cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13544677
title: Additional file 24 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 24: Table S13. Genes that significantly change across time points in liver.
DOI: 10.6084/m9.figshare.13544638.v1
title: Additional file 12 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 12: Table S5. Genes covered by tissue-general and tissue-general changing DMS, or both.
DOI: 10.6084/m9.figshare.13544641
title: Additional file 13 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 13: Table S6. GO terms found for genes associated with tissue-general and tissue-specific changing DMS, subdivided over gene regions and time points.
DOI: 10.6084/m9.figshare.13544665.v1
title: Additional file 20 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 20: Table S9. CpG sites in liver with a significant change in methylation across time points.
DOI: 10.6084/m9.figshare.13544677.v1
title: Additional file 24 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 24: Table S13. Genes that significantly change across time points in liver.
DOI: 10.6084/m9.figshare.13544641.v1
title: Additional file 13 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 13: Table S6. GO terms found for genes associated with tissue-general and tissue-specific changing DMS, subdivided over gene regions and time points.
DOI: 10.6084/m9.figshare.13544665
title: Additional file 20 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 20: Table S9. CpG sites in liver with a significant change in methylation across time points.
DOI: 10.6084/m9.figshare.13544668
title: Additional file 21 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 21: Table S10. CpG sites in RBCs with a significant change in methylation across time points.
DOI: 10.6084/m9.figshare.13544668.v1
title: Additional file 21 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 21: Table S10. CpG sites in RBCs with a significant change in methylation across time points.
DOI: 10.6084/m9.figshare.13544671
title: Additional file 22 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 22: Table S11. Genes that significantly change across time points in hypothalamus.
DOI: 10.6084/m9.figshare.13544707.v1
title: Additional file 33 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 33: Table S14. Number of sites in liver changing in methylation in different gene regions between time point 1 and 2 within genes associated with either Q1 and Q3 or Q2 and Q4 in liver.
DOI: 10.6084/m9.figshare.13544674
title: Additional file 23 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 23: Table S12. Genes that significantly change across time points in ovary.
DOI: 10.6084/m9.figshare.13544710
title: Additional file 34 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 34: Table S15. Number of sites in liver changing in methylation in different gene regions between time point 2 and 3 within genes associated with either Q1 and Q3 or Q2 and Q4 in liver.
DOI: 10.6084/m9.figshare.13544713
title: Additional file 35 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 35: Table S16. Number of sites in RBC changing in methylation in different gene regions between time point 1 and 2 within genes associated with either Q1 and Q3 or Q2 and Q4 in hypothalamus.
DOI: 10.6084/m9.figshare.13544713.v1
title: Additional file 35 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 35: Table S16. Number of sites in RBC changing in methylation in different gene regions between time point 1 and 2 within genes associated with either Q1 and Q3 or Q2 and Q4 in hypothalamus.
DOI: 10.6084/m9.figshare.13544710.v1
title: Additional file 34 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 34: Table S15. Number of sites in liver changing in methylation in different gene regions between time point 2 and 3 within genes associated with either Q1 and Q3 or Q2 and Q4 in liver.
DOI: 10.6084/m9.figshare.13544716.v1
title: Additional file 36 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 36: Table S17. Number of sites in RBC changing in methylation in different gene regions between time point 2 and 3 within genes associated with either Q1 and Q3 or Q2 and Q4 in hypothalamus.
DOI: 10.6084/m9.figshare.13544719
title: Additional file 37 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 37: Table S18. Number of sites in RBC changing in methylation in different gene regions between time point 1 and 2 within genes associated with either Q1 and Q3 or Q2 and Q4 in ovary.
DOI: 10.6084/m9.figshare.13544707
title: Additional file 33 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 33: Table S14. Number of sites in liver changing in methylation in different gene regions between time point 1 and 2 within genes associated with either Q1 and Q3 or Q2 and Q4 in liver.
DOI: 10.6084/m9.figshare.13544725
title: Additional file 39 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 39: Table S20. Number of sites in RBC changing in methylation in different gene regions between time point 1 and 2 within genes associated with either Q1 and Q3 or Q2 and Q4 in liver.
DOI: 10.6084/m9.figshare.13544725.v1
title: Additional file 39 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 39: Table S20. Number of sites in RBC changing in methylation in different gene regions between time point 1 and 2 within genes associated with either Q1 and Q3 or Q2 and Q4 in liver.
DOI: 10.6084/m9.figshare.13544737.v1
title: Additional file 42 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 42: Table S23. Number of CpG sites per tissue (liver, red blood cells (RBCs)) and genomic location (see Methods Lines 545–550). Please note; genomic locations overlap such that a respective CpG sites can be present more than once. Number of genes refers to the total number of genes with (a) CpG site(s) in the respective genomic location and tissue.
DOI: 10.6084/m9.figshare.13544674.v1
title: Additional file 23 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 23: Table S12. Genes that significantly change across time points in ovary.
DOI: 10.6084/m9.figshare.13544722.v1
title: Additional file 38 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 38: Table S19. Number of sites in RBC changing in methylation in different gene regions between time point 2 and 3 within genes associated with either Q1 and Q3 or Q2 and Q4 in ovary.
DOI: 10.6084/m9.figshare.13544671.v1
title: Additional file 22 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 22: Table S11. Genes that significantly change across time points in hypothalamus.
DOI: 10.6084/m9.figshare.13544716
title: Additional file 36 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 36: Table S17. Number of sites in RBC changing in methylation in different gene regions between time point 2 and 3 within genes associated with either Q1 and Q3 or Q2 and Q4 in hypothalamus.
DOI: 10.6084/m9.figshare.13544731
title: Additional file 40 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 40: Table S21. Number of sites in RBC changing in methylation in different gene regions between time point 2 and 3 within genes associated with either Q1 and Q3 or Q2 and Q4 in liver.
DOI: 10.6084/m9.figshare.13544731.v1
title: Additional file 40 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 40: Table S21. Number of sites in RBC changing in methylation in different gene regions between time point 2 and 3 within genes associated with either Q1 and Q3 or Q2 and Q4 in liver.
DOI: 10.6084/m9.figshare.13544722
title: Additional file 38 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 38: Table S19. Number of sites in RBC changing in methylation in different gene regions between time point 2 and 3 within genes associated with either Q1 and Q3 or Q2 and Q4 in ovary.
DOI: 10.6084/m9.figshare.13544737
title: Additional file 42 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 42: Table S23. Number of CpG sites per tissue (liver, red blood cells (RBCs)) and genomic location (see Methods Lines 545–550). Please note; genomic locations overlap such that a respective CpG sites can be present more than once. Number of genes refers to the total number of genes with (a) CpG site(s) in the respective genomic location and tissue.
DOI: 10.6084/m9.figshare.13544746
title: Additional file 45 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 45: Table S26. Methylation levels per sites for females in time point 2 and 3 within the genes of which qPCR data is available.
DOI: 10.6084/m9.figshare.13544746.v1
title: Additional file 45 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 45: Table S26. Methylation levels per sites for females in time point 2 and 3 within the genes of which qPCR data is available.
DOI: 10.6084/m9.figshare.13544734
title: Additional file 41 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 41: Table S22. Details on library preparation and sequencing.
DOI: 10.6084/m9.figshare.13544734.v1
title: Additional file 41 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 41: Table S22. Details on library preparation and sequencing.
DOI: 10.6084/m9.figshare.13544743
title: Additional file 44 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 44: Table S25. Methylation levels per CpG site for females in time point 1 and 2 within the genes of which qPCR data is available.
DOI: 10.6084/m9.figshare.13544749.v1
title: Additional file 46 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 46: Table S27. Expression levels of the individual genes from [39] for which all females show ≥10x coverage for associated CpG sites.
DOI: 10.6084/m9.figshare.13544749
title: Additional file 46 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 46: Table S27. Expression levels of the individual genes from [39] for which all females show ≥10x coverage for associated CpG sites.
DOI: 10.6084/m9.figshare.13544719.v1
title: Additional file 37 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 37: Table S18. Number of sites in RBC changing in methylation in different gene regions between time point 1 and 2 within genes associated with either Q1 and Q3 or Q2 and Q4 in ovary.
DOI: 10.6084/m9.figshare.13544770
title: Additional file 9 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 9: Table S2. CpG sites that showed a differential change between time point 1 and 2 in either RBCs, liver or in both tissues.
DOI: 10.6084/m9.figshare.13544740.v1
title: Additional file 43 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 43: Table S24. Females differed significantly in mean and variance in methylation across all sites in both RBC and liver, as well as when considering only the promoter regions or TSS.
DOI: 10.6084/m9.figshare.13544743.v1
title: Additional file 44 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 44: Table S25. Methylation levels per CpG site for females in time point 1 and 2 within the genes of which qPCR data is available.
DOI: 10.6084/m9.figshare.13544767.v1
title: Additional file 8 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 8: Table S1. CpG sites (n = 302,647) in both red blood cells and liver for which all females show ≥10x coverage.
DOI: 10.6084/m9.figshare.13544770.v1
title: Additional file 9 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 9: Table S2. CpG sites that showed a differential change between time point 1 and 2 in either RBCs, liver or in both tissues.
DOI: 10.6084/m9.figshare.13544740
title: Additional file 43 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 43: Table S24. Females differed significantly in mean and variance in methylation across all sites in both RBC and liver, as well as when considering only the promoter regions or TSS.
DOI: 10.6084/m9.figshare.13544767
title: Additional file 8 of Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

description: Additional file 8: Table S1. CpG sites (n = 302,647) in both red blood cells and liver for which all females show ≥10x coverage.
DOI: 10.6084/m9.figshare.13572080.v1
title: Additional file 2 of Clinical laboratory test-wide association scan of polygenic scores identifies biomarkers of complex disease

description: Additional file 2: Contains all supplementary tables. Table S1. Descriptive statistics generated by the QualityLab pipeline. Table S2. Lipid-altering medications abstracted from free text in clinical notes. Table S3. Characteristics of patients with clean lab and genotyping data. Table S4. Estimates of SNP-based heritability and sample sizes for all labs passing QualityLab using REML. Table S5. Estimates of SNP-based heritability for blood lipid levels across study populations and estimation methods. Table S6. LabWAS of HDLPGS in the European sample in BioVU. Table S7. LabWAS of HDLPGS in the African sample in BioVU. Table S8. LabWAS of LDLPGS in the European sample in BioVU. Table S9. LabWAS of LDLPGS in the African sample in BioVU. Table S10. LabWAS of TGPGS in the European sample in BioVU. Table S11. LabWAS of TGPGS in the African sample in BioVU. Table S12. LabWAS of CADPGS in the European sample in BioVU. Table S13. LabWAS of CADPGS in the European sample in BioVU controlling for CAD diagnosis. Table S14. LabWAS of CADPGS in the African sample in BioVU. Table S15. LabWAS of CADPGS in the African sample in BioVU controlling for CAD diagnosis. Table S16. LabWAS of CAD diagnosis in the European sample in BioVU. Table S17. LabWAS of HDLPGS in the European sample in MGB. Table S18. LabWAS of LDLPGS in the European sample in MGB. Table S19. LabWAS of TGPGS in the European sample in MGB. Table S20. LabWAS of CADPGS in the European sample in MGB. Table S21. LabWAS of CADPGS in the European sample in MGB controlling for CAD diagnosis. Table S22. The GWAS Catalog study accession numbers for summary statistics from GWAS of each lab trait.
DOI: 10.6084/m9.figshare.13572080
title: Additional file 2 of Clinical laboratory test-wide association scan of polygenic scores identifies biomarkers of complex disease

description: Additional file 2: Contains all supplementary tables. Table S1. Descriptive statistics generated by the QualityLab pipeline. Table S2. Lipid-altering medications abstracted from free text in clinical notes. Table S3. Characteristics of patients with clean lab and genotyping data. Table S4. Estimates of SNP-based heritability and sample sizes for all labs passing QualityLab using REML. Table S5. Estimates of SNP-based heritability for blood lipid levels across study populations and estimation methods. Table S6. LabWAS of HDLPGS in the European sample in BioVU. Table S7. LabWAS of HDLPGS in the African sample in BioVU. Table S8. LabWAS of LDLPGS in the European sample in BioVU. Table S9. LabWAS of LDLPGS in the African sample in BioVU. Table S10. LabWAS of TGPGS in the European sample in BioVU. Table S11. LabWAS of TGPGS in the African sample in BioVU. Table S12. LabWAS of CADPGS in the European sample in BioVU. Table S13. LabWAS of CADPGS in the European sample in BioVU controlling for CAD diagnosis. Table S14. LabWAS of CADPGS in the African sample in BioVU. Table S15. LabWAS of CADPGS in the African sample in BioVU controlling for CAD diagnosis. Table S16. LabWAS of CAD diagnosis in the European sample in BioVU. Table S17. LabWAS of HDLPGS in the European sample in MGB. Table S18. LabWAS of LDLPGS in the European sample in MGB. Table S19. LabWAS of TGPGS in the European sample in MGB. Table S20. LabWAS of CADPGS in the European sample in MGB. Table S21. LabWAS of CADPGS in the European sample in MGB controlling for CAD diagnosis. Table S22. The GWAS Catalog study accession numbers for summary statistics from GWAS of each lab trait.
DOI: 10.6084/m9.figshare.13534295.v1
title: Additional file 14 of mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

description: Additional file 14: Table S7. Summary of power test for simulated mix panels. Full version of Table 2. The first sheet includes all designed panels; and sheet 2 ~ 4 filtered on variable ‘Bias’. Sheet 2 presents the panels when half of linked markers are SNPs and the other half of linked markers are STRs; Sheet 3 presents the panels with more linked SNPs than linked STRs; Sheet 4 presents the panels with more linked STRs than linked SNPs.
DOI: 10.6084/m9.figshare.13534283
title: Additional file 10 of mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

description: Additional file 10: Table S3. Table of heterozygosity for example dataset- ‘mixexample’. In each cell, the status of heterozygosity -0 (homozygous) or 1 (heterozygous), for the individual of this row at this locus is presented. Column names are markers’ names, and the row names are individuals.
DOI: 10.6084/m9.figshare.13534295
title: Additional file 14 of mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

description: Additional file 14: Table S7. Summary of power test for simulated mix panels. Full version of Table 2. The first sheet includes all designed panels; and sheet 2 ~ 4 filtered on variable ‘Bias’. Sheet 2 presents the panels when half of linked markers are SNPs and the other half of linked markers are STRs; Sheet 3 presents the panels with more linked SNPs than linked STRs; Sheet 4 presents the panels with more linked STRs than linked SNPs.
DOI: 10.6084/m9.figshare.13534289
title: Additional file 12 of mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

description: Additional file 12: Table S5. Simulations for expected number of heterozygous loci (K) for the example dataset- ‘mixexample’. The first row (also the column names) is the number of heterozygous loci (K) from 0 to 100; and the first column is the index of simulations 1 to 500. Each row denotes each simulation and shows one distribution of K.
DOI: 10.6084/m9.figshare.13534289.v1
title: Additional file 12 of mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

description: Additional file 12: Table S5. Simulations for expected number of heterozygous loci (K) for the example dataset- ‘mixexample’. The first row (also the column names) is the number of heterozygous loci (K) from 0 to 100; and the first column is the index of simulations 1 to 500. Each row denotes each simulation and shows one distribution of K.
DOI: 10.6084/m9.figshare.13534319
title: Additional file 8 of mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

description: Additional file 8: Table S1. Genotypes of example dataset—‘mixexample’. The raw genotypes of the example data. Each row denotes each individual and each column denotes each marker.
DOI: 10.6084/m9.figshare.13534286.v1
title: Additional file 11 of mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

description: Additional file 11: Table S4. Table of shared alleles for example dataset- ‘mixexample’. In each cell, the number of shared alleles -0 or 1 or 2, for the pair of individuals of this row at this locus is presented. Column names are markers’ names, and the row names are pairs of individuals.
DOI: 10.6084/m9.figshare.13534322
title: Additional file 9 of mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

description: Additional file 9: Table S2. Table of allele frequency (expected) for example dataset- ‘mixexample’. Each column denotes each marker. The first column lists all alleles appeared at all loci-0, 1, 2, 3, 4, and 5. There is the probability of the allele of this row at the locus of this column.