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: 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

Journal: Journal of Cancer

Article Title: Modulation of Wnt Activity and Cell Physiology by Butyrate in LT97 Microadenoma Cells

doi: 10.7150/jca.8569

Figure Lengend Snippet: Venn diagrams of microarray data. (A) Venn diagram for “within treatment” comparison of differentially expressed genes in mock or butyrate treatments across cell lines (>3Fold, 9,096 probes). 99 intersection probes are differentially expressed in opposite directions. 2,685 intersection probes are differentially expressed in the same direction. (B) Venn diagram for “within cell lines” comparison of differentially expressed genes in mock treated control (Ctrl) vs. butyrate (NaB) treatments of two cell lines (>3Fold, 8,335 probes). 165 intersection probes are differentially expressed in opposite directions. 1,986 intersection probes are differentially expressed in the same direction.

Article Snippet: After treatment with or without 5 mM butyrate for 17.5 hr, cells were washed with 1 x PBS, scraped into PBS and pelleted; the pellets were snap frozen in liquid nitrogen and sent to Genus Biosystems for RNA extraction and microarray analyses, utilizing the Agilent human whole genome oligo microarray.

Techniques: Microarray, Comparison, Control