Techniques: Microarray, Isolation, Knockdown, Derivative Assay, Infection, Plasmid Preparation, shRNA, Control