Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 36
Release date: Dec 13 2012
Last update date: Mar 14 2013
Access: Public
Diseases: Peroxisomal Disorders
Dataset link Variation in the transcriptional response of threatened coral larvae to elevated temperatures

Experimental Protocol


Hybridization followed a dual channel loop design using two biological replicates (dye-swapped) from each treatment that maximized power to detect differential expression in contrasts between temperatures and batches (within time-points) as well as the amount of data obtained from each slide (Simon and Dobbin 2003). A total of 18 arrays on two 12 plex slides were used (Table S1). Additional samples from other sub-batches (b3/b4) were included in the microarray experiment but are not used in this analysis. Each array measures the expression level of 135,185 genes from the elkhorn coral (Acropora palmata) transcriptome (Polato et al. 2011). Two 60-mer probes were designed for each contig (n = 85,260), and a single probe was designed for each singleton sequence (n = 45,390). Two additional probes each were developed for sequences associated with annotation information relating to calcium metabolism and stress response (n = 4,798). Replicate probes for individual sequences from the assembled transcriptome were not identical; rather they represented multiple different 60-mer sequences from the original template.

Repositories


GEO

GSE36983

ArrayExpress

E-GEOD-36983

BioProject

PRJNA157441

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Contact


Nicholas Polato