Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 12
Release date: Oct 1 2015
Last update date: Oct 28 2015
Access: Public
Chemicals: Iron, Oxygen
Dataset link Intraspecific diversity among partners drives functional variation in coral symbioses

Experimental Protocol


Hybridization followed a dual channel loop design using two biological replicates from each treatment that maximized power to detect differential expression in contrasts between regulationphenotype and temperature as well as the amount of data obtained from each slide (Simon and Dobbin 2003). A total of 12 arrays on one 12 plex slide were used. 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

GSE50926

BioProject

PRJNA219383

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Contact


John Parkinson

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