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SHOX | bioCADDIE Data Discovery Index
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biomedical and healthCAre Data Discovery Index Ecosystem
biomedical and healthCAre Data Discovery Index Ecosystem
ochemical oxygen demand (BOD7), suspended solids (SS), total nitrogen (Tot-N) and total phosphorus (Tot-P) were measured in all effluents (Samuelsson et al., 2011).
The sampling took place during two consecutive days (day 14 and 15) due to the large number of fish. For each day, an equal number of fish from each treatment was sampled in random order and killed by a blow to the head. The fish were weighed, their fork length was measured and their sex was determined by macroscopical observation of their gonads.
Liver samples were collected for several different studies (hence sample size limitations), frozen on dry ice and stored at -70°C until analysis. Homogenization of the frozen liver tissue was carried out using Tissuelyser (Qiagen, Hilden, Germany) and hepatic total RNA was extracted and purified using QIAcube and RNeasy® Plus Mini Kit (Qiagen). The RNA quantity and quality were assessed by spectrophotometric measurements with the Nanodrop 1000 (NanoDrop Technologies, Wilmington, DE). To ensure that no degradation had occurred, the isolated RNA was analyzed using Experion automated electrophoresis (Bio-Rad, Hercules, CA).
A 15k rainbow trout gene expression microarray was designed for the RT analyzer platform (febit, Heidelberg, Germany) by using The Institute for Genomic Research (TIGR) Rainbow Trout Gene Index (RTGI) database version 7.0 (http://compbio.dfci.harvard.edu/tgi/). Details on the probe design strategy, but for eelpout (Zoarces viviparus), and transcript selection strategy are described elsewhere (Kristiansson et al., 2009; Cuklev et al., 2011). However, in the present study, singletons and non-annotated expressed sequence tags (ESTs) were replaced by newly well-annotated ESTs in rainbow trout. When available, transcripts at GenBank (http://www.ncbi.nlm.nih.gov/nucleotide) were used. In our lab, results from similar microarrays using the same platform have shown good correlation with quantitative polymerase chain reaction (qPCR) data (Gunnarsson et al., 2009b; Kristiansson et al., 2009; Cuklev et al., 2011; Lennquist et al., 2011).
To reduce variation in estrogen-responsive genes, only males were used for the subsequent gene expression analyses. Biotinylated antisense RNA (aRNA) was synthesized using MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification Kit (Ambion®). The aRNA samples (20 µg) were vacuum dried in a vacuum centrifuge, dissolved in 10 µl water and fragmented according to the manufacturer’s protocol. The following steps described in this subchapter were all performed by febit. Oligonucleotide arrays were synthesized by photo-controlled in situ synthesis using the Geniom One system (febit). Each biochip consists of eight individually accessible micro channels, each of which is referred to as a microarray in this manuscript. Eight individual samples from each aquarium were included in the analysis. In total, 64 microarrays were analyzed. A customized protocol, described in detail elsewhere (Cuklev et al., 2011), was used for prehybridization and hybridization. All samples were randomly placed on the biochips, with one sample from each exposure on each biochip. Signals were detected using the internal CCD-camera system of the RT analyzer instrument (febit) and quantified using the Geniom Wizard software. Integration times were between 156 and 570 ms, determined automatically by the instrument software.
All microarray data processing and statistical calculations were performed in R-2.12.2 (www.r-project.org; R Development Core Team, 2010). The quality of pre- and post normalized arrays was verified with box- and MA plots. The data analysis was performed in the R-package LIMMA (Smyth, 2005). Data were normalized using the ‘quantile’ method. Moderated t-statistics and adjusted p-values of differential expression were calculated using the empirical Bayes model....
only 50% of their DNA fingerprint bands, whereas SS and SR shared about 80% of bands. Most authorities suggest that WKY alone is not a good control strain, and that for most comparative studies several normotensive strains should be used. There is an extensive literature on the characteristics of SHR. DeJong (1984) provides a useful comparative review of this and other hypertensive strains, and there are regular symposia on hypertensive rat strains (see J. Hypertension 4(suppl):S1-S541, 1986, and Jpn. Heart J. 28:567-648)....
degrees of inflammation from Sjögren's syndrome (SS) patients. SS is a chronic autoimmune disease targeting salivary and lacrimal exocrine glands. Results provide insight into the molecular mechanisms underly...
feasibility, and acceptability of Seeking Safety (SS)
treatment in a sample of incarcerated women with comorbid substance
use disorder (SUD) and comorbid post-traumatic stress disorder
(PTSD). Seeking Safety, a cognitive-behavioral psychoth...
ssue from Sprague Dawley and Dahl salt sensitive (SS/Jr) rats fed 10 day diet of either 0.3% or 8.0% NaCl. Results provide insight into salt adaptation and pathogenesis of hypertension....
6 males exposed to mainstream (MS) or sidestream (SS) cigarette smoke. Smoking and obesity are risk factors for heart disease. Results provide insight into molecular mechanisms underlying cardiac responses of smoke-exposed DIO animals....
components. The School Safety and Discipline (SS&D) component (Part 1)
gathered general perceptions of the school learning environment from
students in grades 6 through 12 and parents/guardians of students in
grades 3 through 12. Respondents were asked about academic challenge,
classroom and school discipline, and student norms for hard work and
good behavior. They also evaluated the safety of their schools
regardless of whether they or their children had been personally
victimized. This component incorporated a broad concept of
victimization, including measures of "secondary victimization," such
as knowledge of an...
United States Department of Education. Institute of Education Sciences. National Center for Education Statistics