Journal: International Journal of Oncology

Article Title: Knockdown of PGBD5 inhibits the malignant progression of glioma through upregulation of the PPAR pathway

doi: 10.3892/ijo.2024.5643

Figure Lengend Snippet: List of primers and shRNA sequences used.

Article Snippet: The GV248 lentiviral vector containing a short hairpin RNA (shRNA) targeting PGBD5 (sh-PGBD5) and the negative control (NC) vector (sh-NC) containing a non-targeting shRNA sequence were established by Shanghai GeneChem Co., Ltd. and were ready to directly infect the cells.

Techniques: shRNA, Sequencing

Journal: Heliyon

Article Title: Long non-coding RNA TTTY14 promotes cell proliferation and functions as a prognostic biomarker in testicular germ cell tumor

doi: 10.1016/j.heliyon.2023.e16082

Figure Lengend Snippet: Expression of Testis-specific transcript, Y-linked 14 (TTTY14). (A) GEPIA was used to analyze the expression of TTTY14 in various tumors. TTTY14 is highly expressed in GBM, PRAD and TGCT. The normalization method is Transcripts Per Million (TPM). The scale of y-axis is log2(TPM+1). (B) The expression of TTTY14 in normal testis samples and testicular tumor samples was analyzed using the GSE3218 dataset in the GEO database. (C) The expression of TTTY14 in non-seminoma and seminoma was analyzed by GEPIA. (D) The TGCT cohort data was downloaded from the UCSC XENA database to analyze the expression of TTTY14 in intratubular germ cell tumors. *P < 0.05, **P < 0.01.

Article Snippet: The TTTY14 siRNA sequences and non-target negative control (NC) was synthesized by Ribobio (Guangzhou, China).

Techniques: Expressing

Journal: Heliyon

Article Title: Long non-coding RNA TTTY14 promotes cell proliferation and functions as a prognostic biomarker in testicular germ cell tumor

doi: 10.1016/j.heliyon.2023.e16082

Figure Lengend Snippet: The association between TTTY14 expression, methylation, and copy number in TCGA TGCT cohort. The UCSC XENA database was used to download the methylation data, expression data, and prognosis data of TTTY14 from the TCGA TGCT cohort. (A–B) The copy number was significantly positively correlated with TTTY14 expression. The copy number column was sorted from smallest to largest values. The redder the color, the larger the value; the bluer the value, smaller the value. (C) Correlation between TTTY14 copy number and overall survival of TGCT cohort from TCGA. Patients with high TTTY14 copy number had lower survival probability. (D) The CpG sites of TTTY14 were showed. (E–F) TTTY14 methylation level was significantly negatively correlated with its expression. The DNA methylation column was sorted from smallest to largest values. The redder the color, the larger the value; the bluer the value, smaller the value. CNV, copy number various. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Article Snippet: The TTTY14 siRNA sequences and non-target negative control (NC) was synthesized by Ribobio (Guangzhou, China).

Techniques: Expressing, Methylation, DNA Methylation Assay

Journal: Heliyon

Article Title: Long non-coding RNA TTTY14 promotes cell proliferation and functions as a prognostic biomarker in testicular germ cell tumor

doi: 10.1016/j.heliyon.2023.e16082

Figure Lengend Snippet: Relationship between TTTY14 and survival prognosis of TGCT patients. Based on TCGA TGCT data, the Kaplan-Meier Plotter online tool was used to analyze relationship between TTTY14 expression and two-year survival in TGCT patients. (A) The relationship between TTTY14 expression and two-year survival in all TGCT patients was analyzed. (B) The relationship between TTTY14 expression and two-year survival in TGCT patients with high tumor mutational burden (TMB) was analyzed. (C) The relationship between TTTY14 expression and two-year survival in TGCT patients with low TMB was analyzed. (D) The relationship between TTTY14 expression and two-year survival in CD8 + T cell-enriched TGCT patients was analyzed. (E) The relationship between TTTY14 expression and two-year survival in patients with TGCT CD8 + T cell-deserted was analyzed.

Article Snippet: The TTTY14 siRNA sequences and non-target negative control (NC) was synthesized by Ribobio (Guangzhou, China).

Techniques: Expressing

Journal: Heliyon

Article Title: Long non-coding RNA TTTY14 promotes cell proliferation and functions as a prognostic biomarker in testicular germ cell tumor

doi: 10.1016/j.heliyon.2023.e16082

Figure Lengend Snippet: Knockdown of TTTY14 inhibits NCCIT cell proliferation. (A) NCCIT cells were transfected with TTTY14 siRNA, and the expression of TTTY14 was detected by qPCR. (B) Edu staining was used to measure the proliferation of NCCIT cells transfected with TTTY14 siRNA. (C) CCK8 assay for cell viability of NCCIT cells transfected with TTTY14 siRNA. (D) Colony formation assay was used to detect the cell cloning ability of NCCIT cells transfected with TTTY14 siRNA. *P < 0.05, **P < 0.01, ***P < 0.001.

Article Snippet: The TTTY14 siRNA sequences and non-target negative control (NC) was synthesized by Ribobio (Guangzhou, China).

Techniques: Knockdown, Transfection, Expressing, Staining, CCK-8 Assay, Colony Assay, Cloning

Journal: Heliyon

Article Title: Long non-coding RNA TTTY14 promotes cell proliferation and functions as a prognostic biomarker in testicular germ cell tumor

doi: 10.1016/j.heliyon.2023.e16082

Figure Lengend Snippet: The correlation between TTTY14 and antitumor drug sensitivity. GSCA online tool was used to analyze the correlation between TTTY14 expression and the sensitivity of Genomics of Drug Sensitivity in Cancer (GDSC) drugs (top 30) in TGCT (A), and the correlation between TTTY14 expression and the sensitivity of cancer therapeutics response portal (CTRP) drugs (top 30) in TGCT (B). (C) Based on anti -PD1 cohort data, the Kaplan-Meier Plotter online tool was used to analyze the correlation between TTTY14 expression and the immune checkpoint inhibitors. Relationship between overall survival and progression-free survival in this cohort of patients was shown. High expression of TTTY14 is a predictive marker for poor outcome of anti -PD1immunotherapy in TGCT patients.

Article Snippet: The TTTY14 siRNA sequences and non-target negative control (NC) was synthesized by Ribobio (Guangzhou, China).

Techniques: Expressing, Marker

Journal: Heliyon

Article Title: Long non-coding RNA TTTY14 promotes cell proliferation and functions as a prognostic biomarker in testicular germ cell tumor

doi: 10.1016/j.heliyon.2023.e16082

Figure Lengend Snippet: The TTTY14-associated genes, proteins, and pathways. Based on the TCGA TGCT expression profile data, LinkedOmics was used to analyze the positively associated genes and negatively associated genes of TTTY14 (A), and the associated proteins of TTTY14 (B). (C) GSEA enrichment was performed to analyze the associated pathway of TTTY14.

Article Snippet: The TTTY14 siRNA sequences and non-target negative control (NC) was synthesized by Ribobio (Guangzhou, China).

Techniques: Expressing

Journal: Heliyon

Article Title: Long non-coding RNA TTTY14 promotes cell proliferation and functions as a prognostic biomarker in testicular germ cell tumor

doi: 10.1016/j.heliyon.2023.e16082

Figure Lengend Snippet: Relationship between TTTY14 expression, immune cells and immune checkpoint molecules. Based on the TCGA TGCT cohort data, the ASSISTANT for Clinical Bioinformatics tool was used to analyze the abundance of various immune cells in TGCT samples (A), the correlation between TTTY14 expression and immune dysregulation score (B), and the correlation between TTTY14 and the abundance of various immune cells (C). (D) The correlation between TTTY14 and three immune checkpoint molecules CD274, CTLA4 and HAVCR2 was analyzed using the GEPIA database.

Article Snippet: The TTTY14 siRNA sequences and non-target negative control (NC) was synthesized by Ribobio (Guangzhou, China).

Techniques: Expressing

Journal: PLoS ONE

Article Title: Distinctive Profile of IsomiR Expression and Novel MicroRNAs in Rat Heart Left Ventricle

doi: 10.1371/journal.pone.0065809

Figure Lengend Snippet: HEK293 cells were transfected with expression plasmids encoding mCherry with a 3′ partial gelsolin sequence and pSM30 containing inserts for miR-133a, miR-133a(v), a random non-targeting sequence (NTC) or siRNA against mCherry (siR-mCh). Cells were imaged and analysed for both green and red fluorescence intensity. A decrease in red/green ratio vs NTC indicates downregulation of target gene expression. Data were log transformed and compared by one-way ANOVA with Bonferroni's Multiple Comparison Test. All pairwise comparisons were significant (p<.001). Comparison of miR-133a vs miR-133a(v) is indicated (***). Number of cells (n): miR-133a 4640; miR-133a(v) 2843; NTC 4088; siR-mCh 3884. Representative of 3 separate experiments in which miR-133a(v) was significantly more effective than miR-133a.

Article Snippet: Complementary pairs of oligonucleotides (25 µM) encoding artificial miRNA sequences (miR-133a canonical isomiR and most common isomiR (miR-133a(v))), a siRNA sequence designed to down regulate mCherry expression (siR-mCh), or a random non-targeting negative control sequence (NTC) were annealed and ligated (T4 DNA ligase; New England Biolabs, Hitchin, UK) into pSM30 restricted with Bsm BI (New England Biolabs, Hitchin, UK).

Techniques: Transfection, Expressing, Sequencing, Fluorescence, Transformation Assay