Technique [55]. Briefly, mice were anesthetized with 1 mg/10 grams body weight ketamine and 0.15 mg/10 grams body weight xylazine. Blood was washed from the animals by perfusion of the heart with Hank’s balanced salt solution (HBSS) followed by intracardiac injection of 26106 Dynabeads M-450/ml (Invitrogen, Carlsbad, CA) in HBSS. After 40 ml was perfused, kidneys were removed and minced with a razor blade on ice, followed by digestion at 37uC with 1 mg/mL collagenase and 100 U/ml DNase I for 30 minutes. Digested kidneys were filtered twice with 100 micron Falcon cell strainers, and tissue was pelleted by gentle centrifugation (200 g, 5 minutes). Glomeruli were isolated with a DynaMag-2 magnetic particle GSK429286A chemical information concentrator (Invitrogen), and resuspended in HBSS containing protease inhibitors (1:100 of protease inhibitor cocktail (PIC), (Sigma-Aldrich Co., St. Louis, MO), and 0.1 mM phenylmethylsulfonyl fluoride, PMSF). After two additional rounds of magnetic isolation and resuspension, the glomeruli were snap frozen in liquid nitrogen and stored at 280uC.2D gel and mass spectrometry analysisGlomerular proteins were solubilized with extraction buffer (7 M urea, 2 M thiourea, 4 CHAPS, 25 mM DTT, 5 mM EDTA, and 30 mM Tris-HCl, pH 8.0) for 20 minutes at room temperature. Magnetic beads and insoluble debris were removed by centrifugation and soluble proteins were recovered in the supernatant. GSK864 biological activity protein concentration was determined with a 2-D Quant kit (GE Healthcare, Piscataway, NJ), and adjusted to 2.0 mg/ml. The mixed internal standard methodology was used as previously described [56], with the following modifications. Briefly, individual glomerular extracts from wild-type or Alport mice were labeled with cy3 or cy5 such that two of the three samples from a given group were labeled with the same dye (such as cy3) and the third sample with the other dye (cy5) to avoid any dye-labeling bias in the data. Cy3/5 pairs of wild-type/Alport samples were then mixed with an aliquot of a cy2-labeled mixture of all six samples, which served as an internal standard. The resulting tripartite mixtures were then added to unlabeled glomerular protein from wild-type animals, and 0.5 mg total protein was loaded per 2D gel. All 2D DIGE equipment was manufactured by GE Healthcare. The resulting three sets of glomerular protein mixtures were then resolved by isoelectric focusing (24 cm IPG pH 4?) using a manifold-equipped IPGphor II, followed by 12 SDS-PAGE (to separate proteins ranging from ,12?50 kDa) in a DALT12 electrophoresis chamber using hand-cast gel cassettes with one plate treated with bind-silane to facilitate robot spot excision, all using the 1317923 manufacturer’s recommended protocols. Fluorescent images consisting of 16-bit .tiff files were acquired at 100 micron resolution at each mutually exclusive excitation/emission setting for cy2, cy3, or cy5 using a Typhoon Multivariable Imager, per the manufacturer’s protocol.DIGE expression values and univariate statistical analysis was carried out using DeCyder-2D v6.5 (GE Healthcare), which normalized the ratios across all six samples relative to the cy2 signal on each gel for each specific protein, one-by-one, thereby reducing influence due to gel-to-gel variation. The threshold for significant change in relative protein abundance was set at .1.5 fold, which was greater than 2 standard deviations of the mean abundance change when considering only pair-wise, wild-type/ Alport comparisons on each gel separately. DIGE.Technique [55]. Briefly, mice were anesthetized with 1 mg/10 grams body weight ketamine and 0.15 mg/10 grams body weight xylazine. Blood was washed from the animals by perfusion of the heart with Hank’s balanced salt solution (HBSS) followed by intracardiac injection of 26106 Dynabeads M-450/ml (Invitrogen, Carlsbad, CA) in HBSS. After 40 ml was perfused, kidneys were removed and minced with a razor blade on ice, followed by digestion at 37uC with 1 mg/mL collagenase and 100 U/ml DNase I for 30 minutes. Digested kidneys were filtered twice with 100 micron Falcon cell strainers, and tissue was pelleted by gentle centrifugation (200 g, 5 minutes). Glomeruli were isolated with a DynaMag-2 magnetic particle concentrator (Invitrogen), and resuspended in HBSS containing protease inhibitors (1:100 of protease inhibitor cocktail (PIC), (Sigma-Aldrich Co., St. Louis, MO), and 0.1 mM phenylmethylsulfonyl fluoride, PMSF). After two additional rounds of magnetic isolation and resuspension, the glomeruli were snap frozen in liquid nitrogen and stored at 280uC.2D gel and mass spectrometry analysisGlomerular proteins were solubilized with extraction buffer (7 M urea, 2 M thiourea, 4 CHAPS, 25 mM DTT, 5 mM EDTA, and 30 mM Tris-HCl, pH 8.0) for 20 minutes at room temperature. Magnetic beads and insoluble debris were removed by centrifugation and soluble proteins were recovered in the supernatant. Protein concentration was determined with a 2-D Quant kit (GE Healthcare, Piscataway, NJ), and adjusted to 2.0 mg/ml. The mixed internal standard methodology was used as previously described [56], with the following modifications. Briefly, individual glomerular extracts from wild-type or Alport mice were labeled with cy3 or cy5 such that two of the three samples from a given group were labeled with the same dye (such as cy3) and the third sample with the other dye (cy5) to avoid any dye-labeling bias in the data. Cy3/5 pairs of wild-type/Alport samples were then mixed with an aliquot of a cy2-labeled mixture of all six samples, which served as an internal standard. The resulting tripartite mixtures were then added to unlabeled glomerular protein from wild-type animals, and 0.5 mg total protein was loaded per 2D gel. All 2D DIGE equipment was manufactured by GE Healthcare. The resulting three sets of glomerular protein mixtures were then resolved by isoelectric focusing (24 cm IPG pH 4?) using a manifold-equipped IPGphor II, followed by 12 SDS-PAGE (to separate proteins ranging from ,12?50 kDa) in a DALT12 electrophoresis chamber using hand-cast gel cassettes with one plate treated with bind-silane to facilitate robot spot excision, all using the 1317923 manufacturer’s recommended protocols. Fluorescent images consisting of 16-bit .tiff files were acquired at 100 micron resolution at each mutually exclusive excitation/emission setting for cy2, cy3, or cy5 using a Typhoon Multivariable Imager, per the manufacturer’s protocol.DIGE expression values and univariate statistical analysis was carried out using DeCyder-2D v6.5 (GE Healthcare), which normalized the ratios across all six samples relative to the cy2 signal on each gel for each specific protein, one-by-one, thereby reducing influence due to gel-to-gel variation. The threshold for significant change in relative protein abundance was set at .1.5 fold, which was greater than 2 standard deviations of the mean abundance change when considering only pair-wise, wild-type/ Alport comparisons on each gel separately. DIGE.
