Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 8
Release date: Aug 24 2009
Last update date: Feb 22 2018
Access: Public
Diseases: Neoplasms, Neoplasms, Germ Cell and Embryonal, Nervous System Diseases
Computational protocol: SAM, EASE
Dataset link GENE PROFILING AND PATHWAY ANALYSIS OF NASP EXPRESSION IN HELA CELLS

Experimental Protocol


Total cellular RNA was purified from HeLa cells using RNeasy ® Mini Kit (Qiagen, Valencia, CA) according to manufacturers’ instructions. RNA samples representing four separate experiments from cells overexpressing tNASP and four experiments from cells treated with NASP siRNA, along with appropriate controls, were submitted for analysis. After the RNA Quality check was performed the samples of RNA from treated cells were amplified with incorporation of Cy5-CTP (fluorescent in the red region), while control samples were labeled by Cy3-CTP (fluorescent in the green region) and purified. The labeled cRNA samples were then fragmented in fragmentation buffer at 60°C for 30 min before the microarray hybridization. Each sample was hybridized to a whole separate Human Genome (4×44K) microarray (Agilent Technologies, Wilmington, DE) overnight at 65°C in a hybridization oven. The hybridization slides were washed, stabilized, dried, and immediately scanned by Agilent Technologies Microarray Scanner (Agilent Technologies, Wilmington, DE). RNA hybridization was performed in the Genomics Core and Microarray Facility (Lineberger Comprehensive Cancer Center, UNC-CH) according to the protocol suggested by Agilent (Agilent Technologies, Wilmington, DE). Statistical analysis – During the initial analysis at UNC Microarray Database, all genes were retrieved, appropriately annotated, and filtered. Eventually, only genes with an absolute value of a Log2 Red/Green Lowess Normalized Ratio of at least 1 (doubled in intensity) for all 4 arrays were selected.

Repositories


GEO

GSE14972

BioProject

PRJNA111869

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Contact


Oleg Alekseev

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