rna oligonucleotide probes  (Celemics Inc)

Journal: bioRxiv

Article Title: Single-nucleus epigenomic dysregulation unmasks genetic risk-associated neurodegenerative glia states

doi: 10.1101/2025.06.02.657512

Figure Lengend Snippet: Diversity and heterogeneity of cellular subtypes in human brain of tauopathies. (A-C) UMAP embedding of subclusters of astrocytes (A), with a heatmap of gene score matrix labeled by log2fc > 1 for marker gene scores (B) and enriched functional terms associated with these marker genes (C). ASC, astrocytes. (D-F) Similar analyses for microglia subclusters. MG, microglia. (G) Gene signatures of astrocyte subclusters (top) and microglia subclusters (bottom), defined by marker gene scores compared within each respective cell type. (H) RNAscope ISH for SOX10 combined with GFAP IHC in human insular tissue from a PSP patient. Representative images show co-localization of SOX10 mRNA and GFAP in a subset of astrocytes (Scale bar: 10 µm). (I) Boxplots displaying the relative abundance of insula ast.C1 (top) and mg.C4 (bottom) across conditions. Changes in cell composition among disease and control groups are modeled using linear regression computed by Limma, adjusted for age and post-mortem interval. *P<0.05. (J) Example tracks showing marker peaks for genes PLP1 , SOT1l in mg.C4; RIN3 and TREM2 in mg.C13 and mg.C6; CD48 in mg.C9 and mg.C6; and LGALS3 in mg.C7 and mg.C14. (K) Example tracks showing marker peaks for genes CNTN2 , KLK6 , and PLP1 in ast.C1; HLA- DMB in ast.C3; and GFAP in multiple astrocyte subclusters.

Article Snippet: Target RNA-specific oligonucleotide probes used for mRNA of human SOX10 (CATALOG # 484128-C4) and PLP1 (CATALOG# 499278) were synthesized by Advanced Cell Diagnostics.

Techniques: Labeling, Marker, Functional Assay, RNAscope, Control

Journal: Experimental & Molecular Medicine

Article Title: LncRNA Gm35585 transcriptionally activates the peroxidase EHHADH against diet-induced fatty liver

doi: 10.1038/s12276-025-01420-5

Figure Lengend Snippet: The oligonucleotide sequences for siRNA experiments in vitro.

Article Snippet: Nucleic-acid-modified targeting Gm35585 oligonucleotide probes and RNA fluorescence in situ hybridization (FISH) kits (GenePharma) were used for RNA FISH of cell migration assays and tissue sections.

Techniques:

Journal: Experimental & Molecular Medicine

Article Title: LncRNA Gm35585 transcriptionally activates the peroxidase EHHADH against diet-induced fatty liver

doi: 10.1038/s12276-025-01420-5

Figure Lengend Snippet: Primers used for qRT–PCR analysis.

Article Snippet: Nucleic-acid-modified targeting Gm35585 oligonucleotide probes and RNA fluorescence in situ hybridization (FISH) kits (GenePharma) were used for RNA FISH of cell migration assays and tissue sections.

Techniques:

Journal: Experimental & Molecular Medicine

Article Title: LncRNA Gm35585 transcriptionally activates the peroxidase EHHADH against diet-induced fatty liver

doi: 10.1038/s12276-025-01420-5

Figure Lengend Snippet: a , f Costaining of liver tissue sections with Nile Red and EHHADH immunofluorescence. Scale bar, 25 μm. b , g Liver peroxidase activity. Reaction time: 30 min (mean ± s.d., n = 5, one-way ANOVA). c , h Liver total FA contents analyzed by LC–MS/MS (mean ± s.d., n = 5, one-way ANOVA). d , i Heat map of 28 FA contents in the liver. (* P <0.05, ** P <0.01, *** P <0.001, NCD+AAV-NC vs HFD+AAV-NC, and NCD+TBG-NC vs HFD+TBG-NC. # P <0.05, ## P <0.01, ### P <0.001, HFD+AAV-NC vs HFD+AAVGm35585, and HFD+TBG-NC vs HFD+TBG-EHHADH.) e , j Changes in hepatic SCFA, MCFA and LCFA levels. Information on the 28 FAs is given in Table . ( a – e The analysis of Gm35585 overexpression experiments in vivo. f – j The analysis of EHHADH overexpression experiments in vivo.).

Article Snippet: Nucleic-acid-modified targeting Gm35585 oligonucleotide probes and RNA fluorescence in situ hybridization (FISH) kits (GenePharma) were used for RNA FISH of cell migration assays and tissue sections.

Techniques: Immunofluorescence, Activity Assay, Liquid Chromatography with Mass Spectroscopy, Over Expression, In Vivo

Journal: Experimental & Molecular Medicine

Article Title: LncRNA Gm35585 transcriptionally activates the peroxidase EHHADH against diet-induced fatty liver

doi: 10.1038/s12276-025-01420-5

Figure Lengend Snippet: a In vivo experimental flow diagram. NCD mice: C57BL/6J mice; HFD mice: 10 weeks of high-fat feeding C57BL/6J mice. b Changes in the body weight of mice within 10 days after AAV-Gm35585 injection (mean ± s.d., n = 5, one-way ANOVA; **** P < 0.0001, NCD + AAV-NC versus HFD + AAV-NC; # P < 0.05, ## P < 0.01, ### P < 0.001, HFD + AAV-NC versus HFD + AAV-Gm35585). c Changes in liver TG and TC levels under Gm35585 overexpression condition (mean ± s.d., n = 5; one-way ANOVA). d Serum biochemical indices included ALT, AST, TG, TC, LDL, and HDL (mean ± s.d., n = 5; one-way ANOVA). e Oil Red O staining of liver tissue sections indicating changes in lipid droplet content. Scale bar, 50 μm. f Differences between groups after Gm35585 overexpression ( n = 3). g The nnumber of upregulated and downregulated genes after Gm35585 overexpression ( n = 3). h KEGG enrichment analysis of RNA sequencing data from HFD + AVV-Gm35585 mouse livers.

Article Snippet: Nucleic-acid-modified targeting Gm35585 oligonucleotide probes and RNA fluorescence in situ hybridization (FISH) kits (GenePharma) were used for RNA FISH of cell migration assays and tissue sections.

Techniques: In Vivo, Injection, Over Expression, Staining, RNA Sequencing

Journal: Experimental & Molecular Medicine

Article Title: LncRNA Gm35585 transcriptionally activates the peroxidase EHHADH against diet-induced fatty liver

doi: 10.1038/s12276-025-01420-5

Figure Lengend Snippet: a , f Costaining of liver tissue sections with Nile Red and EHHADH immunofluorescence. Scale bar, 25 μm. b , g Liver peroxidase activity. Reaction time: 30 min (mean ± s.d., n = 5, one-way ANOVA). c , h Liver total FA contents analyzed by LC–MS/MS (mean ± s.d., n = 5, one-way ANOVA). d , i Heat map of 28 FA contents in the liver. * P < 0.05, ** P < 0.01, *** P < 0.001, NCD+AAV-NC vs HFD+AAV-NC, and NCD+TBG-NC vs HFD+TBG-NC. # P < 0.05, ## P < 0.01, ### P < 0.001, HFD+AAV-NC vs HFD+AAV-Gm35585, and HFD+TBG-NC vs HFD+TBG-EHHADH. e , j Changes in hepatic SCFA, MCFA and LCFA levels. Information on the 28 FAs is given in Table . ( a – e The analysis of Gm35585 overexpression experiments in vivo. f – j The analysis of EHHADH overexpression experiments in vivo).

Article Snippet: Nucleic-acid-modified targeting Gm35585 oligonucleotide probes and RNA fluorescence in situ hybridization (FISH) kits (GenePharma) were used for RNA FISH of cell migration assays and tissue sections.

Techniques: Immunofluorescence, Activity Assay, Liquid Chromatography with Mass Spectroscopy, Over Expression, In Vivo

Journal: Experimental & Molecular Medicine

Article Title: LncRNA Gm35585 transcriptionally activates the peroxidase EHHADH against diet-induced fatty liver

doi: 10.1038/s12276-025-01420-5

Figure Lengend Snippet: a mRNA expression levels of Gm35585, Pparα and Ehhadh with PA and siGm35585 treatment in AML-12 cells. The values were normalized to those of the control group (mean ± s.d., n = 3, one-way ANOVA). b , j , n The protein expression of PPARα and EHHADH in AML-12 cells. c , g , k , o Nile Red staining of AML-12 cells to test changes in lipid content. Scale bar, 50 μm. d , h , l , p Changes in TG levels in AML-12 cells (mean ± s.d., n = 3, one-way ANOVA). e mRNA expression levels of Ehhadh with PA, siEHHADH and pEX-3-Gm35585 treatment in AML-12 cells. The values were normalized to those of the control group (mean ± s.d., n = 3, one-way ANOVA). f The protein expression of EHHADH in AML-12 cells. i mRNA expression levels of Pparα and Ehhadh with PA and GW7647 treatment in AML-12 cells. The values were normalized to those of the control group (mean ± s.d., n = 3, one-way ANOVA). m mRNA expression levels of Pparα and Ehhadh with PA, GW6471 and pEX-3-Gm35585 treatment in AML-12 cells. The values were normalized to those of the control group (mean ± s.d., n = 3, one-way ANOVA). ( b – d The analysis in AML-12 cells with PA and siGm35585 treatment. g , h The analysis in AML-12 cells with PA, siEHHADH, and pEX-3-Gm35585 treatment. j – l The analysis in AML-12 cells with PA, siEHHADH, and GW7646 treatment. n – p The analysis in AML-12 cells with PA, GW6471, and pEX-3-Gm35585 treatment.).

Article Snippet: Nucleic-acid-modified targeting Gm35585 oligonucleotide probes and RNA fluorescence in situ hybridization (FISH) kits (GenePharma) were used for RNA FISH of cell migration assays and tissue sections.

Techniques: Expressing, Control, Staining

Journal: Experimental & Molecular Medicine

Article Title: LncRNA Gm35585 transcriptionally activates the peroxidase EHHADH against diet-induced fatty liver

doi: 10.1038/s12276-025-01420-5

Figure Lengend Snippet: a Gm35585 RNA FISH and EHHADH immunofluorescence costaining under PA and pEX-3-Gm35585 treatment in AML-12 cells. Scale bar, 25 μm. b Gm35585 expression levels in the nucleus and cytoplasm of AML-12 cells. The values were normalized to those of the control group (mean ± s.d., n = 3, two-way ANOVA). c Gm35585 expression in the nucleus and cytoplasm in the liver. The values were normalized to those of the control group (mean ± s.d., n = 3, two-way ANOVA). d RNA pulldown assay flowchart in AML-12 cells. e Silver staining followed by an RNA pulldown assay in AML-12 cells. A U-biotin-labeled Gm35585 probe was used to pull down proteins. f KEGG enrichment analysis of the RNA pulldown protein profile. g Protein expression levels of RXRα and RXRβ in Gm35585 overexpression mouse liver. h mRNA expression levels of Rxrα and Rxrβ in Gm35585 overexpression mouse liver. The values were normalized to those of the control group (mean ± s.d., n = 5; one-way ANOVA). i Protein expression levels of RXRα and RXRβ in AML-12 cells. j mRNA expression levels of Rxrα and Rxrβ in AML-12 cells. The values were normalized to those of the control group (mean ± s.d., n = 4, one-way ANOVA). k Western blot analysis of RNA pulldown proteins. l Mechanistic diagram of Gm35585 binding to RXRα.

Article Snippet: Nucleic-acid-modified targeting Gm35585 oligonucleotide probes and RNA fluorescence in situ hybridization (FISH) kits (GenePharma) were used for RNA FISH of cell migration assays and tissue sections.

Techniques: Immunofluorescence, Expressing, Control, Silver Staining, Labeling, Over Expression, Western Blot, Binding Assay

Journal: Experimental & Molecular Medicine

Article Title: LncRNA Gm35585 transcriptionally activates the peroxidase EHHADH against diet-induced fatty liver

doi: 10.1038/s12276-025-01420-5

Figure Lengend Snippet: a Western blotting assay followed by co-IP assay under IgG and RXRα antibody treatment in AML-12 cells. b The JASPAR database shows the sequence of the PPARα/RXRα transcription factor DAN, which binds to the EHHADH promoter. c The position of the ChIP primer in the EHHADH promoter; the red font represents a DNA sequence similar to that in ( b ). d A ChIP assay combined with RT‒qPCR was performed using the IgG and RXRα antibodies in AML-12 cells (mean ± s.d., n = 4, t test). e mRNA expression levels of Rxrα and Ehhadh with PA, siRXRα and pEX-3-Gm35585 treatment in AML-12 cells. The values were normalized to those of the control group (mean ± s.d., n = 4, one-way ANOVA). f Protein expression levels of RXRα and EHHADH in AML-12 cells. g Changes in TG levels in AML-12 cells (mean ± s.d., n = 4, one-way ANOVA). h Nile Red and EHHADH immunofluorescence costaining in AML-12 cells. Scale bar, 25 μm. i Total mechanism chart.

Article Snippet: Nucleic-acid-modified targeting Gm35585 oligonucleotide probes and RNA fluorescence in situ hybridization (FISH) kits (GenePharma) were used for RNA FISH of cell migration assays and tissue sections.

Techniques: Western Blot, Co-Immunoprecipitation Assay, Sequencing, Expressing, Control, Immunofluorescence

Journal: Frontiers in Neuroanatomy

Article Title: Development of the early fetal human thalamus: from a protomap to emergent thalamic nuclei

doi: 10.3389/fnana.2025.1530236

Figure Lengend Snippet: Details of primary antibodies and RNAScope in situ hybridization probes employed.

Article Snippet: Paired double-Z oligonucleotide probes against target RNA for SOX14, ZIC4 , and CNTNAP2 were designed and supplied by ACD Bio Techne (Abingdon, United Kingdom) and described in .

Techniques: RNAscope, In Situ Hybridization

Journal: Frontiers in Neuroanatomy

Article Title: Development of the early fetal human thalamus: from a protomap to emergent thalamic nuclei

doi: 10.3389/fnana.2025.1530236

Figure Lengend Snippet: C NTNAP2 expression in the developing thalamus. (A) Widespread expression of CNTNAP2 in post-mitotic cells of the thalamus (th) and (Crx), strong expression in the thalamic eminence and cortical hem (arrows) but low expression in the thalamic ventricular zone (VZ) and proliferative regions of cortex and ganglionic eminence (GE). (B–F) A series of sections at 14 PCW from anterior dorsal to posterior ventral thalamus at 14 PCW. (B,C) CNTNAP2 strongly expressed in habenula (Ha) and medial and lateral pulvinar (PM and PL) but less in the inferior pulvinar (PI). Expression moderate in the ventroposterolateral nucleus (VPL) and lateral geniculate nucleus (LGN). Low expression in the medial geniculate nucleus (MGN) and region dorsal to it. (C’) Taken from section adjacent to C double stained for CNTNAP2 and GAD67 and counterstained blue with DAPI; CNTNAP2 mRNA primarily associated with GAD67 immunonegative cells (arrows) and not GAD67+ cell cytoplasm (asterisks). (D,E) Represent mid thalamic regions and demonstrate widespread CNTNAP2 expression, with some areas of low expression such as the parafascicular complex (pF). ( D’,D”) Taken from section adjacent to D double stained for CNTNAP2 and FOXP2, showing that they can be co-expressed, or that expression can be mutually exclusive. (F) At more ventral levels, CNTNAP2 expression highest laterally, posteriorly and close to third ventricle, but relatively weak medially and anteriorly. CM, centromedial nucleus; HIT, habenulo-interpeduncluar tract; LD, laterodorsal nucleus; MD, mediodorsal nucleus; VL, ventrolateral nucleus; VM, ventromedial nucleus; VP, ventroposterior nucleus. Scale bars = 1 mm (A–F) ; 50 μm (C’) .

Article Snippet: Paired double-Z oligonucleotide probes against target RNA for SOX14, ZIC4 , and CNTNAP2 were designed and supplied by ACD Bio Techne (Abingdon, United Kingdom) and described in .

Techniques: Expressing, Staining