Journal: STAR Protocols

Article Title: Protocol for CRISPR-Cas12a genome editing of protein tyrosine phosphatases in human pluripotent stem cells and functional β-like cell generation

doi: 10.1016/j.xpro.2024.103297

Figure Lengend Snippet: Reagents and small molecules used in the β-like cell differentiation

Article Snippet: Sobetirome (GC-1) , Tocris , Cat# 4554.

Techniques: Concentration Assay, Solvent, Recombinant

Journal: STAR Protocols

Article Title: Protocol for CRISPR-Cas12a genome editing of protein tyrosine phosphatases in human pluripotent stem cells and functional β-like cell generation

doi: 10.1016/j.xpro.2024.103297

Figure Lengend Snippet:

Article Snippet: Sobetirome (GC-1) , Tocris , Cat# 4554.

Techniques: Recombinant, Membrane, Knock-Out, Electroporation, Passaging, Transfection, Control, Enzyme-linked Immunosorbent Assay, Software, Microscopy, Pore Size

Journal: PLoS ONE

Article Title: Digital Gene Expression Tag Profiling Analysis of the Gene Expression Patterns Regulating the Early Stage of Mouse Spermatogenesis

doi: 10.1371/journal.pone.0058680

Figure Lengend Snippet: GC-1spg and GC-2spd (ts) DGE library analysis.

Article Snippet: GC-1spg and GC-2spd (ts) cells (ATCC, Manassas, VA, USA) were maintained in DMEM medium containing 10% FBS and 1.5 g/L sodium bicarbonate.

Techniques:

Journal: PLoS ONE

Article Title: Digital Gene Expression Tag Profiling Analysis of the Gene Expression Patterns Regulating the Early Stage of Mouse Spermatogenesis

doi: 10.1371/journal.pone.0058680

Figure Lengend Snippet: Statistics of GC-1spg and GC-2spd (ts) DGE mapping results.

Article Snippet: GC-1spg and GC-2spd (ts) cells (ATCC, Manassas, VA, USA) were maintained in DMEM medium containing 10% FBS and 1.5 g/L sodium bicarbonate.

Techniques:

Journal: PLoS ONE

Article Title: Digital Gene Expression Tag Profiling Analysis of the Gene Expression Patterns Regulating the Early Stage of Mouse Spermatogenesis

doi: 10.1371/journal.pone.0058680

Figure Lengend Snippet: Scatter plot indicates the comparing results of log transformed gene expression levels and differentially expressed genes' distribution between GC-1spg and GC-2spd (ts).

Article Snippet: GC-1spg and GC-2spd (ts) cells (ATCC, Manassas, VA, USA) were maintained in DMEM medium containing 10% FBS and 1.5 g/L sodium bicarbonate.

Techniques: Transformation Assay, Gene Expression

Journal: PLoS ONE

Article Title: Digital Gene Expression Tag Profiling Analysis of the Gene Expression Patterns Regulating the Early Stage of Mouse Spermatogenesis

doi: 10.1371/journal.pone.0058680

Figure Lengend Snippet: Genes up-regulated and down-regulated during the development process from GC-1spg to GC-2spd (ts) are marked in red and green, respectively.

Article Snippet: GC-1spg and GC-2spd (ts) cells (ATCC, Manassas, VA, USA) were maintained in DMEM medium containing 10% FBS and 1.5 g/L sodium bicarbonate.

Techniques:

Journal: PLoS ONE

Article Title: Digital Gene Expression Tag Profiling Analysis of the Gene Expression Patterns Regulating the Early Stage of Mouse Spermatogenesis

doi: 10.1371/journal.pone.0058680

Figure Lengend Snippet: Genes up-regulated and down-regulated during the development process from GC-1spg to GC-2spd (ts) are marked in red and green, respectively.

Article Snippet: GC-1spg and GC-2spd (ts) cells (ATCC, Manassas, VA, USA) were maintained in DMEM medium containing 10% FBS and 1.5 g/L sodium bicarbonate.

Techniques:

Journal: PLoS ONE

Article Title: Digital Gene Expression Tag Profiling Analysis of the Gene Expression Patterns Regulating the Early Stage of Mouse Spermatogenesis

doi: 10.1371/journal.pone.0058680

Figure Lengend Snippet: Genes up-regulated and down-regulated during the development process from GC-1spg to GC-2spd (ts) are marked in red and green, respectively.

Article Snippet: GC-1spg and GC-2spd (ts) cells (ATCC, Manassas, VA, USA) were maintained in DMEM medium containing 10% FBS and 1.5 g/L sodium bicarbonate.

Techniques:

Journal: PLoS ONE

Article Title: Digital Gene Expression Tag Profiling Analysis of the Gene Expression Patterns Regulating the Early Stage of Mouse Spermatogenesis

doi: 10.1371/journal.pone.0058680

Figure Lengend Snippet: Genes up-regulated and down-regulated during the development process from GC-1spg to GC-2spd (ts) are marked in red and green, respectively.

Article Snippet: GC-1spg and GC-2spd (ts) cells (ATCC, Manassas, VA, USA) were maintained in DMEM medium containing 10% FBS and 1.5 g/L sodium bicarbonate.

Techniques:

Journal: PLoS ONE

Article Title: Digital Gene Expression Tag Profiling Analysis of the Gene Expression Patterns Regulating the Early Stage of Mouse Spermatogenesis

doi: 10.1371/journal.pone.0058680

Figure Lengend Snippet: (A) Protein levels of FGF13, SFRP2 and RAC in GC-1spg and GC-2spd (ts) cells were detected by western blotting respectively. β-Actin were used to normalize the individual expression levels. (B) Protein level of WNT10A and FGF7 in the medium supernatants from GC-1spg and GC-2spd (ts) cells were determined by ELISA. The data are presented as the mean plus SEM from a representative of three independent experiments, with each performed in triplicate. Statistically significant differences between GC-1spg and GC-2spd (ts) cells are indicated above the bars: * means P<0.05.

Article Snippet: GC-1spg and GC-2spd (ts) cells (ATCC, Manassas, VA, USA) were maintained in DMEM medium containing 10% FBS and 1.5 g/L sodium bicarbonate.

Techniques: Western Blot, Expressing, Enzyme-linked Immunosorbent Assay

Journal: BMC medicine

Article Title: Nitazoxanide inhibits acetylated KLF5-induced bone metastasis by modulating KLF5 function in prostate cancer.

doi: 10.1186/s12916-023-02763-4

Figure Lengend Snippet: Fig. 1 Screening of FDA-approved drugs for those that inhibit cellular invasion induced by acetylated KLF5. a Schematic of the screening workflow. b Inhibitory effects of 1987 FDA-approved drugs, along with vehicle control (green dots pointed by green arrows), on the invasion of PC-3-KQ cells, as analyzed using the 3D spheroid invasion assay. Each dot represents a drug or control, and the dots are aligned along the X-axis. Y-axis indicates the average invasion area between two well for each drug. The blue horizontal line indicates the mean invasion area of all drugs and controls, while the red horizontal line indicates 50% of the mean invasion area. c Proportions of the 1987 drugs that are approved as non-oncological drugs (purple color), oncological targeted therapeutic drugs (orange color), and oncological chemotherapeutic drugs (red color). d Identification of the most effective 25 drugs by using the 3D spheroid invasion assay with multiple concentrations (μM). The heatmap shows the invasion rates (%) of each drug’s multiple concentrations when compared to the vehicle control, as indicated by blue grids with varying intensities. Names of the 25 drugs are shown at the bottom, with 6 of the most effective ones marked by red boxes. e The chemical structure of nitazoxanide

Article Snippet: After stopping the reaction by adding EDTA, DNA was fragmented by sonication, and the extracts were incubated with KLF5 antibody (Cat #: 21017-1-AP, Proteintech) or IgG (Cat #: 2729P, Cell Signaling Technology).

Techniques: Control, Invasion Assay

Journal: BMC medicine

Article Title: Nitazoxanide inhibits acetylated KLF5-induced bone metastasis by modulating KLF5 function in prostate cancer.

doi: 10.1186/s12916-023-02763-4

Figure Lengend Snippet: Fig. 5 Nitazoxanide reverses the effects of Ac-KLF5 on the expression of many genes in PC-3 cells. a Volcano plots of all quantified genes from the gene expression profiles between the KLF5K369Q and KLF5K369R in PC-3 cells. b Scatter plot of differentially expressed genes (DEGs) between PC-3-KQ cells with and without NTZ treatment and DEGs between PC-3-KQ and PC-3-KR cells. Dots in the upper left quadrant represent genes that were downregulated by KLF5K369Q but upregulated by NTZ, whereas dots in the lower right quadrant indicate genes that were upregulated by KLF5K369Q but downregulated by NTZ in PC-3 cells. An adjusted p value <0.05 was used to define all altered genes. c Heatmap showing DEGs in panel A’s upper left and lower right quadrants. The color bar at the right indicates log2 fold changes (Log2FC)

Article Snippet: After stopping the reaction by adding EDTA, DNA was fragmented by sonication, and the extracts were incubated with KLF5 antibody (Cat #: 21017-1-AP, Proteintech) or IgG (Cat #: 2729P, Cell Signaling Technology).

Techniques: Expressing, Gene Expression

Journal: BMC medicine

Article Title: Nitazoxanide inhibits acetylated KLF5-induced bone metastasis by modulating KLF5 function in prostate cancer.

doi: 10.1186/s12916-023-02763-4

Figure Lengend Snippet: Fig. 6 Association of Ac-KLF5- and NTZ-responsive genes with patient survival. a Higher expression levels of 7 genes correlate with overall survival (OS) in prostate cancer patients, as determined by the Kaplan-Meier analysis using the SU2C dataset. b Expression levels of 7 Ac-KLF5- and NTZ-responsive genes were analyzed using the GSE21034 dataset [29].

Article Snippet: After stopping the reaction by adding EDTA, DNA was fragmented by sonication, and the extracts were incubated with KLF5 antibody (Cat #: 21017-1-AP, Proteintech) or IgG (Cat #: 2729P, Cell Signaling Technology).

Techniques: Expressing

Journal: BMC medicine

Article Title: Nitazoxanide inhibits acetylated KLF5-induced bone metastasis by modulating KLF5 function in prostate cancer.

doi: 10.1186/s12916-023-02763-4

Figure Lengend Snippet: Fig. 8 NTZ binds to KLF5 protein regardless of its acetylation status. a Fluorescence intensities of KLF5, KLF5K369Q, and KLF5K369R proteins were measured after incubation with different concentrations of NTZ. b Calculation of the Kd values for dissociation constant using the Origin software and by fitting the fluorescence quenching data. c Circular dichroism (CD) spectra of KLF5, KLF5K369Q, and KLF5K369R incubated with NTZ. The concentrations of both proteins and NTZ are 0.2 μM. d Binding of NTZ to the purified different forms of KLF5 proteins using HPLC analysis

Article Snippet: After stopping the reaction by adding EDTA, DNA was fragmented by sonication, and the extracts were incubated with KLF5 antibody (Cat #: 21017-1-AP, Proteintech) or IgG (Cat #: 2729P, Cell Signaling Technology).

Techniques: Fluorescence, Incubation, Software, Circular Dichroism, Binding Assay, Purification