DOI: 10.18150/15wh5x
title: Reference genes selection for gene expression analyses in reproductive turkey with yellow semen syndrome: raw data

description: Reference genes selection for gene expression analyses in reproductive turkey (Meleagris gallopavo) with yellow semen syndrome: raw dataThe purpose of the study was to evaluate the most accurate qPCR internal controls that might be used as first-choice-reference genes in studies on the reproductive tract, liver, and immune tissues and cells of adult male turkey breeder producing white semen and with yellow semen syndrome. This dataset contains 9 directories:1. The ditectory ‘The cycle threshold (Ct) values’ contains 9 files in .ods format.-Table 1. Gene expression in testis - Ct values and reaction efficiencies. (.ods)-Table 2. Gene expression in epididymis - Ct values and reaction efficiencies. (.ods)-Table 3. Gene expression in ductus deferens - Ct values and reaction efficiencies. (.ods)-Table 4. Gene expression in bursa of Fabricius - Ct values and reaction efficiencies. (.ods)-Table 5. Gene expression in thymus - Ct values and reaction efficiencies. (.ods)-Table 6. Gene expression in spleen - Ct values and reaction efficiencies (.ods)-Table 7. Gene expression in liver - Ct values and reaction efficiencies. (.ods)-Table 8. Gene expression in whole blood - Ct values and reaction efficiencies. (.ods)-Table 9. Gene expression in peripheral blood mononuclear cells - Ct values and reaction efficiencies. (.ods)2. The ditectory ‘RefFinder’ contains 2 files in .xlsx format.Table 1. Reference gene comprehensive ranking for qPCR analyses only for white semen-producing turkey toms (for studies on healthy individuals). Analysis were performed in male turkeys’ reproductive tract (testis, epididymis, ductus deferens), liver, and immune tissues, and cells i.e. bursa of Fabricius, thymus, whole blood, peripheral blood mononuclear cells (PBMC), and spleen of healthy adult individuals producing white semen. A lower value for each gene is associated with higher expression stability. (.xlsx)Table 2. Reference gene comprehensive ranking for qPCR analyses across white semen (WS) and yellow semen-producing (YSS )turkey toms (for YSS studies). Analysis were performed in male turkeys’ reproductive tract (testis, epididymis, ductus deferens), liver, and immune tissues, and cells i.e. bursa of Fabricius, thymus, whole blood, peripheral blood mononuclear cells (PBMC), and spleen across WS and YSS groups to provide adequate internal controls for YSS. A lower value for each gene is associated with higher expression stability. (.xlsx)3. The ditectory ‘Comparative delta Ct’ contains 2 files in .xlsx format.Table 1. Comparative delta Ct analysis for selecting the best reference genes for qPCR studies only for white semen-producing turkey toms (for studies on healthy individuals). Analysis were performed in male turkeys’ reproductive tract (testis, epididymis, ductus deferens), liver, and immune tissues, and cells i.e. bursa of Fabricius, thymus, whole blood, peripheral blood mononuclear cells (PBMC), and spleen of healthy adult individuals producing white semen. A lower value for each gene is associated with higher expression stability. (.xlsx)Table 2. Comparative delta Ct analysis for selecting the best reference genes for qPCR studies across white semen (WS) and yellow semen-producing (YSS )turkey toms (for YSS studies) Analysis were performed in male turkeys’ reproductive tract (testis, epididymis, ductus deferens), liver, and immune tissues, and cells i.e. bursa of Fabricius, thymus, whole blood, peripheral blood mononuclear cells (PBMC), and spleen across WS and YSS groups to provide adequate internal controls for YSS. A lower value for each gene is associated with higher expression stability. (.xlsx)4. The ditectory ‘BestKeeper’ contains 2 files in .xlsx format.Table 1. Best Keeper analysis for selecting the best reference genes for qPCR only for white semen-producing turkey toms (for studies on healthy individuals). Analysis were performed in male turkeys’ reproductive tract (testis, epididymis, ductus deferens), liver, and immune tissues, and cells i.e. bursa of Fabricius, thymus, whole blood, peripheral blood mononuclear cells (PBMC), and spleen of healthy adult individuals producing white semen.A lower value for each gene is associated with higher expression stability. (.xlsx)Table 2. Best Keeper analysis for selecting the best reference genes for qPCR studies across white semen (WS) and yellow semen-producing (YSS )turkey toms (for YSS studies). Analysis were performed in male turkeys’ reproductive tract (testis, epididymis, ductus deferens), liver, and immune tissues, and cells i.e. bursa of Fabricius, thymus, whole blood, peripheral blood mononuclear cells (PBMC), and spleen across WS and YSS groups to provide adequate internal controls for YSS. A lower value for each gene is associated with higher expression stability. (.xlsx)5. The ditectory ‘NormFinder’ contains 2 files in .xlsx format.Table 1. NormFinder analysis for selecting the best reference genes for qPCR studies only for white semen-producing turkey toms (for studies on healthy individuals). Analysis were performed in male turkeys’ reproductive tract (testis, epididymis, ductus deferens), liver, and immune tissues, and cells i.e. bursa of Fabricius, thymus, whole blood, peripheral blood mononuclear cells (PBMC), and spleen of healthy adult individuals producing white semen. Values represent each gene's average pairwise variation V with all other tested reference genes. (.xlsx)Table 2. NormFinder analysis for selecting the best reference genes for qPCR studies across white semen (WS) and yellow semen-producing (YSS )turkey toms (for YSS studies). Analysis were performed in male turkeys’ reproductive tract (testis, epididymis, ductus deferens), liver, and immune tissues, and cells i.e. bursa of Fabricius, thymus, whole blood, peripheral blood mononuclear cells (PBMC), and spleen across WS and YSS groups to provide adequate internal controls for YSS. Values represent each gene's average pairwise variation V with all other tested reference genes. (.xlsx)6. The ditectory ‘geNorm’ contains 2 files in .xlsx format.Table 1. geNorm analysis for selecting the best reference genes for qPCR studies only for white semen-producing turkey toms (for studies on healthy individuals). Analysis were performed in male turkeys’ reproductive tract (testis, epididymis, ductus deferens), liver, and immune tissues, and cells i.e. bursa of Fabricius, thymus, whole blood, peripheral blood mononuclear cells (PBMC), and spleen of healthy adult individuals producing white semen. Values represent each gene's average pairwise variation V with all other tested reference genes. A lower value for each gene is associated with higher expression stability. (.xlsx)Table 2. geNorm analysis for selecting the best reference genes for qPCR studies across white semen (WS) and yellow semen-producing (YSS )turkey toms (for YSS studies). Analysis were performed in male turkeys’ reproductive tract (testis, epididymis, ductus deferens), liver, and immune tissues, and cells i.e. bursa of Fabricius, thymus, whole blood, peripheral blood mononuclear cells (PBMC), and spleen across WS and YSS groups to provide adequate internal controls for YSS. Values represent each gene's average pairwise variation V with all other tested reference genes. A lower value for each gene is associated with higher expression stability. (.xlsx)7. The ditectory ‘Reference gene ranking’ contains 2 files in .ods format.Table 1. Reference genes ranking (better-good-average) selected for qPCR analyses only for white semen-producing turkey toms (for studies on healthy individuals). (.ods)Table 2. Reference genes ranking (better-good-average) selected for qPCR analyses across white semen (WS) and yellow semen-producing (YSS )turkey toms (for YSS studies). (.ods)8. The ditectory ‘Semen quality parameters’ contains 1 file in .xlsx format.Table 1. Semen quality parameters. (.xlsx)9. The ditectory ‘Figure’ contains 1 file in .tif format.Figure 1. A graphical presentation of the summary results of comparative delta Ct analysis (A, B), BestKeeper (C, D), NormFinder (E, F), geNorm (G, H), and over final ranking (RefFinder) (I-K) of selected reference genes expression stability in white semen producing turkey toms (A, C, E, G, I, K) and respecting yellow semen syndrome occurrence (B, D, F, H, J, L). A lower value calculated for each gene is associated with higher expression stability. (.tif).