Er as the no template control. Relative miRNA expression levels were compared via the 22DDCt method [46]. To normalize the qPCR results, let-7a was chosen as the reference gene based on its high and consistent expression.miRNA Microarray AssayThe Agilent Human MicroRNA Microarray V3 Technology platform was used, which contains 866 mature human miRNAs and 86 viral miRNAs according to the vendor’s protocol. Total RNA (100 ng) was dephosphorylated via 37uC incubation with phosphatase for 30 min. The dephosphorylated RNA was mixed with 2.8 ml of 100 DMSO, and then heated at 100uC for 7 min and immediately cooled on an ice water bath. Labeling reactions were carried out and BMS-5 chemical information samples incubated at 16uC for 2 hr. Asiaticoside A chemical information Labeled RNA samples were dried in a speed vacuum at 55uC for 3 hours. Samples were then reconstituted and mixed with a hybridization cocktail followed by a 5 min 100uC incubation, and then it was immediately transferred to the ice water bath for 5 min. With samples loaded, hybridization chambers were ensconced in the hybridization oven and incubated at 50uC and a 20 rpm rotation for 20 hr. After hybridization, slides were removed from the chambers and submerged in the provided GE Wash Buffer 1, and washed as follows: GE wash buffer 1 (2 ml 10 Triton X-102 added into 4 L wash buffer) at room temperature for 5 min, and overnight pre-warmed GE Wash Buffer 2 at 37uC for 5 min. Slides were briefly dried and scanned by Agilent’s High-Resolution C Scanner.Target Prediction and Pathway AnalysisDownstream targets of the significantly changed miRNAs were predicted using three different algorithms, specifically TargetScan 6.0, Diana microT 3.0 and miRanda (microrna.org). Each Target was regarded as positive only if it was predicted by at least two of the three algorithms. A list of candidate target genes was subjected to GeneSpring GX or IPA (Ingenuity Pathway Analysis) analysis.Anti-miR-21 oligo TransfectionAnti-miR-21 and scrambled mock oligos were purchased from Ambion. On the day of transfection, a total of 240,000 cells wereDeregulated miRNAs in Breast Cancerseeded in each well of a 6-well plate. Dilutions of 90 pmol of oligos or mocks and 5 ml of Lipofectamine 2000 (Invitrogen) in 250 ml OptiMEM serum free medium (Invitrogen) were prepared and incubated at room temperature for 20 min. The 500 ml mixture was applied to each well of the 6-well plate. The cells were cultured on antibiotic-free DMEM medium with 10 FBS at a total volume of 3 ml. Cells were harvested after 48 hrs and the miRNAs were isolated using the mirVana miRNA isolation kit (Ambion).monoclonal antibody (Cat# MA5-15738, Sigma) at a dilution of 1:1,000 in TBS buffer with 0.05 Tween. The membrane was washed 3 times with TBS/0.05 Tween 23977191 and incubated with an anti-rabbit IgG conjugated to horse radish peroxidase (Cat# 7074S, Cell Signaling) for MSH2 and SMAD7, and an anti-mouse IgG (Cat# 7076S, Cell Signaling) for GAPDH at a 1:1,000 dilution in TBS/0.05 Tween (and 5 milk). Super Signal West Femo Maximum Sensitivity Substrate (Thermo) was used according to the manufacturer’s protocol to visualize proteins and quantify band intensity.Western Blot AnalysisThe Western blot experiment was performed as described previously [47]. Cell protein lysates were prepared with SDS gelloading buffer containing b-mercaptoethanol and heated at 95uC for 5 minutes. Proteins were separated by SDS-PAGE using a 12 Mini-PRPTEAN TGX gel (Bio-Rad) and transferred for 2 hours at 100 V. The membrane w.Er as the no template control. Relative miRNA expression levels were compared via the 22DDCt method [46]. To normalize the qPCR results, let-7a was chosen as the reference gene based on its high and consistent expression.miRNA Microarray AssayThe Agilent Human MicroRNA Microarray V3 Technology platform was used, which contains 866 mature human miRNAs and 86 viral miRNAs according to the vendor’s protocol. Total RNA (100 ng) was dephosphorylated via 37uC incubation with phosphatase for 30 min. The dephosphorylated RNA was mixed with 2.8 ml of 100 DMSO, and then heated at 100uC for 7 min and immediately cooled on an ice water bath. Labeling reactions were carried out and samples incubated at 16uC for 2 hr. Labeled RNA samples were dried in a speed vacuum at 55uC for 3 hours. Samples were then reconstituted and mixed with a hybridization cocktail followed by a 5 min 100uC incubation, and then it was immediately transferred to the ice water bath for 5 min. With samples loaded, hybridization chambers were ensconced in the hybridization oven and incubated at 50uC and a 20 rpm rotation for 20 hr. After hybridization, slides were removed from the chambers and submerged in the provided GE Wash Buffer 1, and washed as follows: GE wash buffer 1 (2 ml 10 Triton X-102 added into 4 L wash buffer) at room temperature for 5 min, and overnight pre-warmed GE Wash Buffer 2 at 37uC for 5 min. Slides were briefly dried and scanned by Agilent’s High-Resolution C Scanner.Target Prediction and Pathway AnalysisDownstream targets of the significantly changed miRNAs were predicted using three different algorithms, specifically TargetScan 6.0, Diana microT 3.0 and miRanda (microrna.org). Each Target was regarded as positive only if it was predicted by at least two of the three algorithms. A list of candidate target genes was subjected to GeneSpring GX or IPA (Ingenuity Pathway Analysis) analysis.Anti-miR-21 oligo TransfectionAnti-miR-21 and scrambled mock oligos were purchased from Ambion. On the day of transfection, a total of 240,000 cells wereDeregulated miRNAs in Breast Cancerseeded in each well of a 6-well plate. Dilutions of 90 pmol of oligos or mocks and 5 ml of Lipofectamine 2000 (Invitrogen) in 250 ml OptiMEM serum free medium (Invitrogen) were prepared and incubated at room temperature for 20 min. The 500 ml mixture was applied to each well of the 6-well plate. The cells were cultured on antibiotic-free DMEM medium with 10 FBS at a total volume of 3 ml. Cells were harvested after 48 hrs and the miRNAs were isolated using the mirVana miRNA isolation kit (Ambion).monoclonal antibody (Cat# MA5-15738, Sigma) at a dilution of 1:1,000 in TBS buffer with 0.05 Tween. The membrane was washed 3 times with TBS/0.05 Tween 23977191 and incubated with an anti-rabbit IgG conjugated to horse radish peroxidase (Cat# 7074S, Cell Signaling) for MSH2 and SMAD7, and an anti-mouse IgG (Cat# 7076S, Cell Signaling) for GAPDH at a 1:1,000 dilution in TBS/0.05 Tween (and 5 milk). Super Signal West Femo Maximum Sensitivity Substrate (Thermo) was used according to the manufacturer’s protocol to visualize proteins and quantify band intensity.Western Blot AnalysisThe Western blot experiment was performed as described previously [47]. Cell protein lysates were prepared with SDS gelloading buffer containing b-mercaptoethanol and heated at 95uC for 5 minutes. Proteins were separated by SDS-PAGE using a 12 Mini-PRPTEAN TGX gel (Bio-Rad) and transferred for 2 hours at 100 V. The membrane w.
