human m 6 a-modified lncrna epitranscriptomic microarray  (Arraystar inc)

Journal: Journal of Advanced Research

Article Title: WTAP/YTHDF1-mediated m 6 A modification amplifies IFN-γ-induced immunosuppressive properties of human MSCs

doi: 10.1016/j.jare.2024.06.019

Figure Lengend Snippet: WTAP is required for IFN-γ-licensing immunosuppressive process in hUC-MSCs. (A) log2 (FC) of differential expressed genes of hUC-MSCs with and without IFN-γ (I) treatment (fold change > 2, FDR < 0.05). (B) The correlation of log2 (FC) of differentially expressed transcripts in hUC-MSCs with or without IFN-γ treatment and log2 (FC) of differentially m 6 A modification transcripts in hUC-MSCs with or without IFN-γ treatment are indicated (|log FC| ≥ 1; p-value < 0.05). Group 1 (red) were those transcripts that were upregulated in both RNA-seq and epitranscriptomic microarray; Group 2 (blue) were transcripts that were down-regulated in both groups. (C) Heatmap of representative IFN-γ-licensing immunosuppressive process associated genes by epitranscriptomic microarray. (D) Western blotting analysis of m 6 A writers (METTL3, METTL14, and WTAP) in hUC-MSCs with or without IFN-γ induction. (E) qRT–PCR analysis of the relative mRNA levels of m 6 A writers in hUC-MSCs with or without IFN-γ induction (n = 3). (F) The correlation of log2 (FC) of differentially expressed transcripts in hUC-MSCs with WTAP knockdown (WTAP-KD) and log2 (FC) of differentially m 6 A modification transcripts in hUC-MSCs with WTAP knockdown are indicated (|log FC| ≥ 1; p-value < 0.05). (G) Venn diagram of hypomethylated targets in WTAP-KD hUC-MSCs and hypermethylated-up or hypomethylated-up genes in IFN-γ-licensing hUC-MSCs. Statistical significance was calculated by Student’s t -test. *P < 0.05, **P < 0.01, ***P < 0.001, ns, non-significant. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: In the hybridization step, the cRNA was merged to the Arraystar Human m 6 A Epitranscriptomic Microarray (8 × 60 K; Arraystar, Rockville, USA).

Techniques: Modification, RNA Sequencing, Microarray, Western Blot, Quantitative RT-PCR, Knockdown

Journal: Clinical Epigenetics

Article Title: Comprehensive analyses of molecular features, prognostic values, and regulatory functionalities of m 6 A-modified long non-coding RNAs in lung adenocarcinoma

doi: 10.1186/s13148-023-01475-z

Figure Lengend Snippet: Characteristics of the m 6 A-modified lncRNA microarray in LUAD tumor tissues and adjacent normal tissues. A The source distribution of m 6 A-modified lncRNA transcripts. B The length distribution of m 6 A-modified lncRNA transcripts (≤ 3000 bp). C The chromosomal localization of m 6 A-modified lncRNA transcripts. D Volcano plot showed that in 2846 m 6 A-modified lncRNA transcripts, 143 were differentially modified (|log 2 FC|> 0.585, P < 0.05, unpaired t test), and 123 were hypermethylated and 20 were hypomethylated. E The methylation level heatmap of 143 differentially modified lncRNA transcripts. F Volcano plot showed that in 143 differentially modified lncRNA transcripts, 32 were upregulated and 48 were downregulated (|log 2 FC|> 1, P < 0.05, unpaired t test). G The expression level heatmap of 143 differentially modified lncRNA transcripts

Article Snippet: Importantly, the Arraystar Human M 6 A-modified LncRNA Epitranscriptomic Microarray was utilized to analyze the characteristics of m 6 A-modified lncRNAs and screen out lncRNAs with differential methylation level in LUAD.

Techniques: Modification, Microarray, Methylation, Expressing

Journal: Clinical Epigenetics

Article Title: Comprehensive analyses of molecular features, prognostic values, and regulatory functionalities of m 6 A-modified long non-coding RNAs in lung adenocarcinoma

doi: 10.1186/s13148-023-01475-z

Figure Lengend Snippet: Combined analyses of m 6 A modification and expression profiles of 143 differentially m 6 A-modified lncRNA transcripts in LUAD tissues. A The UpSet diagram was used to divide lncRNAs into six categories. B Spearman correlation analyses between the expression levels and methylation levels of 143 lncRNA transcripts in normal tissues (left), tumor tissues (middle), and all tissues (right). A point’s horizontal and vertical coordinates were the mean m 6 A level and mean expression level of a lncRNA transcript in six normal tissues (left), four tumor tissues (middle), and all ten tissues (right), respectively. C Validation of four lncRNAs’ expression levels in six pairs of clinical tissues; GAPDH served as the reference gene. * P < 0.05 and not significant (ns) P > 0.05. Paired t test. D Validation of four lncRNAs’ m 6 A levels in six pairs of clinical tissues by MeRIP-qPCR assays; Input was used as the reference. * P < 0.05, ** P < 0.01 and *** P < 0.001. Paired t test

Article Snippet: Importantly, the Arraystar Human M 6 A-modified LncRNA Epitranscriptomic Microarray was utilized to analyze the characteristics of m 6 A-modified lncRNAs and screen out lncRNAs with differential methylation level in LUAD.

Techniques: Modification, Expressing, Methylation, Biomarker Discovery

Journal: Clinical Epigenetics

Article Title: Comprehensive analyses of molecular features, prognostic values, and regulatory functionalities of m 6 A-modified long non-coding RNAs in lung adenocarcinoma

doi: 10.1186/s13148-023-01475-z

Figure Lengend Snippet: The screening of prognostic m 6 A-regulated lncRNAs. A The screening criteria of 215 m 6 A-regulated lncRNAs and its expression correlation with m 6 A regulators. B Forest plot of univariate Cox regression analysis of m 6 A-regulated lncRNAs ( P < 0.01). The hazard ratio (HR) value, its 95% confidence interval (CI), as well as the associated P value, were shown. HR > 1 indicated that the lncRNA was a risk factor and its high expression was unfavorable for prognosis, while the high expression of the protective lncRNA of HR < 1 was favorable for prognosis. C The expression correlation between 13 prognostic m 6 A-regulated lncRNAs and m 6 A regulators

Article Snippet: Importantly, the Arraystar Human M 6 A-modified LncRNA Epitranscriptomic Microarray was utilized to analyze the characteristics of m 6 A-modified lncRNAs and screen out lncRNAs with differential methylation level in LUAD.

Techniques: Expressing

Journal: Clinical Epigenetics

Article Title: Comprehensive analyses of molecular features, prognostic values, and regulatory functionalities of m 6 A-modified long non-coding RNAs in lung adenocarcinoma

doi: 10.1186/s13148-023-01475-z

Figure Lengend Snippet: Construction of m 6 A-induced ceRNA Network. A The subcellular localization of 43 differentially m 6 A-modified lncRNAs according to RNALoate. B The construction process of the ceRNA network, which consisted of 11 correlative m 6 A regulators, seven differentially modified lncRNAs, 30 sponged miRNAs, and 110 targeted mRNAs. C The diagram of the ceRNA network. The lines connecting m 6 A regulators and lncRNAs represented RNA co-expression in TCGA-LUAD set (| r |> 0.3 and P < 0.001), and the red line represented the lncRNA-m 6 A regulator protein combination detected by CLIP-seq recorded in the POSTAR3 database. D The chart emphasized the dysregulated targeted mRNAs in LUAD, whose numbers of connecting nodes were greater than or equal to 3 in the ceRNA network. FC represented the expression fold change of T-median/N-median. WilcoxTest. *** P < 0.001

Article Snippet: Importantly, the Arraystar Human M 6 A-modified LncRNA Epitranscriptomic Microarray was utilized to analyze the characteristics of m 6 A-modified lncRNAs and screen out lncRNAs with differential methylation level in LUAD.

Techniques: Modification, Expressing

Journal: Scientific Reports

Article Title: Human m 6 A-mRNA and lncRNA epitranscriptomic microarray reveal function of RNA methylation in hemoglobin H-constant spring disease

doi: 10.1038/s41598-021-99867-9

Figure Lengend Snippet: The differentially expressed profile of m6A-mRNAs in immature red blood cells of Hb CS thalassemia (T) and healthy volunteers controls (N) (* P < 0.05.). Relative mRNA expression, as evidenced by qRT-PCR. The qRT-PCR data ( A ) was consistent with the epitranscriptomic rnicroarray sequence ( B ).

Article Snippet: We conducted the Arraystar Human m 6 A-mRNA and lncRNA epitranscriptomic microarray analysis of 5 pairs of immature erythrocytes, particularly, 5 from HbH-CS thalassemia (T) and 5 from healthy volunteers (N).

Techniques: Expressing, Quantitative RT-PCR, Sequencing

Journal: Scientific Reports

Article Title: Human m 6 A-mRNA and lncRNA epitranscriptomic microarray reveal function of RNA methylation in hemoglobin H-constant spring disease

doi: 10.1038/s41598-021-99867-9

Figure Lengend Snippet: The 20 differentially hypo-methylated m6A other RNAS including lncRNA and other small RNAs.

Article Snippet: We conducted the Arraystar Human m 6 A-mRNA and lncRNA epitranscriptomic microarray analysis of 5 pairs of immature erythrocytes, particularly, 5 from HbH-CS thalassemia (T) and 5 from healthy volunteers (N).

Techniques: