Journal: BMC Molecular Biology

Article Title: Messenger RNA profile analysis deciphers new Esrrb responsive genes in prostate cancer cells

doi: 10.1186/s12867-015-0049-1

Figure Lengend Snippet: Characterization of Esrrb-expressing cancer cell line. Esrrb status of two independent replicates of stable transfected control DU145-pc3.1 and DU145-Esrrb cells are tested by a quantitative PCR b Western blot and c reverse transcriptase PCR. a Relative mRNA concentrations of Esrrb were measured by qPCR, Esrrb transcripts concentration were determined by standard curve method and Esrrb concentration were first normalized to the concentration of house keeping gene GAPDH, then normalized to Esrrb/GAPDH ratio of DU145-pc3.1 cells. b Total protein was extracted form HEK293, DU145-Esrrb and control DU145-pc3.1 cells. Protein concentration of Esrrb was determined by western blot using GAPDH as internal control. c RT-PCR was performed on total RNA extracted from HEK293, DU145-esrrb and control DU145-pc3.1 cells. Esrrb was expressed in DU145-Esrrb cells, while Esrrg is not expressed in either DU145-pc3.1 and DU145-Esrrb cells

Article Snippet: 70 % confluent DU145 cells were transfected with either pcDNA3.1-zeo (+)-Esrrb expression vector [ ], or control empty vector pcDNA3.1-zeo (+) (Promega, Madison, WI, USA).

Techniques: Expressing, Transfection, Real-time Polymerase Chain Reaction, Western Blot, Concentration Assay, Protein Concentration, Reverse Transcription Polymerase Chain Reaction

Journal: BMC Molecular Biology

Article Title: Messenger RNA profile analysis deciphers new Esrrb responsive genes in prostate cancer cells

doi: 10.1186/s12867-015-0049-1

Figure Lengend Snippet: Esrrb-regulated mRNA validation. Left panel qPCR validation of Esrrb-regulated mRNAs. Expression values were firstly normalized to Gapdh and normalized ratios are further normalized to that of DU145-pc3.1. Error bars represent standard deviation. Student t test was performed for statistical analysis (*p < 0.05). Seven genes were differentially expressed in both RNA-seq and qPCR, 1 gene, TGFbeta, is not differentially expressed in either assay and serves as a negative control. Right panel RNA-Seq analysis result, fold change (FC) indicates the ratio of normalized read counts in DU145-Esrrb to that of DU145-pc3.1

Article Snippet: 70 % confluent DU145 cells were transfected with either pcDNA3.1-zeo (+)-Esrrb expression vector [ ], or control empty vector pcDNA3.1-zeo (+) (Promega, Madison, WI, USA).

Techniques: Expressing, Standard Deviation, RNA Sequencing Assay, Negative Control

Journal: BMC Molecular Biology

Article Title: Messenger RNA profile analysis deciphers new Esrrb responsive genes in prostate cancer cells

doi: 10.1186/s12867-015-0049-1

Figure Lengend Snippet: Transcriptome correlation and Esrrb altered mRNAs. a Transcriptome correlation analysis was performed using Spearman Ranking Correlation. Color represents the correlation coefficient. DY131 treatment to DU145-Esrrb cells results in the lowest correlation coefficient with DU145-pc3.1 cells. b Dot plot of Esrrb-induced gene expression alteration. Genes expressed at adequate level are tested for differential gene expression test. The plot was made by plotting the Log2FC (fold change) against the Log2 cpm (count-per-million) difference. Red color marks the genes that are significant differentially expressed (FDR < 0.05), and the blue lines marked the Log2FC cutoff value (Log2FC > 1 or Log2FC < −1). 67 genes passed both thresholds

Article Snippet: 70 % confluent DU145 cells were transfected with either pcDNA3.1-zeo (+)-Esrrb expression vector [ ], or control empty vector pcDNA3.1-zeo (+) (Promega, Madison, WI, USA).

Techniques: Expressing