label it sirna labeling kit  (Mirus Bio)

Journal: bioRxiv

Article Title: Anti-tumor effects of a novel cell penetrating peptide-based therapeutic approach to target Lactate Dehydrogenase C (LDHC) in triple negative breast cancer

doi: 10.1101/2025.03.11.641612

Figure Lengend Snippet: (A) Visualization of 10R:siLDHC#2, 10R-RGD:siLDHC#2, cRGD-10R:siLDHC#2 and iRGD-10R:siLDHC#2 complex formation at different peptide:siRNA molar ratios using gel retardation assay. (B) Serum stability assay of CPP:siLDHC#2 complexes (5:1 peptide:siRNA molar ratio) in 50% human serum.

Article Snippet: To enable visualization of cellular uptake of the CPP:siRNA complexes in cancer cells, siRNA was pre-labeled with CyTM3 using the SilencerTM siRNA Labeling Kit (ThermoFisher scientific, #2960050).

Techniques: Electrophoretic Mobility Shift Assay, Stability Assay

Journal: bioRxiv

Article Title: Anti-tumor effects of a novel cell penetrating peptide-based therapeutic approach to target Lactate Dehydrogenase C (LDHC) in triple negative breast cancer

doi: 10.1101/2025.03.11.641612

Figure Lengend Snippet: (A) Dynamic Light Scattering analysis of 10R:siLDHC#2, 10R-RGD:siLDHC#2, cRGD-10R:siLDHC#2 and iRGD-10R:siLDHC#2 complexes at peptide:siRNA molar ratio of 5:1. Complexes were diluted in Ultra-Pure DNAse/RNAse free water and analyzed at 677nm at room temperature with a constant angle of 90°. Values represent mean and standard error of mean (±SEM) from three independent replicates. (B) Representative negative stain TEM images of CPP:siLDHC#2 complexes. Bar chart represents means and standard error of mean (±SEM) from three independent experiments.

Article Snippet: To enable visualization of cellular uptake of the CPP:siRNA complexes in cancer cells, siRNA was pre-labeled with CyTM3 using the SilencerTM siRNA Labeling Kit (ThermoFisher scientific, #2960050).

Techniques: Staining

Journal: bioRxiv

Article Title: Anti-tumor effects of a novel cell penetrating peptide-based therapeutic approach to target Lactate Dehydrogenase C (LDHC) in triple negative breast cancer

doi: 10.1101/2025.03.11.641612

Figure Lengend Snippet: Immunofluorescent imaging of Cy3-prelabeled CPP:siRNA complexes after 72 hours incubation. Blue, DAPI; red, Cy3-labeled siRNA.

Article Snippet: To enable visualization of cellular uptake of the CPP:siRNA complexes in cancer cells, siRNA was pre-labeled with CyTM3 using the SilencerTM siRNA Labeling Kit (ThermoFisher scientific, #2960050).

Techniques: Imaging, Incubation, Labeling

Journal: bioRxiv

Article Title: Anti-tumor effects of a novel cell penetrating peptide-based therapeutic approach to target Lactate Dehydrogenase C (LDHC) in triple negative breast cancer

doi: 10.1101/2025.03.11.641612

Figure Lengend Snippet: Breast cancer and non-cancerous cell lines were treated with CPP:siRNA complexes (5:1 molar ratio) for 72 hours, and cytotoxicity was determined using CellTiter-Glo luminescent cell viability assay. Lipofectamine-mediated transfection of naked siCTRL was used as a positive control for efficient cellular uptake, and CPPs alone were used to assess the toxicity of the peptides. Error bars represent standard error of mean (±SEM) from three independent experiments. Statistical analysis to assess reduction in cell viability was performed using the one-way ANOVA test with Dunnett correction. * p<0.05, ** p<0.01; **** p<0.0001.

Article Snippet: To enable visualization of cellular uptake of the CPP:siRNA complexes in cancer cells, siRNA was pre-labeled with CyTM3 using the SilencerTM siRNA Labeling Kit (ThermoFisher scientific, #2960050).

Techniques: Cell Viability Assay, Transfection, Positive Control

Journal: bioRxiv

Article Title: Anti-tumor effects of a novel cell penetrating peptide-based therapeutic approach to target Lactate Dehydrogenase C (LDHC) in triple negative breast cancer

doi: 10.1101/2025.03.11.641612

Figure Lengend Snippet: (A) LDHC mRNA expression, normalized to RPLPO, of MDA-MB-468 and (B) BT-549 cells following treatment with CPP:siRNA complexes for 72 hours. (C) Representative images of LDHC protein expression of MDA-MB-468 cells treated with CPP:siRNA complexes for 72 hours. β-actin was used as loading control. Bar chart represent densitometry values from three independent experiments (mean±SEM). Statistical analysis was performed using the one-way ANOVA test with Dunnett correction for comparison of more than two groups and two-tailed unpaired t-test for comparison of two groups. * p<0.05, ** p<0.01, *** p<0.001, **** p<0.0001.

Article Snippet: To enable visualization of cellular uptake of the CPP:siRNA complexes in cancer cells, siRNA was pre-labeled with CyTM3 using the SilencerTM siRNA Labeling Kit (ThermoFisher scientific, #2960050).

Techniques: Expressing, Control, Comparison, Two Tailed Test

Journal: bioRxiv

Article Title: Anti-tumor effects of a novel cell penetrating peptide-based therapeutic approach to target Lactate Dehydrogenase C (LDHC) in triple negative breast cancer

doi: 10.1101/2025.03.11.641612

Figure Lengend Snippet: Representative images of clonogenic assay using 10R-RGD:siRNA and cRGD-10R:siRNA alone or in combination with olaparib short-term treatment (72 hours). Bar chart depicting crystal violet absorbance measurements from three independent experiments (mean ±SEM). Statistical analysis was performed using the one-way ANOVA test with Šídák correction. * p<0.05, ** p<0.01, *** p<0.001.

Article Snippet: To enable visualization of cellular uptake of the CPP:siRNA complexes in cancer cells, siRNA was pre-labeled with CyTM3 using the SilencerTM siRNA Labeling Kit (ThermoFisher scientific, #2960050).

Techniques: Clonogenic Assay

Journal: bioRxiv

Article Title: Anti-tumor effects of a novel cell penetrating peptide-based therapeutic approach to target Lactate Dehydrogenase C (LDHC) in triple negative breast cancer

doi: 10.1101/2025.03.11.641612

Figure Lengend Snippet: (A) Zebrafish mortality and (B) morphological abnormalities following treatment with 10R-RGD:siRNA and cRGD-10R:siRNA complexes. G1: severely affected, G2: mildly affected, G3: normal. (C) Diagram of TNBC xenograft zebrafish model, depicting TNBC cell injection in the yolk at 2 days post-fertilization (dpf) and CPP:siRNA intracardial treatment at 32 hours post-injection (hpi). (D) Change in tumor cell burden, measured as % change in fluorescence intensity following CPP:siRNA treatment. Representative images of fluorescent tumor cells at 24hpi and 72hpi. Scatter dot plots represent fluorescence intensity values from two independent experiments (mean ±SEM). Statistical analysis was performed using the two-tailed unpaired t-test. ** p<0.01, *** p<0.001.

Article Snippet: To enable visualization of cellular uptake of the CPP:siRNA complexes in cancer cells, siRNA was pre-labeled with CyTM3 using the SilencerTM siRNA Labeling Kit (ThermoFisher scientific, #2960050).

Techniques: Injection, Fluorescence, Two Tailed Test

Journal: Communications Biology

Article Title: Exogenous dsRNA triggers sequence-specific RNAi and fungal stress responses to control Magnaporthe oryzae in Brachypodium distachyon

doi: 10.1038/s42003-025-07554-6

Figure Lengend Snippet: Three-day-old Mo liquid cultures were incubated with different RNA molecules for 2 min and subsequently stained for CSLM analysis. A Germinated conidia were treated with 500 ng/µL of poly(I:C) as positive stressor or 10 ng/µL of Pmk1-dsRNA and SHP-siRNA. B Dose-response effect of ROS production in germinating conidia after treatment with SHP-dsRNA. Fluorescence detection with AF488 [λexcitation (nm): 492; λemission (nm): 561]. Scale bar equals 50 µm.

Article Snippet: A silencer siRNA Labeling Kit (ThermoFisher) with Fluorescein dye was used to label Phi6-dsRNA and 21 bp GAPDH siRNA provided with the kit.

Techniques: Incubation, Staining, Fluorescence

Journal: Communications Biology

Article Title: Exogenous dsRNA triggers sequence-specific RNAi and fungal stress responses to control Magnaporthe oryzae in Brachypodium distachyon

doi: 10.1038/s42003-025-07554-6

Figure Lengend Snippet: A Conidia (2000/100 µL) in 0.002% (v/v) Tween20 were incubated with 20 ng/µL of the indicated dsRNA. Potassium chloride (0.25 M) was used as positive stressor control, while geneticin was used as negative control. Images were taken with the AF488 laser at 5 and 60 min after treatment. B Conidia were incubated with 20 ng/µL of the indicated siRNA. C Dose-effect analysis of GFP-MoHog1p nuclear accumulation in Mo conidia treated with various amounts of GFP-dsRNA (476 bp). Scale bar equals 10 µm. AF488 [λexcitation (nm): 492; λemission (nm): 561].

Article Snippet: A silencer siRNA Labeling Kit (ThermoFisher) with Fluorescein dye was used to label Phi6-dsRNA and 21 bp GAPDH siRNA provided with the kit.

Techniques: Incubation, Control, Negative Control

Journal: Communications Biology

Article Title: Exogenous dsRNA triggers sequence-specific RNAi and fungal stress responses to control Magnaporthe oryzae in Brachypodium distachyon

doi: 10.1038/s42003-025-07554-6

Figure Lengend Snippet: ( A ) Infection symptoms on Bd leaves sprayed with a mixture of Mo conidia and dsRNA or siRNA. Intact three-week-old Bd plants were inoculated with a 0.002% (v/v) Tween20 containing conidia (65 × 10³ conidia mL −1 ) and 1 ng/µL of siRNA or long dsRNA. Control plants were sprayed with 0.002% (v/v) Tween (Buffer) or with conidia in Tween solution (Untreated). For imaging, second youngest leaves were detached at 6 dpi and placed on 1% agar plates. Scale bar = 20 mm. B Relative size of necrotic area compared to the whole leaf area calculated with ImageJ. The results of three independent experiments are shown as box plots representing the average with standard deviation. Statistical significance was assessed with Kruskal-Wallis test ( p ≤ 0.05) and asterisks denote difference to the control group (CTR-untreated) according to Dunn’s multiple comparisons test (*: p = 0.046; **: p = 0.0086; ****: p ≤ 0.0001), while differences between GFP and Pmk1 specific RNAs were assessed with two-tailed Welch’s t -test (**: p = 0.0059; ****: p ≤ 0.0001). C Relative fungal growth determined by RT-qPCR comparing Mo housekeeping gene MoGPD with Bd housekeeping gene BdUbi10 . The percentage of reduced fungal growth from three independent experiments was combined and represented as average with standard deviation. Statistical significance assessed with two-tailed t -test (**: p = 0.0013) and one sample t -test to the control (CTR) group (*: p = 0.0207; **: p = 0.0096).

Article Snippet: A silencer siRNA Labeling Kit (ThermoFisher) with Fluorescein dye was used to label Phi6-dsRNA and 21 bp GAPDH siRNA provided with the kit.

Techniques: Infection, Control, Imaging, Standard Deviation, Two Tailed Test, Quantitative RT-PCR

Journal: Communications Biology

Article Title: Exogenous dsRNA triggers sequence-specific RNAi and fungal stress responses to control Magnaporthe oryzae in Brachypodium distachyon

doi: 10.1038/s42003-025-07554-6

Figure Lengend Snippet: A Intact three-week-old Bd seedlings were sprayed with a solution containing conidia (65 × 10³ conidia mL −1 ) and 0.03 ng/µL of the indicated siRNA and dsRNA. Infection symptoms were determined at 6 dpi and the relative size of the necrotic area was quantified using ImageJ. The results of three independent replicates were combined and box plots represent average with standard deviation. Statistical significance was assessed with Kruskal-Wallis test ( p ≤ 0.05) and asterisks denote difference to the control group according to Dunn’s multiple comparisons test (* Pmk1-dsRNA: p = 0.0279; * Pmk1-siRNA: p = 0.0267. B Silencing of the fungal MoPmk1 gene in response to dsRNA treatment of Brachypodium distachyon leaves. Three-week-old Bd seedlings were sprayed with a mixture of Mo conidia and 0.03 ng/µL of fungal target-specific Pmk1-dsRNA, Pmk1-siRNA or GFP -dsRNA or -siRNA. Leaves were harvested at 12 hpi and analysed with RT-qPCR using MoGPD for normalization. Bars represent average of three experiments combined with standard deviation. Statistical significance was assessed with One-way ANOVA test ( p ≤ 0.05) and asterisks denote difference to the control group according to Dunnett test. (** Pmk1-dsRNA: p = 0.0033; ** Pmk1-siRNA: p = 0.0024). Mo indicates a non-treated control.

Article Snippet: A silencer siRNA Labeling Kit (ThermoFisher) with Fluorescein dye was used to label Phi6-dsRNA and 21 bp GAPDH siRNA provided with the kit.

Techniques: Infection, Standard Deviation, Control, Quantitative RT-PCR