cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14220795.v1
title: Additional file 18 of PDX models reflect the proteome landscape of pediatric acute lymphoblastic leukemia but divert in select pathways

description: Additional file 18.
DOI: 10.6084/m9.figshare.14220816
title: Additional file 7 of PDX models reflect the proteome landscape of pediatric acute lymphoblastic leukemia but divert in select pathways

description: Additional file 7.
DOI: 10.6084/m9.figshare.14220863.v1
title: Additional file 1 of Correction for both common and rare cell types in blood is important to identify genes that correlate with age

description: Additional file 1: Table S1. Samples for which all covariates were available and were included in the analyses. LL, LifeLines DEEP; LLS, Leiden Longevity Study; NTR, Netherlands Twin Registry; RS, Rotterdam Study; IQ, interquartile range; BMI, body mass index; RBC, red blood cells; GC, guanine – cytosine. A RBC count was imputed for all LLS samples (see Methods).
DOI: 10.6084/m9.figshare.14220866
title: Additional file 2 of Correction for both common and rare cell types in blood is important to identify genes that correlate with age

description: Additional file 2: Table S2. Missing values expressed in number and percentage per cohort. Values are number (n) and percentage (%). LL, LifeLines DEEP; LLS, Leiden Longevity Study; NTR, Netherlands Twin Registry; RS, Rotterdam Study.
DOI: 10.6084/m9.figshare.14220857
title: Additional file 10 of Correction for both common and rare cell types in blood is important to identify genes that correlate with age

description: Additional file 10: Table S10. Overlap of IM- and EM-related genes with the known aging-related genes in the GenAge database.
DOI: 10.6084/m9.figshare.14220863
title: Additional file 1 of Correction for both common and rare cell types in blood is important to identify genes that correlate with age

description: Additional file 1: Table S1. Samples for which all covariates were available and were included in the analyses. LL, LifeLines DEEP; LLS, Leiden Longevity Study; NTR, Netherlands Twin Registry; RS, Rotterdam Study; IQ, interquartile range; BMI, body mass index; RBC, red blood cells; GC, guanine – cytosine. A RBC count was imputed for all LLS samples (see Methods).
DOI: 10.6084/m9.figshare.14220869
title: Additional file 3 of Correction for both common and rare cell types in blood is important to identify genes that correlate with age

description: Additional file 3: Table S3. Overview of all 33 imputed white blood cell (WBC) subtypes. The codes of each subtype used in the EM model are reported.
DOI: 10.6084/m9.figshare.14220869.v1
title: Additional file 3 of Correction for both common and rare cell types in blood is important to identify genes that correlate with age

description: Additional file 3: Table S3. Overview of all 33 imputed white blood cell (WBC) subtypes. The codes of each subtype used in the EM model are reported.
DOI: 10.6084/m9.figshare.14220872
title: Additional file 4 of Correction for both common and rare cell types in blood is important to identify genes that correlate with age

description: Additional file 4: Table S4. Summary statistics of gene associations with age for the initial model (this sheet) and the extended model (next sheet).
DOI: 10.6084/m9.figshare.14220866.v1
title: Additional file 2 of Correction for both common and rare cell types in blood is important to identify genes that correlate with age

description: Additional file 2: Table S2. Missing values expressed in number and percentage per cohort. Values are number (n) and percentage (%). LL, LifeLines DEEP; LLS, Leiden Longevity Study; NTR, Netherlands Twin Registry; RS, Rotterdam Study.
DOI: 10.6084/m9.figshare.14220872.v1
title: Additional file 4 of Correction for both common and rare cell types in blood is important to identify genes that correlate with age

description: Additional file 4: Table S4. Summary statistics of gene associations with age for the initial model (this sheet) and the extended model (next sheet).
DOI: 10.6084/m9.figshare.14220875
title: Additional file 5 of Correction for both common and rare cell types in blood is important to identify genes that correlate with age

description: Additional file 5: Table S5. The number of total overlapping genes (upper part), the conservation of direction (middle part) and the percentage of genes associated with aging considering the discovery genes (lower part) is reported. EM, Extended Model; IM, Initial Model; GS1, gene set 1 from [3]; GS2, gene set 2 from [4].
DOI: 10.6084/m9.figshare.14220878.v1
title: Additional file 6 of Correction for both common and rare cell types in blood is important to identify genes that correlate with age

description: Additional file 6: Table S6. Mean squared errors, Pearson correlation coefficient (r) and Spearman correlation coefficient (rho) of residual gene expression with age. LL, LifeLines DEEP; LLS, Leiden Longevity Study; NTR, Netherlands Twin Registry; RS, Rotterdam Study; EM, extended model; IM, initial model; EM-age, extended model without age as covariate; IM-age, initial model without age as covariate.
DOI: 10.6084/m9.figshare.14220857.v1
title: Additional file 10 of Correction for both common and rare cell types in blood is important to identify genes that correlate with age

description: Additional file 10: Table S10. Overlap of IM- and EM-related genes with the known aging-related genes in the GenAge database.
DOI: 10.6084/m9.figshare.14220875.v1
title: Additional file 5 of Correction for both common and rare cell types in blood is important to identify genes that correlate with age

description: Additional file 5: Table S5. The number of total overlapping genes (upper part), the conservation of direction (middle part) and the percentage of genes associated with aging considering the discovery genes (lower part) is reported. EM, Extended Model; IM, Initial Model; GS1, gene set 1 from [3]; GS2, gene set 2 from [4].
DOI: 10.6084/m9.figshare.14220881
title: Additional file 7 of Correction for both common and rare cell types in blood is important to identify genes that correlate with age

description: Additional file 7: Table S7. Correlation coefficients per gene; initial model (im); extended model (em).
DOI: 10.6084/m9.figshare.14220881.v1
title: Additional file 7 of Correction for both common and rare cell types in blood is important to identify genes that correlate with age

description: Additional file 7: Table S7. Correlation coefficients per gene; initial model (im); extended model (em).
DOI: 10.6084/m9.figshare.14220884
title: Additional file 8 of Correction for both common and rare cell types in blood is important to identify genes that correlate with age

description: Additional file 8: Table S8. Enrichment of Reactome pathways, KEGG pathways and GO terms.
DOI: 10.6084/m9.figshare.14220884.v1
title: Additional file 8 of Correction for both common and rare cell types in blood is important to identify genes that correlate with age

description: Additional file 8: Table S8. Enrichment of Reactome pathways, KEGG pathways and GO terms.
DOI: 10.6084/m9.figshare.14220878
title: Additional file 6 of Correction for both common and rare cell types in blood is important to identify genes that correlate with age

description: Additional file 6: Table S6. Mean squared errors, Pearson correlation coefficient (r) and Spearman correlation coefficient (rho) of residual gene expression with age. LL, LifeLines DEEP; LLS, Leiden Longevity Study; NTR, Netherlands Twin Registry; RS, Rotterdam Study; EM, extended model; IM, initial model; EM-age, extended model without age as covariate; IM-age, initial model without age as covariate.
DOI: 10.6084/m9.figshare.14220887
title: Additional file 9 of Correction for both common and rare cell types in blood is important to identify genes that correlate with age

description: Additional file 9: Table S9. Overlap of IM- and EM-related genes with platelet-related genes derived from the GO, KEGG and Reactome enrichments described in Table S8.
DOI: 10.6084/m9.figshare.14220887.v1
title: Additional file 9 of Correction for both common and rare cell types in blood is important to identify genes that correlate with age

description: Additional file 9: Table S9. Overlap of IM- and EM-related genes with platelet-related genes derived from the GO, KEGG and Reactome enrichments described in Table S8.
DOI: 10.6084/m9.figshare.14220920.v1
title: Additional file 2 of The cyclase-associated protein UvCap1 is required for mycelial growth and pathogenicity in the rice false smut fungus

description: Additional file 2 : Table S1. Primers used in this study.
DOI: 10.6084/m9.figshare.14220920
title: Additional file 2 of The cyclase-associated protein UvCap1 is required for mycelial growth and pathogenicity in the rice false smut fungus

description: Additional file 2 : Table S1. Primers used in this study.
DOI: 10.6084/m9.figshare.14220929
title: Additional file 2 of Efficacy and safety of nebivolol in Korean patients with hypertension by age and sex: a subanalysis from the BENEFIT-KOREA study

description: Additional file 2. list of IRB site.
DOI: 10.6084/m9.figshare.14220929.v1
title: Additional file 2 of Efficacy and safety of nebivolol in Korean patients with hypertension by age and sex: a subanalysis from the BENEFIT-KOREA study

description: Additional file 2. list of IRB site.
DOI: 10.6084/m9.figshare.14220932
title: Additional file 1 of Genome-scale model reconstruction of the methylotrophic yeast Ogataea polymorpha

description: Additional file 1 Supplementary information.
DOI: 10.6084/m9.figshare.14220932.v1
title: Additional file 1 of Genome-scale model reconstruction of the methylotrophic yeast Ogataea polymorpha

description: Additional file 1 Supplementary information.
DOI: 10.6084/m9.figshare.14220935
title: Additional file 2 of Genome-scale model reconstruction of the methylotrophic yeast Ogataea polymorpha

description: Additional file 2 Experimental data. Excel sheet with comparison of substrate utilization tests conducted in this paper and Suh et al. [9]. Detailed information on the results of Biolog’s Phenotype Microarray™ plates test, namely (i) a list of substrates with abiotic activity, (ii) for plate PM1: OD490/600 and selection of metabolized substrates, (iii) for plate PM1: OD490/600 and selection of metabolized substrates, (iv) shake flask growth results for the eight substrates not grown in phenotype assay (succinate, D-xylose, D-ribose, α-ketoglutarate, α-ketobutyrate, citrate, fumarate, malate).
DOI: 10.6084/m9.figshare.14220938
title: Additional file 3 of Genome-scale model reconstruction of the methylotrophic yeast Ogataea polymorpha

description: Additional file 3 Genome scale metabolic model details. It contains a list of reactions with only one associated gene-protein-reaction association for which no homolog in O. polymorpha was identified. A list of all genes in iMT1026 for which no homologs were identified in O. polymorpha. Lists of new reactions and new genes added to the model. A table of literature values for growth rates and substrate uptake rates and finally the results of the FSEOF analysis.
DOI: 10.6084/m9.figshare.14220938.v1
title: Additional file 3 of Genome-scale model reconstruction of the methylotrophic yeast Ogataea polymorpha

description: Additional file 3 Genome scale metabolic model details. It contains a list of reactions with only one associated gene-protein-reaction association for which no homolog in O. polymorpha was identified. A list of all genes in iMT1026 for which no homologs were identified in O. polymorpha. Lists of new reactions and new genes added to the model. A table of literature values for growth rates and substrate uptake rates and finally the results of the FSEOF analysis.
DOI: 10.6084/m9.figshare.14220935.v1
title: Additional file 2 of Genome-scale model reconstruction of the methylotrophic yeast Ogataea polymorpha

description: Additional file 2 Experimental data. Excel sheet with comparison of substrate utilization tests conducted in this paper and Suh et al. [9]. Detailed information on the results of Biolog’s Phenotype Microarray™ plates test, namely (i) a list of substrates with abiotic activity, (ii) for plate PM1: OD490/600 and selection of metabolized substrates, (iii) for plate PM1: OD490/600 and selection of metabolized substrates, (iv) shake flask growth results for the eight substrates not grown in phenotype assay (succinate, D-xylose, D-ribose, α-ketoglutarate, α-ketobutyrate, citrate, fumarate, malate).
DOI: 10.6084/m9.figshare.14220968
title: Additional file 4 of Circulating proteins associated with allergy development in infants—an exploratory analysis

description: Additional file 4: Table S3. Proteins differing between samples from PCA clusters.
DOI: 10.6084/m9.figshare.14220971
title: Additional file 5 of Circulating proteins associated with allergy development in infants—an exploratory analysis

description: Additional file 5: Table S4. Antibodies used for exploratory analysis.
DOI: 10.6084/m9.figshare.14220974
title: Additional file 6 of Circulating proteins associated with allergy development in infants—an exploratory analysis

description: Additional file 6: Table S5. Proteome annotation of proteins in exploratory analysis.
DOI: 10.6084/m9.figshare.14220971.v1
title: Additional file 5 of Circulating proteins associated with allergy development in infants—an exploratory analysis

description: Additional file 5: Table S4. Antibodies used for exploratory analysis.
DOI: 10.6084/m9.figshare.14220974.v1
title: Additional file 6 of Circulating proteins associated with allergy development in infants—an exploratory analysis

description: Additional file 6: Table S5. Proteome annotation of proteins in exploratory analysis.
DOI: 10.6084/m9.figshare.14220968.v1
title: Additional file 4 of Circulating proteins associated with allergy development in infants—an exploratory analysis

description: Additional file 4: Table S3. Proteins differing between samples from PCA clusters.
DOI: 10.6084/m9.figshare.14220977.v1
title: Additional file 7 of Circulating proteins associated with allergy development in infants—an exploratory analysis

description: Additional file 7: Table S6. Association to allergic status in samples collected at 1 month (T-test).
DOI: 10.6084/m9.figshare.14220977
title: Additional file 7 of Circulating proteins associated with allergy development in infants—an exploratory analysis

description: Additional file 7: Table S6. Association to allergic status in samples collected at 1 month (T-test).
DOI: 10.6084/m9.figshare.14221016
title: Additional file 10 of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

description: Additional file 10: Table S7. MRC5 phosphoproteins identified. List of all phosphoproteins identified in MRC5 cells or MRC5 cells infected for various times with ChAdOx1 nCoV-19.
DOI: 10.6084/m9.figshare.14221016.v1
title: Additional file 10 of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

description: Additional file 10: Table S7. MRC5 phosphoproteins identified. List of all phosphoproteins identified in MRC5 cells or MRC5 cells infected for various times with ChAdOx1 nCoV-19.
DOI: 10.6084/m9.figshare.14221022.v1
title: Additional file 12 of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

description: Additional file 12: Table S9. A549 phospho Peptide Spectral Matches. List of all phospho peptide spectral matches (PSMs) identified in A549 cells or A549 cells infected for various times with ChAdOx1 nCoV-19.
DOI: 10.6084/m9.figshare.14221025
title: Additional file 13 of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

description: Additional file 13: Table S10. MRC5 Peptide Spectral Matches. List of all peptide spectral matches (PSMs) identified in MRC5 cells or MRC5 cells infected for various times with ChAdOx1 nCoV-19.
DOI: 10.6084/m9.figshare.14221025.v1
title: Additional file 13 of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

description: Additional file 13: Table S10. MRC5 Peptide Spectral Matches. List of all peptide spectral matches (PSMs) identified in MRC5 cells or MRC5 cells infected for various times with ChAdOx1 nCoV-19.
DOI: 10.6084/m9.figshare.14221022
title: Additional file 12 of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

description: Additional file 12: Table S9. A549 phospho Peptide Spectral Matches. List of all phospho peptide spectral matches (PSMs) identified in A549 cells or A549 cells infected for various times with ChAdOx1 nCoV-19.
DOI: 10.6084/m9.figshare.14221028
title: Additional file 14 of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

description: Additional file 14: Table S11. MRC5 phospho Peptide Spectral Matches. List of all phospho peptide spectral matches (PSMs) identified in MRC5 cells or MRC5 cells infected for various times with ChAdOx1 nCoV-19.
DOI: 10.6084/m9.figshare.14221031
title: Additional file 15 of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

description: Additional file 15: Table S12. Integrated transcriptomics and proteomics table, A549 cells. Integrated list of transcriptomic, proteomic and phosphoproteomic changes over time in A549 cells.
DOI: 10.6084/m9.figshare.14221019
title: Additional file 11 of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

description: Additional file 11: Table S8. A549 Peptide Spectral Matches. List of all peptide spectral matches (PSMs) identified in A549 cells or A549 cells infected for various times with ChAdOx1 nCoV-19.
DOI: 10.6084/m9.figshare.14221034
title: Additional file 16 of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

description: Additional file 16: Table S13. Integrated transcriptomics and proteomics table, MRC5 cells. Integrated list of transcriptomic, proteomic and phosphoproteomic changes over time in MRC5 cells.
DOI: 10.6084/m9.figshare.14221034.v1
title: Additional file 16 of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

description: Additional file 16: Table S13. Integrated transcriptomics and proteomics table, MRC5 cells. Integrated list of transcriptomic, proteomic and phosphoproteomic changes over time in MRC5 cells.
DOI: 10.6084/m9.figshare.14221037
title: Additional file 1 of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

description: Additional file 1. Features file. A text file delimiting the locations of known features on the ChAdOx1 nCoV-19 genome.
DOI: 10.6084/m9.figshare.14221031.v1
title: Additional file 15 of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

description: Additional file 15: Table S12. Integrated transcriptomics and proteomics table, A549 cells. Integrated list of transcriptomic, proteomic and phosphoproteomic changes over time in A549 cells.
DOI: 10.6084/m9.figshare.14221037.v1
title: Additional file 1 of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

description: Additional file 1. Features file. A text file delimiting the locations of known features on the ChAdOx1 nCoV-19 genome.
DOI: 10.6084/m9.figshare.14221040
title: Additional file 2 of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

description: Additional file 2. Known human transcripts. A fasta file of human transcripts from the EBI data repository and used for mapping of sequence data to the human transcriptome.
DOI: 10.6084/m9.figshare.14221040.v1
title: Additional file 2 of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

description: Additional file 2. Known human transcripts. A fasta file of human transcripts from the EBI data repository and used for mapping of sequence data to the human transcriptome.
DOI: 10.6084/m9.figshare.14221028.v1
title: Additional file 14 of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

description: Additional file 14: Table S11. MRC5 phospho Peptide Spectral Matches. List of all phospho peptide spectral matches (PSMs) identified in MRC5 cells or MRC5 cells infected for various times with ChAdOx1 nCoV-19.
DOI: 10.6084/m9.figshare.14221043
title: Additional file 3 of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

description: Additional file 3. Proteins search list. The protein search list used in the proteomics analysis.
DOI: 10.6084/m9.figshare.14221043.v1
title: Additional file 3 of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

description: Additional file 3. Proteins search list. The protein search list used in the proteomics analysis.
DOI: 10.6084/m9.figshare.14221049
title: Additional file 5 of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

description: Additional file 5: Table S2. A549 transcript groups. An excel spreadsheet describing the structure of all ChAdOx1 nCoV19 derived transcript groups identified and how many transcripts belong to each group. In addition, it also describes what features are present on each transcript group. This list is the combined data from all time points in A549 cells.
DOI: 10.6084/m9.figshare.14221049.v1
title: Additional file 5 of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

description: Additional file 5: Table S2. A549 transcript groups. An excel spreadsheet describing the structure of all ChAdOx1 nCoV19 derived transcript groups identified and how many transcripts belong to each group. In addition, it also describes what features are present on each transcript group. This list is the combined data from all time points in A549 cells.