Journal: Genomics Data

Article Title: Expression-profiling of apoptosis induced by ablation of the long ncRNA TRPM2-AS in prostate cancer cell

doi: 10.1016/j.gdata.2014.10.020

Figure Lengend Snippet: Validation of microarray data by qRT-PCR. Ten transcripts were quantified by qRT-PCR both in control and in TRPM2-AS KO PC3 cells. The resulting expression fold change is plotted against the expression fold change obtained from the Illumina HumanHT-12 V3.0 microarray data. A correlation coefficient of 0.97 was found between the two datasets.

Article Snippet: The human, androgen-independent prostate cancer cell line PC3 was obtained from ATCC (CRL-1435, ATCC).

Techniques: Biomarker Discovery, Microarray, Quantitative RT-PCR, Control, Expressing

Journal: Genomics Data

Article Title: Expression-profiling of apoptosis induced by ablation of the long ncRNA TRPM2-AS in prostate cancer cell

doi: 10.1016/j.gdata.2014.10.020

Figure Lengend Snippet:

Article Snippet: The human, androgen-independent prostate cancer cell line PC3 was obtained from ATCC (CRL-1435, ATCC).

Techniques: Expressing, Microarray, Gene Expression

Journal: PLoS ONE

Article Title: The Response of the Prostate to Circulating Cholesterol: Activating Transcription Factor 3 (ATF3) as a Prominent Node in a Cholesterol-Sensing Network

doi: 10.1371/journal.pone.0039448

Figure Lengend Snippet: ( A ) A provisional network was generated from integration of two microarray data sets. Node color represents increases (red), no significant changes (yellow), and decreases (green) in gene expression in murine prostate tissue after cholesterol alteration as ascertained by cDNA microarray. Changes in RNA expression levels of the corresponding nodes in LNCaP cells are shown as colored node boundaries (donut shape) and the color represents increases (red), no significant change (yellow), and decreases (green) in gene expression under CDM conditions compared to control. Arrows indicate direct activation, T-shaped lines direct repression, dashed arrows indirect activation, and lines physical interaction. ( B ) Gene expression under Normo and Hyper conditions ( in vivo ). To verify in vivo microarray data obtained from SCID experiments, mRNA levels of the indicated genes were determined. GAPDH expression was used to normalize gene expression. Error bars represent SD (n = 3). ( C ) Gene expression under Control and Cholesterol-depleted conditions ( in vitro ). LNCaP cells were incubated in CDM for 0, 3 or 16 h, and mRNA levels of the indicated genes were measured by RT-PCR analysis to validate cDNA microarray data. Error bars represent SD (n = 3). * p <0.05 (Student’s t-test).

Article Snippet: LNCaP human prostate tumor cells were purchased from American Type Culture Collection (ATCC, Manassas, VA) and maintained in RPMI1640 media (Invitrogen, Carlsbad, CA) supplemented with 10% FBS and 1% Penicillin/Streptomycin at 37°C under 5% CO 2 .

Techniques: Generated, Microarray, Gene Expression, RNA Expression, Control, Activation Assay, In Vivo, Expressing, In Vitro, Incubation, Reverse Transcription Polymerase Chain Reaction

Journal: PLoS ONE

Article Title: The Response of the Prostate to Circulating Cholesterol: Activating Transcription Factor 3 (ATF3) as a Prominent Node in a Cholesterol-Sensing Network

doi: 10.1371/journal.pone.0039448

Figure Lengend Snippet: ( A ) RT-PCR analysis in vivo . ATF3 levels are reduced in all prostatic lobes from Hyper mice, compared to those from the Normo group (AP = anterior prostate; VP = ventral prostate; DLP = dorsal prostate). ( B ) Immunoblot analysis. Immunoblot of PrEC lysates showed induction of ATF3 protein by CDM (left panel) and by β-cyclodextrin (right panel). MG132, a proteasome inhibitor, also increased ATF3 expression. ( C ) Immunofluorescence analysis. Induction of ATF3 protein by CDM in LNCaP cells as shown by IF. LNCaP cells were treated with CDM for 18 h, stained with anti-ATF3 antibody and nuclei were counterstained with DAPI (left panel: ATF3; middle panel: DAPI; right panel: overlay). ( D ) RT-PCR analysis. ATF3 mRNA levels in LNCaP cells treated with CDM were normalized to levels of GAPDH. RT-PCR analysis shows induction of ATF3 mRNA levels by CDM. ( E–F ) Promoter reporter analysis. A full-length ATF3 promoter was cloned into a luciferase reporter vector and transfected into LNCaP (D) or PrEC (E). Cells were then incubated in Control and CDM medium. ATF3 promoter activity was plotted as arbitrary units (± SD) after normalization with total protein concentration.

Article Snippet: LNCaP human prostate tumor cells were purchased from American Type Culture Collection (ATCC, Manassas, VA) and maintained in RPMI1640 media (Invitrogen, Carlsbad, CA) supplemented with 10% FBS and 1% Penicillin/Streptomycin at 37°C under 5% CO 2 .

Techniques: Reverse Transcription Polymerase Chain Reaction, In Vivo, Western Blot, Expressing, Immunofluorescence, Staining, Clone Assay, Luciferase, Plasmid Preparation, Transfection, Incubation, Control, Activity Assay, Protein Concentration

Journal: Oncotarget

Article Title: Isolation and genome-wide expression and methylation characterization of CD31 + cells from normal and malignant human prostate tissue

doi:

Figure Lengend Snippet: (A) Representative photomicrographs of hematoxylin and eosin stained frozen sections of benign (left) and malignant (right) prostatic tissues of macrodissected tissues used for ECs isolation. ECs are highlighted in the frozen sections by CD31 immunostaining (Original magnification, x200). (B) Representative immunofluorescent photomicrographs of CD31 (green) and vWF (red) expression and uptake of DiI-Ac-LDL (red) (original magnification, ×200) in CD31 + prostate TdECs and NdECs. Absence of pan-cytokeratin expression by immunofluorescence was observed in CD31 + prostate TdECs and NdECs. LNCaP was used as positive control for pan-cytokeratin immunofluorescence. Nuclei are stained with DAPI (blue). Endothelial tube network was formed by primary cultures of prostate TdECs and NdECs (original magnification, x100). (C) Representative reverse transcription-PCR analysis of RNA from primary cultures of TdECs and NdECs, HUVECs, or LNCaP cells using human-specific primers for human CD31, CD34, ICAM-1, VCAM-1, VEGFR1, VEGFR2, AR and PSA. GAPDH was used as a loading control.

Article Snippet: Primary cultures of human prostate endothelial cells (NdECs and TdECs) were cultured in endothelial growth medium [Endothelial Cell Growth Medium MV2 with Supplement Mix (PromoCell GmbH, Heidelberg, Germany) and 100 U/ml penicillin and 100 μg/ml streptomycin (Invitrogen)].

Techniques: Staining, Isolation, Immunostaining, Expressing, Immunofluorescence, Positive Control

Journal: Oncotarget

Article Title: Isolation and genome-wide expression and methylation characterization of CD31 + cells from normal and malignant human prostate tissue

doi:

Figure Lengend Snippet: Quantitative real-time PCR was used to validate gene expression of AREG , JMY , EPB41 , GMNN and FAM53C in endothelial cells derived from malignant lesions vs benign lesions in AA and CA patients with prostate cancer. Relative gene expression level for qRT-PCR was normalized to the reference gene GAPDH . Gene expression from microarray was plotted together with the qRT-PCR results. Results were shown as Mean ± SD (triplicate). “*” represents p value <0.05 by t-Test.

Article Snippet: Primary cultures of human prostate endothelial cells (NdECs and TdECs) were cultured in endothelial growth medium [Endothelial Cell Growth Medium MV2 with Supplement Mix (PromoCell GmbH, Heidelberg, Germany) and 100 U/ml penicillin and 100 μg/ml streptomycin (Invitrogen)].

Techniques: Real-time Polymerase Chain Reaction, Expressing, Derivative Assay, Quantitative RT-PCR, Microarray