Dataset of liver proteins changed in eu- and hypothyroid female rats upon in vivo exposure to hexabromocyclododecane (HBCD)

Female Wistar rats with different thyroid status (eu-, hypothyroid) were exposed to 0, 3 or 30 mg/kg body weight of the flame retardant HBCD for 7 days. Changes in protein patterns obtained by 2D-DIGE were evaluated, and different animal groups compared taking into account their exposure and thyroid status. Proteins significantly altered in abundance in any of these comparisons were identified by mass spectrometry. These data, together with hormone data of the animals, are discussed in “Hexa-bromocyclododecane (HBCD) induced changes in the liver proteome of eu- and hypothyroid female rats” (Miller et al., 2016) [1].


Subject area
Biology More specific subject area

Environmental Toxicology
Type of data Tables, image (annotated gel image) How data was acquired 2D Fluorescence Difference Gel Electrophoresis (2D-DIGE) and mass spectrometry Data format Analyzed and filtered data Experimental factors Liver lysates of eu-and hypothyroid female rats differently exposed to HBCD

Experimental features
Comparative proteomic analysis of rat liver lysates using 2D-DIGE. Proteins present in differentially abundant protein spots (regarding HBCD exposure, amount, and thyroid status) were identified using MALDI TOF/TOF analysis. Data source location Origin of samples: Wageningen University, Wageningen, The Netherlands Data collection: Luxembourg Institute of Science and Technology, Esch-sur-Alzette, Luxembourg Data accessibility

MS-and regulation data is with this article as Supplementary material
Value of the data Identification of liver proteins from female rats altered due to HBCD exposure. Identification of liver proteins from female rats changed in hypothyroid status.
Data showing single and combined effects (HBCD exposure, hypothyroidism). Identified liver proteins form the basis for further studies to achieve a more detailed understanding of involved mechanism.

Data
Two-dimensional electrophoresis of liver protein lysates showed complex patterns of about 3000 spots per gel. Patterns of 24 gels from different exposures of eu-and hypothyroid rats were evaluated quantitatively. The data from different animals groups were compared, taking different aspects into account (HBCD exposure, thyroid status). Statistically significant fold-changes of at least 30% between groups (P o0.05 within group) were considered to be relevant.
The master gel is presented in Fig. 1, and all spots with significant abundance changes in any of the performed comparisons are labelled. Spot numbers refer to the protein identifications listed in Table 1 (peptide list in Supplemental Table 1), and to abundance changes in the various animal groups (Supplemental Table 2).

Animals, treatment and experimental protocol
The animal experiment was detailed in [1] and was approved under number 2007-041 by the Animal Welfare Committee of Wageningen University. In brief, female Wistar WU (HsdCpbWU) rats with normal or reduced thyroid function (hypothyroid) were orally exposed to 0, 3 or 30 mg/kg bw/d HBCD, respectively, for 7 consecutive days. Four liver samples per group were analyzed by proteomic methods.

Proteomic analysis
Two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) was performed as previously described, with minor modifications [2,3]. Rat livers were homogenized using the GE sample grinding kit in lysis buffer (urea 7 M; thiourea 2 M; CHAPS 2% w/w; tris 30 mM) containing protease inhibitor Complete Mini (Roche, Brussels, Belgium). Supernatants obtained after centrifugation (15 min at 30,000 g) were collected and stored at À 20°C until use. Protein concentration was determined according to Bradford [4]. Fifty mg per sample were labelled with CyDyes according to the manufacturer's instructions and separated on IPGs of a non-linear 3-10 pH-range. The second dimensional SDS-PAGE was performed in 12.5% precast gels (SERVA Electrophoresis GmbH, Heidelberg, Germany). Gel images (acquired on a Typhoon 9400) were analyzed with the DeCyder 7.0 software package (both GE Healthcare, Diegem, Belgium). Gels were matched and subjected to univariate and multivariate analysis in order to highlight differentially regulated spots (fold change at least 1.3) with a P-value in the respective univariate ANOVA or two way ANOVA o 0.05.
Differentially abundant spots were automatically picked, tryptically digested and spotted on the MALDI target by the use of the Ettan Spot Handling Workstation (GE Healthcare, Diegem, Belgium). Protein identification was carried out on the Applied Biosystems MALDI-Tof-Tof 4800 Proteomics Analyser (Applied Biosystem, Gent, Belgium) as previously described [2]. Protein identification was performed by searching protein mass fingerprints (PMF) and MS/MS spectra against the SwissProt database with "Rattus norvegicus" as taxonomy. Searches were performed using the ProteinPilot software (Sciex, Nieuwerkerk aan den Ijssel, The Netherlands) and the searching algorithm MASCOT (Matrix Science, www.matrixscience.com, London, UK). For each spot one protein mass fingerprint and up to 8 MS/MS spectra were generated. Parameters for the search were set as follow: up to two Fig. 1. Image of a rat liver 2D-DIGE gel (master gel, grey level image). All spots with statistically significant abundance changes are labelled; spot numbers refer to identifications in Table 1. For details on protein identification see Supplemental Table 1, for data on protein abundance, see Supplemental Table 2. Statistics, including univariate analysis (ANOVA and t-test) and multivariate analysis (two way ANOVA), was performed using the Extended Data Analysis (EDA) module, which is present inside the Decyder 7.0 software package.