ddx21 antibody - bsa free  (Bio-Techne corporation)

Journal: Nature

Article Title: GlycoRNA complexed with heparan sulfate regulates VEGF-A signalling

doi: 10.1038/s41586-025-10052-8

Figure Lengend Snippet: a , Representative images of U2OS cells co-stained with Siglec-11 (yellow) and 9D5 (magenta). An enlargement of the hatched box is shown, and a bright field (BF) is shown to represent the outline of the cell membrane. The nearest neighbour distance analysis of the Siglec pairs is also imaged (bottom). For each pair, the distance (µm) from that anchor (left side protein name in the figure key) to the other pair was calculated across the indicated number of cells. These values were plotted in a density histogram. b , Dot plot of genes identified in the genome-wide CRISPR-KO screen for the loss of Siglec-11 cell surface binding ranked by CRISPR score. The top 15 gene names are displayed, with cut-off shown. The inset illustrates how Siglec-11 could interact with a glycoRNA. c , Dot plot of genes identified in the genome-wide KO screen as in panel b , for the loss of 9D5 cell surface binding. The inset illustrates how 9D5 could interact with a glycoRNA. d , Upset plot analysis of genes with a score cut-off of −0.8 from the Siglec-11, 9D5 and MAA-I genome-wide KO screens. The common overlapping hits between 9D5 and Siglec-11 are highlighted in blue. The total number of hits for each intersection is noted. Statistical assessment was performed with a hypergeometric test and P values are shown without adjustment. e , Representative images of WT and KO U2OS cells stained live with 10E4, Siglec-11–Fc, 9D5 and Siglec-7 (all in red). Ab, antibody; dsRNA, double-stranded RNA; mE, mEmerald. f , Quantification of the indicated signal dot numbers and intensity per cell from panels e , g from three independent experiments. Mut, mutant. g , Representative images of the indicated cell lines stained live with anti-DDX21 and anti-hnRNP-U (both in red).

Article Snippet: For DDX21 and hnRNP-U staining, 2.5 μg ml −1 of anti-DDX21 (Novus Biological) and anti-hnRNP-U (Proteintech) were incubated with cells for 45 min on ice.

Techniques: Staining, Membrane, Genome Wide, CRISPR, Binding Assay, Mutagenesis

Journal: Nature

Article Title: GlycoRNA complexed with heparan sulfate regulates VEGF-A signalling

doi: 10.1038/s41586-025-10052-8

Figure Lengend Snippet: a . Sequence alignment of partial EXT2 coding sequences from WT and EXT2 knockout (KO) U2OS cells. Protospacer adjacent motif (PAM), green; sgRNA target, blue; mutated sequence, red. b . Western blot analysis of whole cell lysate. (left) from wild-type (WT) and (right) EXT2 KO U2OS cell lines. 2 independent experiments were performed. c . Representative images of WT and EXT2 KO U2OS cells stained with Siglec-9 (red). Scale bar, 10 µm. 3 independent experiments were performed. d . Number of cells quantified in Fig. , and EDF4C across 3 independent experiments. e . Representative images of WT and EXT2 KO U2OS cells fixed, permeabilized, and stained with 9D5. Scale bar, 10 µm. Quantification of 9D5 intensity counted from 3 independent experiments. Data are mean ± s.e.m. f . Western blot analysis of whole cell lysate from the indicated cell lines. 2 independent experiments were performed. g . Western blot analysis of whole cell lysate (right) and sequence alignment of partial EXT1 coding sequences (left) from WT and EXT1 KO U2OS cells. 2 independent experiments were performed. h . Sequence alignment of partial UXS1 coding sequences from WT and UXS1 KO U2OS cells. i . Representative images of WT, EXT1 KO, and UXS1 KO U2OS cells stained with 10E4, Siglec-11, 9D5, DDX21, and hnRNP-U (all in red), separately. Scale bar, 10 µm. 3 independent experiments were performed. j . Representative images of U2OS cells co-stained live with 9D5 (green) and anti-DDX21 (red) or anti-hnRNP-U (red). An enlargement of the hatched box is shown, and a bright field (BF) is shown to represent the outline of the cell membrane. Scale bar, 10 µm. 2 independent experiments were performed. k . Western blot analysis of whole cell lysate from WT and EXT2 KO U2OS cell lines. Quantification of the ratio of total DDX21 and hnRNP-U to GAPDH is calculated across the biological triplicates. Statistical assessment was performed with a two-sided Student's t -test and P values are shown. Data are mean ± s.e.m.

Article Snippet: For DDX21 and hnRNP-U staining, 2.5 μg ml −1 of anti-DDX21 (Novus Biological) and anti-hnRNP-U (Proteintech) were incubated with cells for 45 min on ice.

Techniques: Sequencing, Knock-Out, Western Blot, Staining, Membrane

Journal: Nature

Article Title: GlycoRNA complexed with heparan sulfate regulates VEGF-A signalling

doi: 10.1038/s41586-025-10052-8

Figure Lengend Snippet: a . Representative images of U2OS cells treated with heparinase pool for 30 min, and stained live with 10E4, Siglec-11, 9D5, anti-DDX21, anti-hnRNP-U, Siglec-7-Fc, and Siglec-9-Fc (all in red), separately. Scale bar, 10 µm. b . Quantification of data in A with the number of cells per condition from 3 independent experiments is shown. Statistical assessment was performed with a two-sided Student's t -test and P values are shown. Data are mean ± s.e.m. c . Nearest neighbor distance analysis of the 10E4 and Siglec-11 in Fig. . For each pair, the nm distance from 10E4 to Siglec-11 was calculated across each time point. These values were plotted in a density histogram. d . Quantification fraction of 10E4-occupied, Siglec-11 dots in Fig. from 3 independent experiments. e . Representative images of U2OS cells co-stained with the indicated 10E4 (Cyan), Siglec-11 (yellow), and DDX21 (magenta). An enlargement of the hatched box is shown, and a bright field (BF) is shown to represent the outline of the cell membrane. Scale bar, 10 µm. 2 independent experiments were performed.

Article Snippet: For DDX21 and hnRNP-U staining, 2.5 μg ml −1 of anti-DDX21 (Novus Biological) and anti-hnRNP-U (Proteintech) were incubated with cells for 45 min on ice.

Techniques: Staining, Membrane

Journal: Nature

Article Title: GlycoRNA complexed with heparan sulfate regulates VEGF-A signalling

doi: 10.1038/s41586-025-10052-8

Figure Lengend Snippet: a , Representative images of U2OS cells treated with a heparinase pool for 30 min, recovering for the indicated times and co-stained with 10E4 (cyan), Siglec-11 (yellow) and 9D5 (magenta). An enlargement of the hatched box is shown, and a bright field is shown to represent the outline of the cell membrane. Three independent experiments were performed. b , Schematic of a HSPG with the regions of activity for the various enzymes and HS oligos perturbed in the following experiments. 2S, 2- O -sulfation; 6S, 6- O -sulfation; NS, N -sulfation. c , Representative images of WT, NDST1 -KO-treated, HS6ST1 -KO-treated, HS2ST1 -KO-treated, Sulf1 stably overexpressing (OE)-treated, Sulf2 stably OE-treated, Tega HS #09-treated and Tega HS #37-treated U2OS cells stained with 10E4, Siglec-11, 9D5, anti-DDX21 and anti-hnRNP-U (all in red) separately. d , Quantification of data in panel c with the number of cells counted from three independent experiments. Data are mean ± s.e.m.

Article Snippet: For DDX21 and hnRNP-U staining, 2.5 μg ml −1 of anti-DDX21 (Novus Biological) and anti-hnRNP-U (Proteintech) were incubated with cells for 45 min on ice.

Techniques: Staining, Membrane, Activity Assay, Stable Transfection

Journal: Nature

Article Title: GlycoRNA complexed with heparan sulfate regulates VEGF-A signalling

doi: 10.1038/s41586-025-10052-8

Figure Lengend Snippet: a . Representative zoom-out images of Fig. . Scale bar, 10 µm. 3 independent experiments were performed. b . Sequence alignment of partial NDST1 , HS6ST1 , and HS2ST1 coding sequences from wild-type (WT) and the indicated knock-out (KO) U2OS cell lines. Protospacer adjacent motif (PAM), green; sgRNA target, blue; mutated sequence, red. c . Western blot analysis of whole cell lysate from WT, NDST1 , HS6ST1 , and HS2ST1 KO U2OS cells. 2 independent experiments were performed. d . Representative images of WT and NaCl or NaClO 3 treated U2OS cells stained with 10E4, Siglec-11, 9D5, anti-DDX21, and anti-hnRNP-U (all in red). Scale bar, 10 µm. 3 independent experiments were performed. e . Representative images of WT and NaCl or NaClO 3 treated U2OS cells stained with 3G10 (red). Scale bar, 10 µm. 1 independent experiment was performed. f . Representative images of mEmerald-Sufl1 and mEmerald-Sulf2 stably overexpressing U2OS cells. Scale bar, 10 µm. 2 independent experiments were performed. g . Western blot analysis of whole cell lysate isolated from mEmerald-Sufl1 and mEmerald-Sulf2 stably overexpressing U2OS cells. 2 independent experiments were performed.

Article Snippet: For DDX21 and hnRNP-U staining, 2.5 μg ml −1 of anti-DDX21 (Novus Biological) and anti-hnRNP-U (Proteintech) were incubated with cells for 45 min on ice.

Techniques: Sequencing, Knock-Out, Western Blot, Staining, Stable Transfection, Isolation

Journal: Nature

Article Title: GlycoRNA complexed with heparan sulfate regulates VEGF-A signalling

doi: 10.1038/s41586-025-10052-8

Figure Lengend Snippet: a . Representative images of HUVECs treated with the RNase pool or heparinase pool, and stained live with 10E4, Siglec-11, 9D5, anti-DDX21, and anti-hnRNP-U (all in red). Scale bar, 10 µm. b . Representative images of keratinocytes with the RNase pool or heparinase pool, and stained live with 10E4, Siglec-11, 9D5, anti-DDX21, and anti-hnRNP-U (all in red). Scale bar, 10 µm. c . Quantification of 10E4, Siglec-11, 9D5, cs-DDX21, and cs-hnRNP-U intensity per cell from 3 independent staining experiments on keratinocytes. Data are mean ± s.e.m.

Article Snippet: For DDX21 and hnRNP-U staining, 2.5 μg ml −1 of anti-DDX21 (Novus Biological) and anti-hnRNP-U (Proteintech) were incubated with cells for 45 min on ice.

Techniques: Staining