Journal: Cancer Research

Article Title: DLGAP1-AS2–Mediated Phosphatidic Acid Synthesis Activates YAP Signaling and Confers Chemoresistance in Squamous Cell Carcinoma

doi: 10.1158/0008-5472.can-22-0717

Figure Lengend Snippet: Figure 4. D-AS2 reduces H3K27ac enrichment at the FAM3D enhancer region. A, FISH detection of D-AS2 localization in KYSE30 and NCI-H1703 cells. Scale bar, 30 mm. B, qRT-PCR measurement of the D-AS2 level in precipitates from RIP assays performed using IgG or specific antibodies. The data are presented as the mean SD values; n ¼ 3 technical replicates. C, Western blot analyses of histones in precipitates from RNA pulldown assays performed using antisense or sense sequences of D-AS2. Representative results of at least three biological replicates are shown. D, Numbers of genes that exhibited shared or unique peaks identified by ATAC-seq in D-AS2–silenced and control NCI-H1703 cells. E, Numbers of genes with significant differences in the number of peaks in the gene collections that exhibited shared peaks. F, Unique peak identified by ATAC-seq in D-AS2–silenced NCI-H1703 cells. Four independent qPCR primer sets were designed within 1,000 bp upstream/downstream (blue bar) of the ATAC-seq peak (red bar). G–I, CUT&RUN assay of the FAM3D enhancer region in D-AS2–depleted and D-AS2–overexpressing SCC cells with antibodies against H3K27ac. The data are presented as the mean SD values; two-tailed t test; , P < 0.01; , P < 0.001; n ¼ 3 technical replicates.

Article Snippet: To determine the mRNA expression levels, qRT-PCR was performed using a StepOnePlus Real-Time PCR system (Applied Biosystems) and PowerUp SYBR Green Master Mix (A25918; Applied Biosystems). lncRNAs were reverse transcribed into cDNA using a lnRcute lncRNA First-Strand cDNA Kit (4992908; Tiangen Biotech), and lncRNA expression was quantified using a lnRcute lncRNA qPCR Kit (4992886; Tiangen Biotech).

Techniques: Quantitative RT-PCR, Western Blot, Control, Two Tailed Test

Journal: BMC Plant Biology

Article Title: Integrated microRNA and transcriptome profiling reveal key miRNA-mRNA interaction pairs associated with seed development in Tartary buckwheat ( Fagopyrum tataricum )

doi: 10.1186/s12870-021-02914-w

Figure Lengend Snippet: Expression profiles of Tartary buckwheat miRNA biosynthesis genes in different organs and during seed development. The different colors represent the expression abundance of the genes

Article Snippet: The qRT-PCR was performed on a CFX96 Real-time System (BIO-RAD, USA) using the miRcute Plus miRNA qPCR Kit (SYBR Green) (Tiangen, Beijing, China).

Techniques: Expressing

Journal: BMC Plant Biology

Article Title: Integrated microRNA and transcriptome profiling reveal key miRNA-mRNA interaction pairs associated with seed development in Tartary buckwheat ( Fagopyrum tataricum )

doi: 10.1186/s12870-021-02914-w

Figure Lengend Snippet: DEMs during Tartary buckwheat seed development. a Venn diagram represented the overlap of DEMs among the comparisons. b Number of DEMs in the comparisons of S1 vs. S2, S1 vs. S3, and S2 vs. S3. Green and yellow bars represented the number of up- or down-regulated genes, respectively. c Expression heat map of DEMs. The different colors represent the expression abundance of the miRNAs

Article Snippet: The qRT-PCR was performed on a CFX96 Real-time System (BIO-RAD, USA) using the miRcute Plus miRNA qPCR Kit (SYBR Green) (Tiangen, Beijing, China).

Techniques: Expressing

Journal: BMC Plant Biology

Article Title: Integrated microRNA and transcriptome profiling reveal key miRNA-mRNA interaction pairs associated with seed development in Tartary buckwheat ( Fagopyrum tataricum )

doi: 10.1186/s12870-021-02914-w

Figure Lengend Snippet: Identified key miRNA-mRNA interaction pairs for tartary buckwheat seed development

Article Snippet: The qRT-PCR was performed on a CFX96 Real-time System (BIO-RAD, USA) using the miRcute Plus miRNA qPCR Kit (SYBR Green) (Tiangen, Beijing, China).

Techniques: Binding Assay, Cell Differentiation, Starch, Transduction, Inhibition, Phospho-proteomics, Membrane

Journal: BMC Plant Biology

Article Title: Integrated microRNA and transcriptome profiling reveal key miRNA-mRNA interaction pairs associated with seed development in Tartary buckwheat ( Fagopyrum tataricum )

doi: 10.1186/s12870-021-02914-w

Figure Lengend Snippet: miRNA-mRNA interaction pairs showed significant negative correlation (R ≥ 0.5, P < 0.05) of expression during Tartary buckwheat seed development. Left: Heat map of DEMs. Right: Heat map of the differentially expressed target mRNAs of DEMs. The different colors represent the expression abundance of the miRNAs and their corresponding target mRNAs

Article Snippet: The qRT-PCR was performed on a CFX96 Real-time System (BIO-RAD, USA) using the miRcute Plus miRNA qPCR Kit (SYBR Green) (Tiangen, Beijing, China).

Techniques: Expressing

Journal: BMC Plant Biology

Article Title: Integrated microRNA and transcriptome profiling reveal key miRNA-mRNA interaction pairs associated with seed development in Tartary buckwheat ( Fagopyrum tataricum )

doi: 10.1186/s12870-021-02914-w

Figure Lengend Snippet: Quantitative real-time PCR validation of six identified key miRNA-mRNA interaction pairs for Tartary buckwheat seed development. Green and blue bars represented the miRNAs and their corresponding target mRNAs, respectively. The error bar represents the error values of three biological replicates

Article Snippet: The qRT-PCR was performed on a CFX96 Real-time System (BIO-RAD, USA) using the miRcute Plus miRNA qPCR Kit (SYBR Green) (Tiangen, Beijing, China).

Techniques: Real-time Polymerase Chain Reaction, Biomarker Discovery

Journal: BMC Plant Biology

Article Title: Integrated microRNA and transcriptome profiling reveal key miRNA-mRNA interaction pairs associated with seed development in Tartary buckwheat ( Fagopyrum tataricum )

doi: 10.1186/s12870-021-02914-w

Figure Lengend Snippet: 5′ RLM-RACE verification of six identified key miRNA-mRNA interaction pairs for Tartary buckwheat seed development. The numbers above sequences indicate the detected cleavage site of independent clones

Article Snippet: The qRT-PCR was performed on a CFX96 Real-time System (BIO-RAD, USA) using the miRcute Plus miRNA qPCR Kit (SYBR Green) (Tiangen, Beijing, China).

Techniques: Clone Assay

Journal: Shock

Article Title: Characterization and Identification of Novel Serum MicroRNAs in Sepsis Patients With Different Outcomes

doi: 10.1097/shk.0b013e3182940cb8

Figure Lengend Snippet: FIG. 3. AYF, Receiver operating characteristic curves for serum miRNAs of sepsis nonsurvivors (n = 24) and survivors (n = 32). G, These six miRNAs were confirmed by qRT-PCR. Areas under the ROC curves are also shown. H, Conjoint analysis of the six miRNAs.

Article Snippet: A miRNA first-strand cDNA synthesis kit and miRcute miRNA qPCR detection kit (SYBR) (Tiangen Biotech Company, Beijing, China) were used for qRT-PCR validation of the novel predicted miRNAs.

Techniques: Quantitative RT-PCR

Journal: Journal for Immunotherapy of Cancer

Article Title: Nanoparticle delivery of miR-21-3p sensitizes melanoma to anti-PD-1 immunotherapy by promoting ferroptosis

doi: 10.1136/jitc-2021-004381

Figure Lengend Snippet: The expression profile of miRNAs in IFN-γ-potentiated ferroptosis in melanoma. (A) A schematic view of the treatment plan that C57BL/6 mice burdened with B16F10 tumors received anti-PD-1 antibody and liprostatin-1 treatment as indicated. (B-D) Images of isolated tumors from mice that received indicated treatment. Tumor volumes and weights in each group were calculated and displayed in (C) and (D). (E) Relative lipid ROS in isolated transplanted tumors with indicated treatment. (F-G) Relative cell viability and lipid ROS level in A2058 and A375 melanoma cells after indicated treatment with IFN-γ, RSL3, erastin and Fer-1. (H) The average abundance of the differentially expressed miRNAs related to . (I) The relative expression of the most significantly differentially-expressed miRNAs after the treatment with RSL3 or RSL3 combined with IFN-γ in A375 melanoma cell. Erastin was used at 10 µM in both cell lines. RSL3 was used at 0.5 µM in A375 and 1 µM in A2058 cell line. Fer-1 was used at 2 µM in both cell lines. IFN-γ was used at 50 ng/mL in both cell lines. Data represent the mean±SD of triplicates. P value was calculated by two-tailed Student’s t-test. * P<0.05, ** p<0.01, *** p<0.001. IFN, interferon; miRNA, microRNA; ns, non-significant; PD-1, programmed cell death protein 1; ROS, reactive oxygen species.

Article Snippet: Total RNA was extracted using TRIzol reagent (cat. 15596018, Invitrogen). cDNA was synthesized from miRNA using miRNA cDNA First Strand Synthesis kit (cat. KR211-01, Tiangen Biotech, Beijing, China) and qRT-PCR was performed using miRNA SYBR qRT-PCR Kit (cat. FP411-01, Tiangen Biotech).

Techniques: Expressing, Isolation, Two Tailed Test

Journal: Journal for Immunotherapy of Cancer

Article Title: Nanoparticle delivery of miR-21-3p sensitizes melanoma to anti-PD-1 immunotherapy by promoting ferroptosis

doi: 10.1136/jitc-2021-004381

Figure Lengend Snippet: Synthesis and characterization of miR-21–3p-conjugated nanoparticles miR-21–3p-AuNp. (A) A schematic view of the design and construction process of miR-21–3p-AuNp. (B) UV-Vis absorption spectra of AuNp and miR-21–3p-AuNp. (C) Hydrodynamic diameter distributions of AuNp and miR-21–3p-AuNp, showing the successful self-assembly process of the nanoengineering miRNA into an auric sphere hybrid system. (D-E) Transmission electron micrograph images (TEM) of Au and miR-21–3p-AuNp. (F) The zeta potential of miR-21–3p-AuNp measured in PBS at pH 7.4. (G-H) Relative mRNA level of miR-21–3p and TXNRD1 after the treatment with miR-21–3p-AuNp or AuNp in melanoma cell. (I) Immunoblotting analysis of TXNRD1 after the treatment with miR-21–3p-AuNp or AuNp in melanoma cell. (J) Relative cell viability of melanoma cells treated with ferroptosis inducer, IFN-γ and miR-21–3p-AuNp or AuNp. Erastin was used at 10 µM in both cell lines. RSL3 was used at 0.5 µM in A375 and 1 µM in A2058 cell line. IFN-γ was used at 50 ng/mL in both cell lines. Data represent the mean±SD of triplicates. P value was calculated by two-tailed Student’s t-test. * P<0.05, ** p<0.01, *** p<0.001. AuNp, gold nanoparticles; IFN, interferon; miRNA, microRNA; ns, non-significant; TXNRD1, thioredoxin reductase 1.

Article Snippet: Total RNA was extracted using TRIzol reagent (cat. 15596018, Invitrogen). cDNA was synthesized from miRNA using miRNA cDNA First Strand Synthesis kit (cat. KR211-01, Tiangen Biotech, Beijing, China) and qRT-PCR was performed using miRNA SYBR qRT-PCR Kit (cat. FP411-01, Tiangen Biotech).

Techniques: Transmission Assay, Zeta Potential Analyzer, Western Blot, Two Tailed Test