Journal: Frontiers in Cell and Developmental Biology

Article Title: Infrapatellar Fat Pad Stem Cells Responsiveness to Microenvironment in Osteoarthritis: From Morphology to Function

doi: 10.3389/fcell.2019.00323

Figure Lengend Snippet: Antibodies used for flow cytometry analysis.

Article Snippet: A350 anti-human IL1R1 , bs-2594R , Bioss.

Techniques: Flow Cytometry

Journal: Computational and Structural Biotechnology Journal

Article Title: Identification of potential diagnostic and prognostic biomarkers for sepsis based on machine learning

doi: 10.1016/j.csbj.2023.03.034

Figure Lengend Snippet: Differentially expressed genes.

Article Snippet: Western blotting Western blotting was performed as per standard protocols using primary antibodies for YOD1 (25370-1-AP, Protein Tech, Wuhan, China), GADD45A (A11768, ABclonal, Wuhan, China), BCL11B (A19804, ABclonal, Wuhan, China), IL1R2 (60262-1-Ig, ProteinTech, Wuhan, China) and GAPDH (60004-1-Ig, ProteinTech, Wuhan, China), and an electrochemiluminescence detection system (Tanon, China).

Techniques:

Journal: Computational and Structural Biotechnology Journal

Article Title: Identification of potential diagnostic and prognostic biomarkers for sepsis based on machine learning

doi: 10.1016/j.csbj.2023.03.034

Figure Lengend Snippet: Expression analysis of the 11 candidate DEGs in the GSE65682 and GSE134347 datasets between sepsis and healthy control groups. The relative expression levels of (A) YOD1, (B) GADD45A, (C) BCL11B, (D) IL1R2, (E) UGCG, (F) TLR5, (G) S100A12, (H) ITK, (I) HP, (J) CCR7 and (K) C19orf59 mRNAs are shown.

Article Snippet: Western blotting Western blotting was performed as per standard protocols using primary antibodies for YOD1 (25370-1-AP, Protein Tech, Wuhan, China), GADD45A (A11768, ABclonal, Wuhan, China), BCL11B (A19804, ABclonal, Wuhan, China), IL1R2 (60262-1-Ig, ProteinTech, Wuhan, China) and GAPDH (60004-1-Ig, ProteinTech, Wuhan, China), and an electrochemiluminescence detection system (Tanon, China).

Techniques: Expressing, Control

Journal: Computational and Structural Biotechnology Journal

Article Title: Identification of potential diagnostic and prognostic biomarkers for sepsis based on machine learning

doi: 10.1016/j.csbj.2023.03.034

Figure Lengend Snippet: Specificity at 0.85 sensitivity, PPV, and NPV of these 11 DEGs.

Article Snippet: Western blotting Western blotting was performed as per standard protocols using primary antibodies for YOD1 (25370-1-AP, Protein Tech, Wuhan, China), GADD45A (A11768, ABclonal, Wuhan, China), BCL11B (A19804, ABclonal, Wuhan, China), IL1R2 (60262-1-Ig, ProteinTech, Wuhan, China) and GAPDH (60004-1-Ig, ProteinTech, Wuhan, China), and an electrochemiluminescence detection system (Tanon, China).

Techniques:

Journal: Computational and Structural Biotechnology Journal

Article Title: Identification of potential diagnostic and prognostic biomarkers for sepsis based on machine learning

doi: 10.1016/j.csbj.2023.03.034

Figure Lengend Snippet: Diagnostic value of DEGs for sepsis in the GSE65682 and GSE134347 datasets. The ROC curves of (A) YOD1, (B) GADD45A, (C) BCL11B, (D) IL1R2, (E) UGCG, (F) TLR5, (G) S100A12, (H) ITK, (I) HP, (J) CCR7 and (K) C19orf59 are shown.

Article Snippet: Western blotting Western blotting was performed as per standard protocols using primary antibodies for YOD1 (25370-1-AP, Protein Tech, Wuhan, China), GADD45A (A11768, ABclonal, Wuhan, China), BCL11B (A19804, ABclonal, Wuhan, China), IL1R2 (60262-1-Ig, ProteinTech, Wuhan, China) and GAPDH (60004-1-Ig, ProteinTech, Wuhan, China), and an electrochemiluminescence detection system (Tanon, China).

Techniques: Diagnostic Assay

Journal: Computational and Structural Biotechnology Journal

Article Title: Identification of potential diagnostic and prognostic biomarkers for sepsis based on machine learning

doi: 10.1016/j.csbj.2023.03.034

Figure Lengend Snippet: Prognostic value of DEGs for patients in the GSE65682 dataset. The Kaplan-Meier survival curves of the high- and low-expression groups of (A) YOD1, (B) GADD45A, (C) BCL11B, (D) IL1R2, (E) UGCG, (F) TLR5, (G) S100A12, (H) ITK, (I) HP, (J) CCR7 and (K) C19orf59 are shown.

Article Snippet: Western blotting Western blotting was performed as per standard protocols using primary antibodies for YOD1 (25370-1-AP, Protein Tech, Wuhan, China), GADD45A (A11768, ABclonal, Wuhan, China), BCL11B (A19804, ABclonal, Wuhan, China), IL1R2 (60262-1-Ig, ProteinTech, Wuhan, China) and GAPDH (60004-1-Ig, ProteinTech, Wuhan, China), and an electrochemiluminescence detection system (Tanon, China).

Techniques: Expressing

Journal: Computational and Structural Biotechnology Journal

Article Title: Identification of potential diagnostic and prognostic biomarkers for sepsis based on machine learning

doi: 10.1016/j.csbj.2023.03.034

Figure Lengend Snippet: GSEA results of IL1R2. (A) T cell receptor signaling pathway. (B) Primary immunodeficiency. (C) Antigen processing and presentation. (D) Abnormal eosinophil. (E) Immunological. (F) T cell Differentiation.

Article Snippet: Western blotting Western blotting was performed as per standard protocols using primary antibodies for YOD1 (25370-1-AP, Protein Tech, Wuhan, China), GADD45A (A11768, ABclonal, Wuhan, China), BCL11B (A19804, ABclonal, Wuhan, China), IL1R2 (60262-1-Ig, ProteinTech, Wuhan, China) and GAPDH (60004-1-Ig, ProteinTech, Wuhan, China), and an electrochemiluminescence detection system (Tanon, China).

Techniques: Cell Differentiation

Journal: Computational and Structural Biotechnology Journal

Article Title: Identification of potential diagnostic and prognostic biomarkers for sepsis based on machine learning

doi: 10.1016/j.csbj.2023.03.034

Figure Lengend Snippet: Validation of biomarkers in a mouse model of sepsis. (A-D) YOD1, GADD45A, BCL11B and IL1R2 mRNA levels in the heart, liver, lungs and kidneys (n = 3, compared with the Mann-Whitney test); (E-H) YOD1, GADD45A, BCL11B and IL1R2 protein levels in the heart, liver, lung and kidney tissues (n = 6, *p < 0.05, **p < 0.01, ***p < 0.001).

Article Snippet: Western blotting Western blotting was performed as per standard protocols using primary antibodies for YOD1 (25370-1-AP, Protein Tech, Wuhan, China), GADD45A (A11768, ABclonal, Wuhan, China), BCL11B (A19804, ABclonal, Wuhan, China), IL1R2 (60262-1-Ig, ProteinTech, Wuhan, China) and GAPDH (60004-1-Ig, ProteinTech, Wuhan, China), and an electrochemiluminescence detection system (Tanon, China).

Techniques: Biomarker Discovery, MANN-WHITNEY

Journal: Nature Communications

Article Title: Specific multivalent molecules boost CRISPR-mediated transcriptional activation

doi: 10.1038/s41467-024-51694-y

Figure Lengend Snippet: a – d Relative mRNA expression of NTF3 , ASCL1 , MYOD1 , and IL1RN in HEK293T cells transfected with dCas9-VP64 or dCas9-VP64-FUS and a single guide RNA (gRNA) targeting each gene promoter as well as a scrambled gRNA (gScr) control. Data are shown as mean ± SD ( n = 3 independent experiments). Statistical significance was determined by two-sided Welch’s t-test. e , f Relative mRNA expression of NTF3 and ASCL1 in HEK293T cells transfected with dCas9-VPR or dCas9-VPR-FUS and a gRNA targeting each gene promoter. Data are shown as mean ± SD ( n = 3 independent experiments). Statistical significance was determined by two-sided Welch’s t-test. g , h Relative mRNA expression of NTF3 and ASCL1 in HEK293T cells transfected with dCpf1-VP64 or dCpf1-VP64-FUS and a gRNA targeting each gene promoter. Data are shown as mean ± SD ( n = 3 independent experiments). Statistical significance was determined by two-sided Welch’s t-test. Source data are provided as a Source data file.

Article Snippet: HEK293T cells transfected with Flag-tagged dCas9 activators along with gRNAs targeting NTF3 or IL1RN promoter were harvested and homogenized in lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, protease inhibitor cocktail (TargetMol, C0001) with 2 h of rotation.

Techniques: Expressing, Transfection, Control

Journal: Nature Communications

Article Title: Specific multivalent molecules boost CRISPR-mediated transcriptional activation

doi: 10.1038/s41467-024-51694-y

Figure Lengend Snippet: a Boxplot illustrating the GFP intensity in HEK293R cells expressing different dCas9 activators together with gTetO. The results are presented as the median GFP intensity, along with the 25th and 75th quartiles, as well as the 5th and 95th percentiles, and are representative of three independent experiments. Statistical significance was determined by two-sided Wilcoxon rank-sum test. Cell numbers from left to right ( n = 17198, 17379, 9902). b , c Relative mRNA expression of NTF3 and ASCL1 in HEK293T cells expressing different dCas9 activators and a single gRNA targeting the indicated genes. Data are shown as mean ± SD ( n = 3 independent experiments). Statistical significance was determined by one-way ANOVA versus the dCas9-VP64-FUS group. d , e Fluorescence recovery after photobleaching (FRAP) analysis of HEK293R cells expressing BFP-tagged dCas9-VP64-FUS or dCas9-VP64-TDP-43 with gTetO. Up, representative timelapse images after photobleaching. Yellow arrowheads indicate bleached condensates. Scale bar, 10 μm. Down: FRAP curves showing mean ± SD fluorescence recovery of condensates ( n = 5 puncta per group). f Boxplot illustrating the GFP intensity in HEK293R cells expressing different dCas9 activators together with gTetO. The results are presented as the median GFP intensity, along with the 25th and 75th quartiles, as well as the 5th and 95th percentiles, and are representative of three independent experiments. Statistical significance was determined by two-sided Wilcoxon rank-sum test. Cell numbers from left to right ( n = 19,096, 16,734, 13,743, 14,080, 12,071, 17,691). g , h Relative mRNA expression of NTF3 and ASCL1 in HEK293T cells expressing different dCas9 activators and a single gRNA targeting the indicated genes. Data are shown as mean ± SD ( n = 3 independent experiments). Statistical significance was determined by one-way ANOVA versus the dCas9-VP64-FUS group. i Co-immunoprecipitation (co-IP) of Flag-tagged dCas9 activators and BRG1, MED1 or RPB1. Three independent experiments were performed and similar results were obtained. j , k Enrichment of Flag-tagged dCas9 activators, BRG1, RPB1, and MED1 at the NTF3 or IL1RN promoter. Data are presented as mean values ± SD ( n = 3 independent experiments). Statistical significance was determined by two-sided Welch’s t-test. Source data are provided as a Source data file.

Article Snippet: HEK293T cells transfected with Flag-tagged dCas9 activators along with gRNAs targeting NTF3 or IL1RN promoter were harvested and homogenized in lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, protease inhibitor cocktail (TargetMol, C0001) with 2 h of rotation.

Techniques: Expressing, Fluorescence, Immunoprecipitation, Co-Immunoprecipitation Assay

Journal: Nature Communications

Article Title: Specific multivalent molecules boost CRISPR-mediated transcriptional activation

doi: 10.1038/s41467-024-51694-y

Figure Lengend Snippet: a , b Relative mRNA expression of ASCL1 and MYOD1 in HEK293T cells transfected with a single gRNA targeting the indicated genes along with the labeled dCas9-activators. Data are shown as mean ± SD ( n = 3 independent experiments). Statistical significance was determined by one-way ANOVA versus the dCas9-VP64 or the dCas9-VP64-FUS group. c , d Relative mRNA expression of ASCL1 and MYOD1 in HEK293T cells transfected with dCas9-VP64-FUS-Shank3, dCas9-VP64-FUS-Shank3MA, or dCas9-VP64-FUS-Shank3 ME and a single gRNA targeting the indicated genes. Data are shown as mean ± SD ( n = 3 independent experiments). Statistical significance was determined by one-way ANOVA test versus the dCas9-VP64-FUS-Shank3 group. e , f Relative mRNA expression of ASCL1 and MYOD1 in HEK293T cells transfected with dCas9-VP64-FUS-HOTag activators and a single gRNA targeting the indicated genes. Data are shown as mean ± SD ( n = 3 independent experiments). Statistical significance was determined by one-way ANOVA test versus the dCas9-VP64-FUS group. g Relative mRNA expression of NTF3 , ASCL1 , MYOD1, and IL1RN in HEK293T cells transfected with a single gRNA targeting the indicated genes along with the dCas9-VP64-FUS-HOTag3 or dCas9-VP64-HOTag3-FUS. Data are shown as mean ± SD ( n = 3 independent experiments). Statistical significance was determined by two-sided Welch’s t-test. h Boxplot showing relative GFP intensity in 1xTetO-GFP, 7xTetO-GFP or 14xTetO-GFP reporter cells expressing dCas9, dCas9-VP64, dCas9-VP64-FUS, dCas9-VP64-FUS-Shank3 or dCas9-VP64-FUS-HOTag3 together with gTetO. The results are presented as the relative median GFP intensity, along with the 25th and 75th quartiles, as well as the 5th and 95th percentiles, and are representative of three independent experiments. Statistical significance was determined by two-sided Wilcoxon rank-sum test. Cell numbers from left to right ( n = 24,461, 17,298, 21,807, 17,611, 11,280, 22,233, 14,347, 16,136, 15,605, 13,372, 23,028, 11,938, 15,760, 15,641, 12,923). Source data are provided as a Source data file.

Article Snippet: HEK293T cells transfected with Flag-tagged dCas9 activators along with gRNAs targeting NTF3 or IL1RN promoter were harvested and homogenized in lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, protease inhibitor cocktail (TargetMol, C0001) with 2 h of rotation.

Techniques: Expressing, Transfection, Labeling

Journal: Bioengineered

Article Title: MicroRNA-155-5p modulates the progression of acute respiratory distress syndrome by targeting interleukin receptors

doi: 10.1080/21655979.2022.2071020

Figure Lengend Snippet: Identification of IL17RB, IL18R1, and IL22RA2 as potential targets of miR-155-5p. IL17RB, IL18R1, and IL22RA2 were identified as potential targets of miR-155-5p by the databases (a); this was confirmed by the dual-luciferase report assay (b). The levels of IL17RB, IL18R1, and IL22RA2 were measured by qRT-PCR (c). *p < 0.05 and **p < 0.01, ANOVA.

Article Snippet: In brief, LPS reagent was injected into the medium for 24 hours and the relative levels of human IL17RB (EK0785), IL18R1 (EK1260), IL22RA2, IL-1β, IL-6, IL-8, and TNF-α were measured in the treated cells using an ELISA kit (Boster, Wuhan, China) in accordance with the manufacturer’s protocol [ ].

Techniques: Luciferase, Quantitative RT-PCR

Journal: Bioengineered

Article Title: MicroRNA-155-5p modulates the progression of acute respiratory distress syndrome by targeting interleukin receptors

doi: 10.1080/21655979.2022.2071020

Figure Lengend Snippet: Upregulated levels of the inflammatory cytokines in patients with ARDS. The levels of IL17RB, IL18R1, and IL22RA2 in serum samples from patients with ARDS (a). Serum concentrations of IL17RB, IL18R1, and IL22RA2 (b), and IL-1β, IL-6, IL-8, and TNF-α (c) in patients with ARDS were analyzed by ELISA. *p < 0.05, **p < 0.01, and ***p < 0.001 compared with the control.

Article Snippet: In brief, LPS reagent was injected into the medium for 24 hours and the relative levels of human IL17RB (EK0785), IL18R1 (EK1260), IL22RA2, IL-1β, IL-6, IL-8, and TNF-α were measured in the treated cells using an ELISA kit (Boster, Wuhan, China) in accordance with the manufacturer’s protocol [ ].

Techniques: Enzyme-linked Immunosorbent Assay, Control

Journal: Bioengineered

Article Title: MicroRNA-155-5p modulates the progression of acute respiratory distress syndrome by targeting interleukin receptors

doi: 10.1080/21655979.2022.2071020

Figure Lengend Snippet: miR-155-5p inhibited the NF-kB signaling pathway. The expression levels of the inflammatory cytokine receptors (IL17RB, IL18R1, and IL22R2) and NF-kB-related proteins (NF-kB, STAT1, and STAT3) were measured by western blotting analysis with β-actin used as the internal control. *p < 0.05, **p < 0.01, and ***p < 0.001 compared with the control.

Article Snippet: In brief, LPS reagent was injected into the medium for 24 hours and the relative levels of human IL17RB (EK0785), IL18R1 (EK1260), IL22RA2, IL-1β, IL-6, IL-8, and TNF-α were measured in the treated cells using an ELISA kit (Boster, Wuhan, China) in accordance with the manufacturer’s protocol [ ].

Techniques: Expressing, Western Blot, Control