Journal: The EMBO Journal

Article Title: A novel non-coding RNA lncRNA-JADE connects DNA damage signalling to histone H4 acetylation

doi: 10.1038/emboj.2013.221

Figure Lengend Snippet: ATM-dependent regulation of lncRNA expression in response to DNA damage. (A) Experimental layout to identify ATM-dependent lncRNAs. Atm+/+ and Atm−/− mouse embryonic fibroblasts (MEFs) were treated with NCS (200 ng/ml) and harvested at indicated time points for microarray analyses. (B) The number of ATM-dependent lncRNAs upon DNA damage. (C) A representative group of ATM-dependent and DNA damage-induced lncRNAs. Green or red colour on the heat map indicates a decrease or an increase in the lncRNA level and colour intensities correspond to relative signal levels on a logarithmic scale. (D) Quantitative PCR validation of representative lncRNAs. Data represent the mean of three experimental replicates, with error bars depicting s.d.

Article Snippet: For lncRNA microarray analyses, RNA was extracted from a pair of primary Atm+/+ and Atm−/− MEFs treated with NCS (500 ng/ml) for 4, 8, and 24 h. RNA samples were subjected to mouse genome-wide lncRNA microarray analysis at ArrayStar, Rockville, MD.

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

Journal: The EMBO Journal

Article Title: A novel non-coding RNA lncRNA-JADE connects DNA damage signalling to histone H4 acetylation

doi: 10.1038/emboj.2013.221

Figure Lengend Snippet: Knockdown of lncRNA-JADE inhibits mammary tumour growth in vivo. (A) Higher levels of lncRNA-JADE in human breast cancer tissues in comparison with normal breast tissues. In situ hybridization of lncRNA-JADE was performed on tissue microarray comprised of human normal breast and breast cancer tissues. (B) Correlation between lncRNA-JADE and Jade1 up-expression in breast cancer tissue cDNA array. The level of lncRNA-JADE and Jade1 was measured by RT–PCR. The lncRNA-JADE expression demonstrated a significant correlation with the Jade1 expression according to the Spearman correlation coefficient (r=0.6983 and P=0.0294). (C) Comparison of survival curves between patients with Jade1 overexpression and patients with normal Jade1 expression using TCGA data in breast invasive carcinomas. (D) Knockdown of lncRNA-JADE inhibits xenografted 4T1 tumour growth in vivo. One million luciferase expressing 4T1 cells stably expressing control or lncRNA-JADE shRNA were injected into the mammary fat pad of each Balb/cSCID mouse. Two weeks after injection, luciferase activity was measured and quantified by an IVIS device (left panel and upper right panel). Breast tumour size was measured in the mice for 24 days (bottom right panel). Graphic data present the mean of five mice and error bars depict s.d.

Article Snippet: For lncRNA microarray analyses, RNA was extracted from a pair of primary Atm+/+ and Atm−/− MEFs treated with NCS (500 ng/ml) for 4, 8, and 24 h. RNA samples were subjected to mouse genome-wide lncRNA microarray analysis at ArrayStar, Rockville, MD.

Techniques: In Vivo, In Situ Hybridization, Microarray, Expressing, Reverse Transcription Polymerase Chain Reaction, Over Expression, Luciferase, Stable Transfection, shRNA, Injection, Activity Assay

Journal: Data in Brief

Article Title: Expression profiling of long noncoding RNAs in neonatal and adult mouse testis

doi: 10.1016/j.dib.2015.06.004

Figure Lengend Snippet: Validation of microarray results by qRT-PCR [3] .

Article Snippet: 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the lncRNA expression microarray slide (Mouse Stringent LncRNA microarray, 4×44 K, ArrayStar).

Techniques: Biomarker Discovery, Microarray

Journal: Data in Brief

Article Title: Expression profiling of long noncoding RNAs in neonatal and adult mouse testis

doi: 10.1016/j.dib.2015.06.004

Figure Lengend Snippet: List of primers used in the validation of microarray results by qRT-PCR.

Article Snippet: 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the lncRNA expression microarray slide (Mouse Stringent LncRNA microarray, 4×44 K, ArrayStar).

Techniques: Biomarker Discovery, Microarray, Sequencing, Amplification

Journal: Data in Brief

Article Title: Expression profiling of long noncoding RNAs in neonatal and adult mouse testis

doi: 10.1016/j.dib.2015.06.004

Figure Lengend Snippet:

Article Snippet: 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the lncRNA expression microarray slide (Mouse Stringent LncRNA microarray, 4×44 K, ArrayStar).

Techniques: Microarray, Comparison

Journal: Journal of Immunology Research

Article Title: Identification of Differentially Expressed lncRNAs in a CpG ODN-Activated Macrophage

doi: 10.1155/2020/1407654

Figure Lengend Snippet: Changed expression profiles of lncRNAs and mRNAs during CpG ODN-induced macrophage activation. (a) The heat map of all lncRNA expression at different time points during CpG ODN-induced macrophage activation from microarray data. (b) Scatter plots showing differentially expressed lncRNAs between macrophages with the stimulation with CpG ODN at 0 h and activated macrophages at different time points (4 h, 8 h, and 16 h). (c) Often differentially expressed lncRNAs between macrophages with the stimulation with CpG ODN at 0 h and activated macrophages at different time points (4 h, 8 h, and 16 h). (d) Hierarchical clustering showing often upregulated and downregulated lncRNAs among the four groups (macrophages stimulated for 0 h, 4 h, 8 h, and 16 h). (e) The heat map of all mRNA expression at different time points during CpG ODN-induced macrophage activation from microarray data. (f) Scatter plots showing differentially expressed mRNAs between macrophages with the stimulation with CpG ODN at 0 h and activated macrophages at different time points (4 h, 8 h, and 16 h). (g) Often differentially expressed mRNAs between macrophages with the stimulation with CpG ODN at 0 h and activated macrophages at different time points (4 h, 8 h, and 16 h). (h) Hierarchical clustering showing often up- and downregulated mRNAs among the four groups (macrophages stimulated for 0 h, 4 h, 8 h, and 16 h).

Article Snippet: The lncRNA microarray was conducted by CapitalBio Technology (Beijing, China).

Techniques: Expressing, Activation Assay, Microarray