Journal: Journal of Cellular and Molecular Medicine

Article Title: Deregulated lncRNA expression profile in the mouse lung adenocarcinomas with KRAS‐G12D mutation and P53 knockout

doi: 10.1111/jcmm.14584

Figure Lengend Snippet: Construction of P53 re‐expression KP cells and identification of lncRNAs regulated by P53. A, P53 was efficiently re‐expressed in the primary KP cells. The P53‐re‐expressed KP cells (KP‐P53) were developed by PCDH‐Flag‐P53 lentiviral infection and puromycin selection （4 μg/mL）, using PCDH‐Flag empty vector lentivirus as negative control. Western blot analysis was used to analyse the expression of P53 in lysates from KP cells. B, Comparison between microarray data and qPCR results of lncRNAs regulated by P53. Among the selected 210 lncRNAs, qPCR results determined 11 lncRNAs, whose expression was altered by the re‐expression of P53 in KP cells and exhibited opposite expression alteration direction to that in the microarray of the mouse lung adenocarcinoma tissues. The heights of the columns in the chart represent the log‐transformed median fold changes (tumour sample/normal tissues in microarray data or KP‐ p53 cells/KP‐NC cells in qPCR results). Mean ± SD are shown, n = 3 or 2

Article Snippet: For microarray analysis, lncRNA + mRNA mouse Gene Expression Microarray v1.0, 4x180K chip (CapitalBio Corp), was employed and conducted by CapitalBio Corp according to the manufacturer's protocols.

Techniques: Expressing, Infection, Selection, Plasmid Preparation, Negative Control, Western Blot, Comparison, Microarray, Transformation Assay

Journal: Journal of Cellular and Molecular Medicine

Article Title: Deregulated lncRNA expression profile in the mouse lung adenocarcinomas with KRAS‐G12D mutation and P53 knockout

doi: 10.1111/jcmm.14584

Figure Lengend Snippet: Construction of KP cell lines with Kras gene disruption and identification of Kras related lncRNAs in KP cells. A, Messy peak figure reporting the results of DNA sequencing showed mutations induced by Cas9/gRNA in the Kras guide RNA. The stable Cas9 expression KP cells (KP‐Cas9) were developed by pCDH‐bla‐Cas9 lentivirus infection and selection with 10 μg/mL blasticidin. KP‐Cas9 cells were further infected by the Kras ‐targeting guide RNA expression lentivirus and selected by 4 μg/mL puromycin, lenti‐guide empty vector lentivirus as negative control. The DNA fragment containing the Kras guide RNA binding site was amplified by using PCR with the genomic DNA of guide RNA‐infected KP‐cas9 cells. B, Comparison between microarray data and qPCR results of lncRNAs regulated by Kras . Among the selected 210 lncRNAs, qPCR results determined 33 lncRNAs, whose expression was altered by the Kras deletion in KP cells and exhibited opposite expression alteration direction to that in the microarray of the mouse lung adenocarcinoma tissues. The heights of the columns in the chart represent the log‐transformed median fold changes (tumour sample/normal tissues in microarray data of the mouse lung adenocarcinoma tissues or KP‐Kras‐guide cells/ KP‐guide‐NC cells in qPCR results). Mean ± SD are shown, n = 3 or 2

Article Snippet: For microarray analysis, lncRNA + mRNA mouse Gene Expression Microarray v1.0, 4x180K chip (CapitalBio Corp), was employed and conducted by CapitalBio Corp according to the manufacturer's protocols.

Techniques: Disruption, DNA Sequencing, Expressing, Infection, Selection, RNA Expression, Plasmid Preparation, Negative Control, RNA Binding Assay, Amplification, Comparison, Microarray, Transformation Assay

Journal: Journal of Cellular and Molecular Medicine

Article Title: Deregulated lncRNA expression profile in the mouse lung adenocarcinomas with KRAS‐G12D mutation and P53 knockout

doi: 10.1111/jcmm.14584

Figure Lengend Snippet: Identification of hypoxia‐related lncRNAs in KP cells. A, KP cells were incubated under hypoxia with 1% O 2 and normoxia (20% O 2 ). Immunoblot (left) was used to detect HIF1α protein levels and was quantified by measuring the grey value of the bands. Data are shown as means ± SD. All P values are from two‐sided t tests. B, Comparison between microarray data and qPCR results of lncRNAs associated with hypoxia. The qPCR result validated the 13 out of 210 selected lnRNAs were regulated by hypoxia, whose expression exhibited same expression alteration direction to that in the microarray of the mouse lung adenocarcinoma tissues. The heights of the columns in the chart represent the log‐transformed median fold changes (tumour sample/normal tissues in microarray data of the mouse lung adenocarcinoma tissues or KP cells cultured in hypoxia/KP cells cultured in normoxia in qPCR results) in expression across the three lung adenocarcinoma tissues and KP cells cultured in hypoxia. Mean ± SD are shown, n = 3 or 2

Article Snippet: For microarray analysis, lncRNA + mRNA mouse Gene Expression Microarray v1.0, 4x180K chip (CapitalBio Corp), was employed and conducted by CapitalBio Corp according to the manufacturer's protocols.

Techniques: Incubation, Western Blot, Comparison, Microarray, Expressing, Transformation Assay, Cell Culture

Journal: Journal of Cellular and Molecular Medicine

Article Title: Deregulated lncRNA expression profile in the mouse lung adenocarcinomas with KRAS‐G12D mutation and P53 knockout

doi: 10.1111/jcmm.14584

Figure Lengend Snippet: Confirmation of the p53‐ , Kras‐ or hypoxia‐ associated lncRNAs. A, Overlapped differentially expressed lncRNAs. B, Among the total 52 lncRNAs identified to be associated with p53 , Kras or hypoxia, 19 lncRNAs, with expression change fold greater than 3.5 in the microarray results, were selected to further confirmed by using quantitative RT‐PCR in another group of mouse lung adenocarcinoma tissues (6 lung adenocarcinoma samples and 6 normal lung tissues). The heights of the columns in the chart represent the log‐transformed median fold changes (tumour sample/normal tissues). The validation results of the 19 lncRNAs indicated that the microarray data correlated well with the qPCR results. Mean ± SD are shown, n = 3 or 6. C, Long noncoding RNA (lncRNA)‐lncRNA co‐expression network (LLCN) related to the 19 selected lncRNAs was constructed. Among the 19 lncRNAs, 6 lncRNAs had no significant co‐expression with other lncRNAs. The circles represent nodes of differential expressed lncRNAs (DE lncRNAs). The nodes in green colour represent the 13 remained lncRNAs. The LLCN contained a total of 4086 lncRNAs with 19 595 edges between them

Article Snippet: For microarray analysis, lncRNA + mRNA mouse Gene Expression Microarray v1.0, 4x180K chip (CapitalBio Corp), was employed and conducted by CapitalBio Corp according to the manufacturer's protocols.

Techniques: Expressing, Microarray, Quantitative RT-PCR, Transformation Assay, Biomarker Discovery, Construct

Journal: Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology

Article Title: Propofol Alters Long Non-Coding RNA Profiles in the Neonatal Mouse Hippocampus: Implication of Novel Mechanisms in Anesthetic-Induced Developmental Neurotoxicity

doi: 10.1159/000493875

Figure Lengend Snippet: Propofol alters messenger RNA (mRNA) profiles in the mouse hippocampus. (A) The images of denaturing agarose gel electrophoresis of total RNAs isolated from 4 intralipid- or 4 propofol-treated mouse hippocampal tissues. (B) The box plots display similar distributions of normalized mRNA intensity values across 4 control and 4 propofol samples, suggesting that the microarray data can be used for further analysis. Each box plot consists of a box with a central line and two tails. The central line represents the median of mRNA intensity values whereas the tails represent the upper and lower quartiles. (C) Heatmap showing profiles and the hierarchical clustering of differentially expressed mRNAs between intralipid- and propofol-treated mouse hippocampus (n=4; p<0.05). The red signal refers to high relative expression and the green signal referred to low relative expression.

Article Snippet: Microarray assay Mouse LncRNA Expression Microarray V3.0 assay and data analysis were performed by Arraystar Inc. (Rockville, MD) to evaluate global expression levels of 35, 923 lncRNAs and 24, 881 mRNAs in the hippocampus.

Techniques: Agarose Gel Electrophoresis, Isolation, Control, Microarray, Expressing

Journal: Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology

Article Title: Propofol Alters Long Non-Coding RNA Profiles in the Neonatal Mouse Hippocampus: Implication of Novel Mechanisms in Anesthetic-Induced Developmental Neurotoxicity

doi: 10.1159/000493875

Figure Lengend Snippet: Propofol alters profiles of long non-coding RNAs (lncRNAs) in the mouse hippocampus. (A) The box plots showing the similar distributions of normalized lncRNA intensity values from 4 control and 4 propofol samples. Each box plot consists of a box with a central line and two tails. The central line represents the median of lncRNA intensity values, whereas the tails represent the upper and lower quartiles. (B) The volcano plot illustrating the differentially expressed lncRNAs (red dots) between control and propofol groups. These altered lncRNAs were either downregulated (left red dots) or upregulated (right red dots) following propofol exposure. (C) Heat map showing the profiles and hierarchical clustering of differentially expressed lncRNAs in intralipid- and propofol-treated mouse hippocampus (n=4; p<0.05). The red signals refer to high relative expression and the green signals indicate low relative expression. Among 24,881 lncRNAs analyzed, 159 lncRNAs were differentially expressed following propofol exposure. (D) Pie chart showing the ratio of various types of dysregulated lncRNAs. Specifically, over 50% total dysregulated lncRNAs were intergenic lncRNAs.

Article Snippet: Microarray assay Mouse LncRNA Expression Microarray V3.0 assay and data analysis were performed by Arraystar Inc. (Rockville, MD) to evaluate global expression levels of 35, 923 lncRNAs and 24, 881 mRNAs in the hippocampus.

Techniques: Control, Expressing

Journal: Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology

Article Title: Propofol Alters Long Non-Coding RNA Profiles in the Neonatal Mouse Hippocampus: Implication of Novel Mechanisms in Anesthetic-Induced Developmental Neurotoxicity

doi: 10.1159/000493875

Figure Lengend Snippet: Propofol-induced individual dysregulated lncRNAs and their neighbor protein-coding genes which are also altered following propofol exposure. Note: chr is the abbreviated chromosome. P value and fold change is shown as propofol vs. control. Expression changes are shown compared with control group

Article Snippet: Microarray assay Mouse LncRNA Expression Microarray V3.0 assay and data analysis were performed by Arraystar Inc. (Rockville, MD) to evaluate global expression levels of 35, 923 lncRNAs and 24, 881 mRNAs in the hippocampus.

Techniques: Control, Expressing

Journal: Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology

Article Title: Propofol Alters Long Non-Coding RNA Profiles in the Neonatal Mouse Hippocampus: Implication of Novel Mechanisms in Anesthetic-Induced Developmental Neurotoxicity

doi: 10.1159/000493875

Figure Lengend Snippet: Bioinformatics analysis of neuro-degenerative signaling pathways of top 50-ranked altered lncRNAs. The green and red arrows, respectively, representative lncRNA downregulation and upregulation following propofol exposure.

Article Snippet: Microarray assay Mouse LncRNA Expression Microarray V3.0 assay and data analysis were performed by Arraystar Inc. (Rockville, MD) to evaluate global expression levels of 35, 923 lncRNAs and 24, 881 mRNAs in the hippocampus.

Techniques: Protein-Protein interactions