Journal: Genome Medicine

Article Title: A cell-of-origin epigenetic tracer reveals clinically distinct subtypes of high-grade serous ovarian cancer

doi: 10.1186/s13073-020-00786-7

Figure Lengend Snippet: OriPrint is a solid stratifier and establishes the tissue of origin as a major source of variance for HGSOC. a Diffusion map with pseudotime timeline performed on OriPrint CpGs for samples of all cohorts. The origin is situated either in the distal FI (purple origin) or OSE (orange origin) samples. b Diffusion maps showing the classification output for the three indicated clustering methods. The overlap plot shows in white the samples that are concordantly classified by all three methods and in green the samples that have a different classification in at least one of the three methods. c PCA analysis coupled to Gaussian Mixture Model (GMM) clustering of the Melbourne tumor cohort. Left: First two components of global variance in DNA methylation for the considered samples. Middle: The two probability distributions calculated by GMM. Right: Overlay of the OriPrint classification, showing a consistent overlap with GMM’s distributions

Article Snippet: For each sample, 500 ng of genomic DNA was bisulfite converted using the EZ-DNA methylation Gold Kit (Zymo research) according to the kit’s manual, except that the final elution volume was reduced to 12 μl.

Techniques: Diffusion-based Assay, DNA Methylation Assay

Journal: Genome Medicine

Article Title: A cell-of-origin epigenetic tracer reveals clinically distinct subtypes of high-grade serous ovarian cancer

doi: 10.1186/s13073-020-00786-7

Figure Lengend Snippet: PAX8, a defining marker of HGSOC, is differentially methylated and expressed in FI-like vs. OSE-like tumors. a Graphical representation of the methylation of CpGs in PAX8 promoter across the indicated sample groups . b Dotplot depicting the gene expression level of PAX8 by RNAseq (blue bars, left Y -axis) and the DNA methylation level of its promoter by array (orange bars, right Y -axis) in the considered categories. The table summarizes the results of Mann-Whitney U tests (two-tailed) performed in the indicated comparisons. Data are shown as mean ± standard deviation. c PAX8 IHC performed on a tissue microarray of FFPE HGSOC. Samples were divided according to staining intensity. FI-like and OSE-like tumors were compared for the enrichment in the indicated categories by chi-square testing. d Dotplot depicting the DNA methylation level of PAX8 promoter in TCGA samples stratified as FI-like and OSE-like tumors. Mann-Whitney U test (two-tailed) for significance

Article Snippet: For each sample, 500 ng of genomic DNA was bisulfite converted using the EZ-DNA methylation Gold Kit (Zymo research) according to the kit’s manual, except that the final elution volume was reduced to 12 μl.

Techniques: Marker, Methylation, Expressing, DNA Methylation Assay, MANN-WHITNEY, Two Tailed Test, Standard Deviation, Microarray, Staining

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Activation of murine CD4+ and CD8+ T lymphocytes leads to dramatic remodeling of N-linked glycans.

doi: 10.4049/jimmunol.177.4.2431

Figure Lengend Snippet: FIGURE 1. Purification of B cells and T cells from mixed splenocytes before and after activation. CD8 T cells, CD4 T cells, and B cells were purified from mixed splenocytes before or after activation using the MACS system with anti-CD8-, anti-CD4-, or anti-CD19-coated magnetic beads, respectively. Phenotypic analysis of purified fresh and activated cell populations was performed by flow cytometry and showed 90% purity of all cell preparations, as indicated. Purified cells were used either for RNA preparation for microarray analysis, or were processed to extract glycans for MALDI profiling and methylation analysis.

Article Snippet: 6 The online version of this article contains supplemental material. at B row n U niversity on M ay 30, 2014 http://w w w .jim m unol.org/ D ow nloaded from Microarray analysis of the expression of cytokine and glycan transferase genes For gene expression analysis, mRNAs were extracted from purified cell populations of fresh and activated lymphocytes and subjected to analysis on a custom Affymetrix-based DNA microarray containing murine and human glycosyltransferase, sulfotransferase, and cytokine genes, made available by the Consortium for Functional Glycomics.

Techniques: Activation Assay, Magnetic Beads, Cytometry, Microarray, Methylation

Journal: PeerJ

Article Title: Exosomes in cancer: small vesicular transporters for cancer progression and metastasis, biomarkers in cancer therapeutics

doi: 10.7717/peerj.4763

Figure Lengend Snippet: Overview of the role of exosomes in multiple kinds of cancer.

Article Snippet: ACTB, TUBA1A, FN1, FNLA, CD61, HLA-A, LGALS3BP, Alix, RAB5B, RAB5C, SDCBP, VPF37B, CLTC, ARF1, ANXA2, ANXA5, HSC70, HSP72, RAC1, STOM, MFGE8, MVP, GNA12, PTGFRN, HBA1, tumor susceptibility gene-101 (TSG-101), and Grp94 , The inhoused established human HCC cell lines HKCI-C3 and HKCI-8 cells The hepatocellular carcinoma (HCC) cell line MHCC97L cells The immortalized hepatocyte cell line MIHA cells , qRT-PCR analysis, Ion Torrent Next-Generation Sequencing, and Western blotting , The internalization of exosomes could activate PI3K/AKT and MAPK signaling pathway, and promote secretion of MMP-2 and MMP-9 that favored cell invasion. Also, by proteome analysis Syndecan–syntenin–ALIX is known to support biogenesis of exosomes and the segregation of signaling cargo to these vesicles. The research also detected the components of endosomal protein sorting complex, such as VPS28 and VPS37, whose functions are required for exosome cargo sorting Process. , .

Techniques: Western Blot, Immunofluorescence, AChE Assay, Immunocytochemistry, Inhibition, Chromatin Immunoprecipitation, Marker, Expressing, Activity Assay, Enzyme-linked Immunosorbent Assay, Derivative Assay, Biomarker Assay, In Vitro, In Silico, Diagnostic Assay, Isolation, Flow Cytometry, Variant Assay, In Vivo, Sampling, Modification, Transgenic Assay, Migration, Luciferase, Plasmid Preparation, In Vivo Imaging, Purification, Ex Vivo, Activation Assay, Injection, Endothelial Tube Formation Assay, Viability Assay, Matrigel Assay, Immunoprecipitation, Microscopy, Functional Assay, Knock-Out, Mass Spectrometry, Dot Blot, Electron Microscopy, Methylation, Chromatography, Over Expression, Mutagenesis, Microarray, Binding Assay, Transferring, Real-time Polymerase Chain Reaction, Bradford Assay, Transformation Assay, Animal Model, MTT Assay, Fluorescence, FACS, Diffusion-based Assay, Next-Generation Sequencing, Transplantation Assay, Sequencing, Histone Deacetylase Assay, Infection, Incubation, Transmission Assay, Blocking Assay, Luminex, Fractionation, Irradiation, Reporter Assay

Journal: BMC Biology

Article Title: N6-methyladenosine regulates metabolic remodeling in kidney aging through transcriptional regulator GLIS1

doi: 10.1186/s12915-024-02100-y

Figure Lengend Snippet: The abnormal m6A modification and protein levels of GLIS1 in human aged kidney tissues. A Total m6A RNA levels in the H/aged ( n = 10) and H/control group ( n = 10) detected by m6A methylation quantification kit; B differential methylated mRNA expressions between H/aged (A) and H/control (Y) group by using m6A-mRNA epitranscriptomic microarray analysis ( n = 3); C analysis of significant changes in methylated mRNA expression levels between the H/aged and H/control group; D the Gene Ontology (GO) biological process enrichment analysis pathways of predicted mRNA targets; E enriched m6A modification of GLIS1 in the H/aged and H/control group by MeRIP assay ( n = 4); F , G protein level of GLIS1 in the H/aged and H/control group by western blot, and its semi-quantitative analyses ( n = 6). The data are expressed as the mean ± SD of three independent experiments. *** P < .001 indicates a significant difference versus the H/control group by Student’s t -test

Article Snippet: Human m6A epitranscriptomic microarray and mRNA microarray analyses were performed based on Arraystar’s standard protocols.

Techniques: Modification, Control, Methylation, Microarray, Expressing, Western Blot

Journal: BMC Biology

Article Title: N6-methyladenosine regulates metabolic remodeling in kidney aging through transcriptional regulator GLIS1

doi: 10.1186/s12915-024-02100-y

Figure Lengend Snippet: METTL3 directly interacted with GLIS1 in kidney aging. A The mRNA level of METTL3 in the vector and siMETTL3 group in HK-2 cells by RT-qPCR ( n = 3); B , C protein level of GLIS1 by western blot in the vector and siMETTL3 group in HK-2 cells, and its semi-quantitative analysis ( n = 3); D protein levels of METTL3, METTL14, and WTAP by western blot in the 24-month-old and 6-month-old group ( n = 6); E , F the expression of METTL3 in the 24-month-old and 6-month-old group by IHC assay, and its semi-quantitative analysis ( n = 6), scale bar = 50 μm; G immunostaining for METTL3 (green), with DAPI (blue) counterstaining by IF staining in the 24-month-old and 6-month-old group ( n = 6), scale bar = 50 μm; H immunostaining for METTL3 (green), GLIS1 (red), with DAPI (blue) counterstaining by IF staining in HK-2 cells ( n = 3), scale bar = 50 μm; I , J METTL3 RIP and RT-PCR confirmed the interaction between METTL3 and GLIS1 mRNA, and its semi-quantitative analysis ( n = 3); K the lower m6A level of GLIS1 in siMETTL3 group compared with the vector group in HK-2 cells by using MeRIP-qPCR ( n = 3); L the mRNA level of GLIS1 in the vector and siMETTL3 group in HK-2 cells by RT-qPCR ( n = 3); M mutations at the two putative m6A sites in GLIS1 (A to G); N m6A level of GLIS1 in HK-2 cells with co-expression of siMETTL3 and GLIS1-WT/Muts by MeRIP-qPCR ( n = 3); O the mRNA level of GLIS1 in the vector and GLIS1-Mut3 group by RT-qPCR ( n = 3). The data are expressed as the mean ± SD of three independent experiments. ** P < .01 or *** P < .001 versus the vector group ( A , C , K ) or 6-month-old group ( E ) or IgG group ( J ) by Student’s t -test; ## P < .01, ### P < .001 versus the vector-WT group, ++ P < .01, +++ P < .001 versus the siMETTL3-WT group, ** P < .01 versus vector group by two way-ANOVA ( N )

Article Snippet: Human m6A epitranscriptomic microarray and mRNA microarray analyses were performed based on Arraystar’s standard protocols.

Techniques: Plasmid Preparation, Quantitative RT-PCR, Western Blot, Expressing, Immunostaining, Staining, Reverse Transcription Polymerase Chain Reaction

Journal: BMC Biology

Article Title: N6-methyladenosine regulates metabolic remodeling in kidney aging through transcriptional regulator GLIS1

doi: 10.1186/s12915-024-02100-y

Figure Lengend Snippet: METTL3 ameliorated age-related renal fibrosis in accelerated aging mouse model. A , B Downregulated protein levels of METTL3, METTL14, and GLIS1 in an accelerated aging mouse model were reversed in the presence of AAV-METTL3, and the upregulated protein levels of P16 INK4A and FN by western blot in the accelerated aging mouse model were reduced by introducing AAV-METTL3 ( n = 6); C the enriched m6A modification of GLIS1 in the control, AAV-Vector and AAV-METTL3 group by MeRIP-qPCR assay ( n = 6); D GLIS1 mRNA levels in the control, AAV-Vector, and AAV-METTL3 group detected by RT-qPCR ( n = 5); E protein levels of GLIS1, P16 INK4A , and FN in the control, AAV-Vector and AAV-METTL3 group by Masson staining and IHC assay and their semi-quantitative analyses ( n = 6), scale bar = 50 μm; F immunostaining for PPARα (red) and CPT1A (green), HK2 (pink), and PDK1 (yellow), with DAPI (blue) counterstaining by IF staining in the control, AAV-Vector, and AAV-METTL3 group ( n = 6), scale bar = 50 μm. The data are expressed as the mean ± SD of three independent experiments. ** P < .01 or *** P < .001 versus the AAV-vector group by one-way ANOVA

Article Snippet: Human m6A epitranscriptomic microarray and mRNA microarray analyses were performed based on Arraystar’s standard protocols.

Techniques: Western Blot, Modification, Control, Plasmid Preparation, Quantitative RT-PCR, Staining, Immunostaining

Journal: BMC Biology

Article Title: N6-methyladenosine regulates metabolic remodeling in kidney aging through transcriptional regulator GLIS1

doi: 10.1186/s12915-024-02100-y

Figure Lengend Snippet: YTHDF1 identified with m6A-meditated GLIS1 mRNA and participated the translation process of GLIS1 protein. A The expression of YTHDF1 in the 24-month-old and 6-month-old group by IHC assay, and its semi-quantitative analysis ( n = 6), scale bar = 50 μm; B immunostaining for YTHDF1 (green), with DAPI (blue) counterstaining by IF staining in the 24-month-old and 6-month-old group ( n = 6), scale bar = 50 μm; C , D protein level of YTHDF1 in the 24-month-old and 6-month-old group by western blot, and its semi-quantitative analysis ( n = 6); E mRNA level of YTHDF1 by RT-qPCR in HK-2 cells within vector or siYTHDF1 ( n = 3); F protein level of GLIS1 in HK-2 cells within vector or siYTHDF1, and its semi-quantitative analysis ( n = 3); G double immunostaining for GLIS1 (red) and YTHDF1 (green) by IF staining in HK-2 cells ( n = 3), scale bar = 50 μm; H , I RIP and RT-PCR assays confirmed the interaction between YTHDF1 and GLIS1 mRNA, and its semi-quantitative analysis ( n = 3); J the expression of GLIS1 with RPL22-FLAG label by ribosomal immunoprecipitation in HK-2 cells ( n = 3); K the mRNA level of GLIS1 by RT-qPCR in HK-2 cells within vector or siYTHDF1 ( n = 3); L , M relative luciferase activity of the GLIS1-WT or GLIS1-Mut 3′UTR luciferase reporter in the vector and siMETTL3 group, n = 3. The data are expressed as the mean ± SD of three independent experiments. ** P < .01 or *** P < .001 versus the 6-month-old group, or vector group, or IgG group by Student’s t -test

Article Snippet: Human m6A epitranscriptomic microarray and mRNA microarray analyses were performed based on Arraystar’s standard protocols.

Techniques: Expressing, Immunostaining, Staining, Western Blot, Quantitative RT-PCR, Plasmid Preparation, Double Immunostaining, Reverse Transcription Polymerase Chain Reaction, Immunoprecipitation, Luciferase, Activity Assay

Journal: Cancer Cell International

Article Title: The emerging functions and clinical implications of circRNAs in acute myeloid leukaemia

doi: 10.1186/s12935-025-03772-4

Figure Lengend Snippet: Biogenesis, degradation and regulatory functions of circRNAs. A Biogenesis of exonic circRNAs (ecircRNAs), exon‒intron circRNAs (EIciRNAs), intronic circRNAs (ciRNAs), intergenic circRNAs, read‒through circRNAs (rt-circRNAs), fusion circRNAs (f-circRNAs), tRNA intronic circular RNAs (tricRNAs), and mitochondria‒encoded circRNAs (mecciRNAs) and the potential mechanisms of circRNA degradation. B Potential regulatory mechanisms of circRNAs. ( a ) CircRNAs can serve as microRNA sponges to block microRNA-mediated target gene silencing. ( b ) CircRNAs can interact with DNA to form circR loops. ( c ) CircRNAs can regulate the functions of RBPs (I), recruit transcription activators (II), act as protein scaffolds (III), and interact with specific proteins (IV). ( d ) CircRNAs can be translated into proteins or peptides

Article Snippet: GSE116618 , Normal individuals (n = 4) and AML patients (n = 8) based on GSE116617 , Arraystar Human CircRNA Array , 19 circRNAs were differentially expressed , [ ] .

Techniques: Blocking Assay

Journal: Cancer Cell International

Article Title: The emerging functions and clinical implications of circRNAs in acute myeloid leukaemia

doi: 10.1186/s12935-025-03772-4

Figure Lengend Snippet: CircRNA profiles in AML

Article Snippet: GSE116618 , Normal individuals (n = 4) and AML patients (n = 8) based on GSE116617 , Arraystar Human CircRNA Array , 19 circRNAs were differentially expressed , [ ] .

Techniques: Expressing, Control, Microarray, Modification

Journal: Cancer Cell International

Article Title: The emerging functions and clinical implications of circRNAs in acute myeloid leukaemia

doi: 10.1186/s12935-025-03772-4

Figure Lengend Snippet: Databases or tools for predicting the translation potential of circRNA

Article Snippet: GSE116618 , Normal individuals (n = 4) and AML patients (n = 8) based on GSE116617 , Arraystar Human CircRNA Array , 19 circRNAs were differentially expressed , [ ] .

Techniques: Sequencing, Modification, Mass Spectrometry

Journal: Cancer Cell International

Article Title: The emerging functions and clinical implications of circRNAs in acute myeloid leukaemia

doi: 10.1186/s12935-025-03772-4

Figure Lengend Snippet: Databases for predicting the potential regulatory mechanisms of circRNA

Article Snippet: GSE116618 , Normal individuals (n = 4) and AML patients (n = 8) based on GSE116617 , Arraystar Human CircRNA Array , 19 circRNAs were differentially expressed , [ ] .

Techniques: Mutagenesis, Binding Assay, Methylation, Expressing

Journal: Cancer Cell International

Article Title: The emerging functions and clinical implications of circRNAs in acute myeloid leukaemia

doi: 10.1186/s12935-025-03772-4

Figure Lengend Snippet: Summary of significant associations between circRNA and AML survival

Article Snippet: GSE116618 , Normal individuals (n = 4) and AML patients (n = 8) based on GSE116617 , Arraystar Human CircRNA Array , 19 circRNAs were differentially expressed , [ ] .

Techniques:

Journal: PLoS ONE

Article Title: DNA Methylation in Multiple Myeloma Is Weakly Associated with Gene Transcription

doi: 10.1371/journal.pone.0052626

Figure Lengend Snippet: (A) Pearson correlation was used to measure linear relationships between DNA methylation and gene expression levels for 1505 CpG probes represented on the GoldenGate Methylation BeadArray. The panels represent examples of a gene with high (left) and low (right) Pearson correlation coefficients when analyzing DNA methylation levels (x axis) against gene expression levels (y axis). (B) A discretization approach was used to classify samples into methylated (M) or unmethylated (U) groups based on the mean ( μ ) methylation value and standard deviation ( σ ) of a given probe. Statistically significant gene expression differences between M and U groups indicated a methylation-expression correlation for the gene in question.

Article Snippet: For these approaches we used DNA methylation data obtained with the GoldenGate BeadArray technology along with corresponding array-based gene expression data from 193 human MM samples.

Techniques: DNA Methylation Assay, Expressing, Methylation, Standard Deviation

Journal: PLoS ONE

Article Title: DNA Methylation in Multiple Myeloma Is Weakly Associated with Gene Transcription

doi: 10.1371/journal.pone.0052626

Figure Lengend Snippet: Box plots represent gene expression levels generated by either microarray or qRT-PCR. Data are shown for samples classified as U or M based on the methylation status of p16 (A), DLC1 (B), IGF1R (C), or IL17RB (D). For microarray data, probe intensities are plotted on the y-axis. Relative fold-change differences are plotted for data generated by qRT-PCR. The number of samples in each group is displayed above each plot. The GoldenGate BeadArray probe names are indicated above each pair of box plots.

Article Snippet: For these approaches we used DNA methylation data obtained with the GoldenGate BeadArray technology along with corresponding array-based gene expression data from 193 human MM samples.

Techniques: Expressing, Generated, Microarray, Quantitative RT-PCR, Methylation

Journal: BMC Biology

Article Title: N6-methyladenosine regulates metabolic remodeling in kidney aging through transcriptional regulator GLIS1

doi: 10.1186/s12915-024-02100-y

Figure Lengend Snippet: The abnormal m6A modification and protein levels of GLIS1 in human aged kidney tissues. A Total m6A RNA levels in the H/aged ( n = 10) and H/control group ( n = 10) detected by m6A methylation quantification kit; B differential methylated mRNA expressions between H/aged (A) and H/control (Y) group by using m6A-mRNA epitranscriptomic microarray analysis ( n = 3); C analysis of significant changes in methylated mRNA expression levels between the H/aged and H/control group; D the Gene Ontology (GO) biological process enrichment analysis pathways of predicted mRNA targets; E enriched m6A modification of GLIS1 in the H/aged and H/control group by MeRIP assay ( n = 4); F , G protein level of GLIS1 in the H/aged and H/control group by western blot, and its semi-quantitative analyses ( n = 6). The data are expressed as the mean ± SD of three independent experiments. *** P < .001 indicates a significant difference versus the H/control group by Student’s t -test

Article Snippet: Human m6A epitranscriptomic microarray and mRNA microarray analyses were performed based on Arraystar’s standard protocols.

Techniques: Modification, Control, Methylation, Microarray, Expressing, Western Blot

Journal: BMC Biology

Article Title: N6-methyladenosine regulates metabolic remodeling in kidney aging through transcriptional regulator GLIS1

doi: 10.1186/s12915-024-02100-y

Figure Lengend Snippet: METTL3 directly interacted with GLIS1 in kidney aging. A The mRNA level of METTL3 in the vector and siMETTL3 group in HK-2 cells by RT-qPCR ( n = 3); B , C protein level of GLIS1 by western blot in the vector and siMETTL3 group in HK-2 cells, and its semi-quantitative analysis ( n = 3); D protein levels of METTL3, METTL14, and WTAP by western blot in the 24-month-old and 6-month-old group ( n = 6); E , F the expression of METTL3 in the 24-month-old and 6-month-old group by IHC assay, and its semi-quantitative analysis ( n = 6), scale bar = 50 μm; G immunostaining for METTL3 (green), with DAPI (blue) counterstaining by IF staining in the 24-month-old and 6-month-old group ( n = 6), scale bar = 50 μm; H immunostaining for METTL3 (green), GLIS1 (red), with DAPI (blue) counterstaining by IF staining in HK-2 cells ( n = 3), scale bar = 50 μm; I , J METTL3 RIP and RT-PCR confirmed the interaction between METTL3 and GLIS1 mRNA, and its semi-quantitative analysis ( n = 3); K the lower m6A level of GLIS1 in siMETTL3 group compared with the vector group in HK-2 cells by using MeRIP-qPCR ( n = 3); L the mRNA level of GLIS1 in the vector and siMETTL3 group in HK-2 cells by RT-qPCR ( n = 3); M mutations at the two putative m6A sites in GLIS1 (A to G); N m6A level of GLIS1 in HK-2 cells with co-expression of siMETTL3 and GLIS1-WT/Muts by MeRIP-qPCR ( n = 3); O the mRNA level of GLIS1 in the vector and GLIS1-Mut3 group by RT-qPCR ( n = 3). The data are expressed as the mean ± SD of three independent experiments. ** P < .01 or *** P < .001 versus the vector group ( A , C , K ) or 6-month-old group ( E ) or IgG group ( J ) by Student’s t -test; ## P < .01, ### P < .001 versus the vector-WT group, ++ P < .01, +++ P < .001 versus the siMETTL3-WT group, ** P < .01 versus vector group by two way-ANOVA ( N )

Article Snippet: Human m6A epitranscriptomic microarray and mRNA microarray analyses were performed based on Arraystar’s standard protocols.

Techniques: Plasmid Preparation, Quantitative RT-PCR, Western Blot, Expressing, Immunostaining, Staining, Reverse Transcription Polymerase Chain Reaction

Journal: BMC Biology

Article Title: N6-methyladenosine regulates metabolic remodeling in kidney aging through transcriptional regulator GLIS1

doi: 10.1186/s12915-024-02100-y

Figure Lengend Snippet: METTL3 ameliorated age-related renal fibrosis in accelerated aging mouse model. A , B Downregulated protein levels of METTL3, METTL14, and GLIS1 in an accelerated aging mouse model were reversed in the presence of AAV-METTL3, and the upregulated protein levels of P16 INK4A and FN by western blot in the accelerated aging mouse model were reduced by introducing AAV-METTL3 ( n = 6); C the enriched m6A modification of GLIS1 in the control, AAV-Vector and AAV-METTL3 group by MeRIP-qPCR assay ( n = 6); D GLIS1 mRNA levels in the control, AAV-Vector, and AAV-METTL3 group detected by RT-qPCR ( n = 5); E protein levels of GLIS1, P16 INK4A , and FN in the control, AAV-Vector and AAV-METTL3 group by Masson staining and IHC assay and their semi-quantitative analyses ( n = 6), scale bar = 50 μm; F immunostaining for PPARα (red) and CPT1A (green), HK2 (pink), and PDK1 (yellow), with DAPI (blue) counterstaining by IF staining in the control, AAV-Vector, and AAV-METTL3 group ( n = 6), scale bar = 50 μm. The data are expressed as the mean ± SD of three independent experiments. ** P < .01 or *** P < .001 versus the AAV-vector group by one-way ANOVA

Article Snippet: Human m6A epitranscriptomic microarray and mRNA microarray analyses were performed based on Arraystar’s standard protocols.

Techniques: Western Blot, Modification, Control, Plasmid Preparation, Quantitative RT-PCR, Staining, Immunostaining

Journal: BMC Biology

Article Title: N6-methyladenosine regulates metabolic remodeling in kidney aging through transcriptional regulator GLIS1

doi: 10.1186/s12915-024-02100-y

Figure Lengend Snippet: YTHDF1 identified with m6A-meditated GLIS1 mRNA and participated the translation process of GLIS1 protein. A The expression of YTHDF1 in the 24-month-old and 6-month-old group by IHC assay, and its semi-quantitative analysis ( n = 6), scale bar = 50 μm; B immunostaining for YTHDF1 (green), with DAPI (blue) counterstaining by IF staining in the 24-month-old and 6-month-old group ( n = 6), scale bar = 50 μm; C , D protein level of YTHDF1 in the 24-month-old and 6-month-old group by western blot, and its semi-quantitative analysis ( n = 6); E mRNA level of YTHDF1 by RT-qPCR in HK-2 cells within vector or siYTHDF1 ( n = 3); F protein level of GLIS1 in HK-2 cells within vector or siYTHDF1, and its semi-quantitative analysis ( n = 3); G double immunostaining for GLIS1 (red) and YTHDF1 (green) by IF staining in HK-2 cells ( n = 3), scale bar = 50 μm; H , I RIP and RT-PCR assays confirmed the interaction between YTHDF1 and GLIS1 mRNA, and its semi-quantitative analysis ( n = 3); J the expression of GLIS1 with RPL22-FLAG label by ribosomal immunoprecipitation in HK-2 cells ( n = 3); K the mRNA level of GLIS1 by RT-qPCR in HK-2 cells within vector or siYTHDF1 ( n = 3); L , M relative luciferase activity of the GLIS1-WT or GLIS1-Mut 3′UTR luciferase reporter in the vector and siMETTL3 group, n = 3. The data are expressed as the mean ± SD of three independent experiments. ** P < .01 or *** P < .001 versus the 6-month-old group, or vector group, or IgG group by Student’s t -test

Article Snippet: Human m6A epitranscriptomic microarray and mRNA microarray analyses were performed based on Arraystar’s standard protocols.

Techniques: Expressing, Immunostaining, Staining, Western Blot, Quantitative RT-PCR, Plasmid Preparation, Double Immunostaining, Reverse Transcription Polymerase Chain Reaction, Immunoprecipitation, Luciferase, Activity Assay