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6 protocols using mircury lna microrna array kit

1

Microarray Analysis of Human miRNA

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Analysis of human miRNA expression was initiated by using a miRCURY LNA microRNA Array kit (Exiqon, Vedbaek, Denmark). Processed microarray slides were then scanned with an Agilent G2565CA Microarray Scanner System (Agilent Technologies). Scanned images were imported by Agilent Feature Extraction software version 10.7.3.1 (Agilent Technologies), and fluorescence intensities of each image were quantified by applying the modified manufacturer’s protocol.
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2

miRNA Expression Profiling via LNA Microarray

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The MiRNA expression profiling was performed using the miRCURY LNA microRNA array kit (Exiqon, Vedbaek, Denmark) according to the manufacturer's protocol. This array contains 3100 capture probes covering human miRNAs in miRBase v. 19.0. Slides were scanned using an Agilent C scanner (Agilent Technologies). Next, scanned images were imported into GenePix Pro 5.1 software (Axon Instruments, Foster City, CA) for grid alignment and data extraction. Expressed data were normalized using quantile normalization. After normalization, miRNAs that were significantly differentially expressed between the 2 groups were identified through fold changes (>1.5) and P-values (<.05). The sample number was limited; thus, we did not perform a multiple hypotheses testing, such as false discovery rate.
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3

miRNA Expression Profiling of Tumor and Normal Tissues

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In total, three paired tumor and adjacent normal tissue specimens were randomly selected. Total RNA was isolated with TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and an miRNeasy Mini kit (Qiagen, Valencia, CA, USA) according to the manufacturers’ instructions. Samples with an RNA integrity number >8 were processed for hybridization. Total RNA was labeled with a miRCURY™ Array Power labeling kit (Exiqon, Copenhagen, Denmark) and hybridized to the miRNA microarray with a miRCURY LNA™ microRNA Array kit (Exiqon). Images were then obtained with a GenePix 4000B microarray scanner and imported with the associated software (Axon Instruments, Sunnyvale, CA, USA). SpotData Pro software was used for data analysis. Hierarchical clustering was performed with Data Matching Software.
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4

In Situ Hybridization and Immunohistochemistry

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In situ hybridization was performed using a 5′- and 3′-digoxigenin- (DIG-) labeled locked nucleic acid- (LNA-) based probe specific for miR-7-5p (E38915; Exiqon, Denmark). The probe was detected using antidigoxigenin-AP (11093274910; Roche) and NBT/BCIP ready-to-use tables (11697471001; Roche). The hybridization was conducted according to the manual of the miRCURY LNA™ microRNA Array Kit (Exiqon, Denmark) using a hybridization station (ThermoBrite).
Immunohistochemistry was performed on tissue microarray chips. The slides were probed with the following primary antibodies: rabbit anti-human LDHA (ab47010; Abcam) and rabbit anti-human LC3 (12741; Cell Signaling Technology), and then incubated with HRP-conjugated goat anti-rabbit secondary antibody. The proteins were visualized in situ with DAB chromogenic substrate. The results of immunostaining and hybridization were evaluated according to the reference [14 (link)].
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5

Exosomal miRNA Profiling by Array

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Exosomes were isolated from the conditioned media of A375-P & -R cells by ultracentrifugation as previously described43 (link). RNA was extracted from the exosomes using TRIzol method following the standard protocol (ThermoFisher Scientific, Waltham, MA). The purified RNA (1 µg each) was subjected to miR profiling using miRCURY LNA™ microRNA array kit (Qiagen, Germantown, MD), as reported43 (link).
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6

RT-qPCR Analysis of Hippocampal Gene and miRNA Expression

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For RT-qPCR analysis, total RNA was extracted from hippocampus tissues 7 days after anesthesia using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc., Waltham, MA, USA). Then, 2 µg of total RNA was used as a template to synthesize the first-strand cDNA using iScriptTM Reverse Transcription Supermix (Bio-Rad Laboratories, Inc., Hercules, CA, USA), and the mRNA and miRNA expression levels were determined using a Ssofast EvaGreen Supermix kit (Bio-Rad Laboratories, Inc.) with an ABI 7500 Fast Real-Time PCR system (Applied Biosystems; Thermo Fisher Scientific, Inc.) and a miRCURY LNA microRNA Array kit (version 14.0; Exiqon; Qiagen, Hilden, Germany). The primers (Table I) were synthesized by Shanghai Sangon Biologic Engineering Technology and Services Co., Ltd. (Shanghai, China). GAPDH was used as the internal control for mRNA quantifications and U6 was used as the internal control for miRNA quantification. The reaction conditions were as follows: 95°C 10 min, followed by 95°C for 30 sec, 60°C for 40 sec and 72°C for 10 sec for 40 cycles. All reactions were run in triplicate. The relative mRNA expression level was calculated by the 2−ΔΔCq method (27 (link)).
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