Whole Mouse Genome Microarray Kit, 4x44K

Protocol tips

Upstream tips	Protocol tips	Downstream tips
Avoid touching the surface of the glass with your fingers. Skin oils and other substances, such as lotions or ink, can fluoresce. If the surface of the glass is noticeably dirty, it can be carefully cleaned with a nonabrasive laboratory tissue.

Upstream tips
Avoid touching the surface of the glass with your fingers. Skin oils and other substances, such as lotions or ink, can fluoresce. If the surface of the glass is noticeably dirty, it can be carefully cleaned with a nonabrasive laboratory tissue.

Publication protocol

Total RNA from four samples per genotype (LT2 Control, LT2‐MYC) was extracted as per manufacturer's instructions (mirVana™ miRNA isolation kit, Ambion). RNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies). Three LT2 Control and four LT2‐MYC samples were selected for Agilent stock mouse 44K (014868) array analysis—one LT2 Control RNA sample did not meet quality selection criteria and was thus removed from downstream applications. Sample preparation, labeling, and array hybridizations were performed according to standard protocols from UCSF Shared Microarray Core Facilities and Agilent Technologies (http://www.arrays.ucsf.edu; http://www.agilent.com). RNA was amplified and labeled with Cy3‐CTP using the Agilent Low RNA Input Fluorescent Linear Amplification kits following the manufacturer's protocol (Agilent). Labeled cRNA was assessed using Nandrop ND‐100 (Nanodrop Technologies Inc.). Cy3‐labeled target was hybridized to Agilent whole mouse genome 4x44K Ink‐jet arrays (Agilent). Hybridization samples were randomized on the 4x44K format to correct any batch bias. Hybridizations were performed for 14 h, according to the manufacturer's protocol (Agilent). Arrays were scanned using the Agilent microarray scanner (Agilent), and raw signal intensities were extracted with Feature Extraction v9.5 software (Agilent). Primary normalization and data extraction were performed by the Microarray Core Facility. Briefly, single channel data were normalized using quantile normalization method. No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization.

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Manufacturer protocol

Download the product protocol from Agilent Technologies for Whole Mouse Genome Microarray Kit, 4x44K below.

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