Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 46
Release date: Nov 21 2007
Last update date: Mar 16 2012
Access: Public
Taxon: Sus scrofa, Homo sapiens, Mus musculus
Dataset link Microarray gene expression profiling of 27k cDNAs in 23 healthy porcine tissues

Experimental Protocol


The microarray experiment was carried out using a two-channel common reference design with two independent RNA extractions from each tissue sample. For each total-RNA extraction, 20 μg was labeled with Alexa 594 and 20 μg with Alexa 488 using SuperScript Indirect cDNA labeling System from Invitrogen. The RNA extracts labeled with Alexa 488 was collected from all tissue samples, mixed and used as reference sample referred to here as a the common reference. The RNA extracts labeled with Alexa 594 were used individually as labeled tissue samples. The labeled RNA extracts were used in two batches of 23 hybridizations corresponding to the two independent RNA extraction batches. One labeled tissue sample RNA (Alexa 594) and one labeled common reference sample RNA (Alexa 488) was thus hybridized to each of 46 microarrays. The same common reference sample was thus used in all the 46 (2x23) hybridizations. Two rounds of hybridizations on a Discovery XT hybridization station from Ventana were carried out corresponding to the two RNA batches. The hybridized microarrays were scanned and converted into TIFF images using Scanner and ScanArray Express software from Perkin Elmer.

Repositories


GEO

GSE4918

ArrayExpress

E-GEOD-4918

BioProject

PRJNA95861

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Contact


Henrik Hornshøj
Henrik Hornshøj