Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 8
Release date: Nov 12 2010
Last update date: Mar 22 2012
Access: Public
Genes: AtRbcX1, SSBP3, LDB1, FXYD1, PKN2
Taxon: Caenorhabditis elegans, Homo sapiens
Dataset link Gene expression regulation by C. elegans SAM-10

Experimental Protocol


Animals were grown on fresh 8P plates (Wormbook.org) until gravid. Eggs were collected by bleaching and hatched in M9 buffer overnight. L1 animals were fed on fresh food for 2 hours at room temperature, harvested and separated from worm debris using a 25μm mesh. RNA was isolated using a standard Trizol protocol. RNA preps were stored at -80C. Quality of RNA preps was first estimated using Agilent 2100 Bioanalyzer. RNA was then reverse-transcribed using the Genisphere Array 350 kit, which generate tagged cDNA. Resulted products are hybridized to the microarrays. Four independent high quality RNA preps (RIN>=7) were chosen for microarray assay using long oligomer-based spotted microarray (Washington University, St. Louis, MO). For dye-swap controls, we ran a technical replicate hybridization for each pair of samples in which the dyes are reversed. Gene spots with “found/good” signals (defined by ScanArray, channel flag 3) in all scans were chosen for gene expression analysis.

Repositories


GEO

GSE25285

ArrayExpress

E-GEOD-25285

BioProject

PRJNA134831

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Contact


Michael Nonet