Agilent human mirna microarray kit

Total RNAs were extracted from tissues of six primary colorectal cancer patients using the mirVana miRNA extraction kit (Ambion) according to the manufacturer's instructions. The quality control of RNA was performed by a 2100 Bioanalyzer using the RNA 6000 Pico LabChip kit (Agilent Technologies, Santa Clara, CA). The microarray was performed at the Shanghai Biochip Company by using the Agilent Human miRNA microarray Kit version 12.0. Total RNA (100 ng) derived from each of the specimens were used as inputs for labelling via Cy3 incorporation. Microarray slides were scanned by XDR Scan (PMT100, PMT5). The labelling and hybridization were performed according to the protocols in the Agilent miRNA microarray system.

To complete the microRNA chip analysis, total RNA was extracted from eight ovarian tumor samples, using the Agilent Human miRNA Microarray Kit (DesignID:070156), four of which were platinum resistant and four of which were platinum sensitive. The NanoDrop ND-2000 (Thermo Scientific, Waltham, MA, USA) was used to measure total RNA, while the RNA integrity was evaluated by the Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA). The standard chip-processing procedure was implemented, which included sample labeling, microarray hybridization, and washing. Total RNA was first dephosphorylated before being tagged with Cyanine-3-CTP. The tagged RNAs were then hybridized onto the microarray after purification. The arrays were then scanned using an Agilent Scanner G2505C (Agilent Technologies) to get raw pictures, and raw data were extracted using Feature Extraction software (version 10.7.1.1; Agilent Technologies). In the end, the raw data were quantile normalized and filtered by at least 75% detached probes in each sample.

mRNA and miRNA expression profiles were obtained for the same samples using the Agilent Whole Human Genome Oligo Microarray (8 × 60K; G4851A; #028004; Agilent Technologies), which detects 27,958 target Entrez gene mRNAs and 7,419 lincRNAs. Briefly, 600 ng Cy3-labeled fragmented cRNA was hybridized overnight to an Agilent Whole Human Genome Oligo Microarray, washed twice, blocked, and scanned using Agilent’s microarray scanner.
Agilent human miRNA microarray Kit (8×60K; G4872A; #031181) based on miRBase release 16.0 and detecting 1,205 human miRNAs was used to analyze miRNA expression. Briefly, 100 ng total RNA was labeled and hybridized to an Agilent human miRNA microarray overnight at 55°C. The microarray was washed twice and fluorescence detected using Agilent’s microarray scanner System. Agilent’s Feature Extraction software was used for image analysis. Microarray gene analysis was performed by Milteny (Milteny Biotec GmBH, Germany).
Both mRNA and miRNA data were generated according to the MIAME guidelines [20 (link)] and are available on the Gene Expression Omnibus (GEO) website (http://www.ncbi.nlm.nih.gov/geo/) under accession number GEO: GSE55955.