Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 53
Release date: Dec 13 2013
Last update date: Apr 25 2014
Access: Public
Dataset link Using transcriptomic tools to evaluate biological effects across effluent gradients at a diverse set of study sites in Minnesota, USA

Experimental Protocol


At the specific locations (UP, EF, DS), sexually mature female fathead minnows (SI-SM2) were exposed to location specific water in mini-mobile environmental monitoring units (MMU)14 for a period of 4d, at each of three sites (R, H, E) during the summer and fall of 2010 (SI-SM3). The MMUs allowed for consistency in aeration, temperature, and feeding. In the case of the riverine R and H sites, the MMU was supplied with a continuous flow of location-specific water. Due to logistical constraints, exposures at the lake site (E) were conducted under static renewal conditions within the MMUs. However, the cumulative number of daily water exchanges were equivalent to those in the flow-through studies. After exposure fish were anesthetized (buffered MS-222), and necropsied at a facility near the site, specific tissues were excised and flash frozen in liquid nitrogen, and stored at -80°C. Gonads were removed from female and flash-frozen for gene expression analyses using microarray. Ovarian transcripts from six females per location (three locations per site, three sites) were analyzed using a custom 15,000 feature microarray (GEO Platform Accession GPL9248). Data sets for this phase (n=53 microarrays) were normalized independently using Fastlo (Ballman et al., 2004) implemented in R (http://www.r-project.org/), but analyzed using parallel approaches.

Repositories


GEO

GSE53204

ArrayExpress

E-GEOD-53204

BioProject

PRJNA231237

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Contact


Jason Berninger