cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14759828.v1
title: Additional file 2 of Sex-specific recombination patterns predict parent of origin for recurrent genomic disorders

description: Additional file 2: Table S1. Exclusion/Inclusion statuses and literature search results of genomic disorder loci conducted January 2021.
DOI: 10.6084/m9.figshare.14759820.v1
title: Additional file 1 of Genetic and morphological estimates of androgen exposure predict social deficits in multiple neurodevelopmental disorder cohorts

description: Additional file 1: Table 1. Counts of individuals with reported genetic syndromes in devGenes. Table 2. Parent-report items in devGenes. Reliability for each domain wasassessed using Cronbach's alpha. Table 3. Individual-level data for devGenes participants. The results of ouranalyses may be reproduced using code available at https://research-git.uiowa.edu/michaelson-lab-public/facial-masculinity-2021 . Table 4. Factor loadings for devGenes parent-report items. Table 5. Counts of autosomal genes in GO terms related to androgen signaling and sex differentiation.
DOI: 10.6084/m9.figshare.14759799.v1
title: Additional file 1 of Glycoproteomics identifies HOMER3 as a potentially targetable biomarker triggered by hypoxia and glucose deprivation in bladder cancer

description: Additional file 1.
DOI: 10.5281/zenodo.4922063
title: Molecular dynamics simulation data of a toy model (epsilon = 2.5 kJ/mol)

description: Molecular dynamics simulations of a toy model (after PBC treatment and pocket-ligand only coordinates). More details can be found here: https://chemrxiv.org/articles/preprint/Estimation_of_Binding_Rates_and_Affinities_from_Multiensemble_Markov_Models_and_Ligand_Decoupling/14728206/1
DOI: 10.5281/zenodo.4922062
title: Molecular dynamics simulation data of a toy model (epsilon = 2.5 kJ/mol)

description: Molecular dynamics simulations of a toy model (after PBC treatment and pocket-ligand only coordinates). More details can be found here: https://chemrxiv.org/articles/preprint/Estimation_of_Binding_Rates_and_Affinities_from_Multiensemble_Markov_Models_and_Ligand_Decoupling/14728206/1
DOI: 10.6084/m9.figshare.14759774.v1
title: Additional file 9 of The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis

description: Additional file 9: Supplemental Table 6. Summary of the linear model test of all the identified TE-gene loci pairs. A. AT2 linear model analysis summary. B. AM linear model analysis summary. The association between the log2-transformed TE expression (independent variable) and the log2-transformed gene expression (dependent variable) was tested using a linear model. Genes, TE locus, distance from the gene and the genomic region of the TE locus are shown. The p value1 represents relationship between gene expression and adjacent TE-locus expression, and the p value2 - represent difference in the regression slopes between the two groups (IPF and donor). The p-value correction was performed using the Benjamini and Hochberg (BH) test and (p.adjust1 and p.adjust2).
DOI: 10.6084/m9.figshare.14759771.v1
title: Additional file 8 of The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis

description: Additional file 8: Supplemental Table 5. Summary of the differential analysis of the TE loci and genes between the IPF patients and the donors in different cells. A. Whole-lung (WL) tissue, B. Alveolar type II (AT2) cells. C. Alveolar macrophages (AM). The columns represent the gene expression base mean (baseMean), log2 fold change (log2FoldChange), lfcSE (log fold standard error), stat (Wald statistics; lfc/standard error), p-value, p.adj (BH adjusted p-value). The plus and minus signs next to the gene names indicate the gene orientation.
DOI: 10.6084/m9.figshare.14759768.v1
title: Additional file 7 of The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis

description: Additional file 7: Supplemental Table 4. Summary of the differential analysis and correlation between the L1HS and their functionally related genes in AT2 cells. A. Manually curated list of genes known to be part of the L1HS defense and antiviral interferon-stimulating genes [25, 39]. B. List of all significant differentially expressed genes in AT2 cells, with functional annotation of L1HS related genes. Only significant genes are shown. The columns represent the gene names, gene expression base mean (baseMean), log2 fold change (log2FoldChange), lfcSE (log fold standard error), stat (Wald statistics; lfc/standard error), p-value, p.adj (BH adjusted p-value). C. Summary of the linear model test of association between the expression of L1HS -related genes and L1HS. The p value1 represents relationship between gene expression and L1HS-locus expression, and the p value2 - represent difference in the regression slopes between the two groups (IPF and donor). The p-value correction was performed using the Benjamini and Hochberg (BH) test and (p.adjust1 and p.adjust2). Model: Gene expression∼L1HS expression + group (IPF/Donor).
DOI: 10.6084/m9.figshare.14759765.v1
title: Additional file 6 of The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis

description: Additional file 6: Supplemental Table 3. Summary of the differential analysis of the TE families between the IPF patients and the donors in AT2 cells based on genomics regions and SQuIRE and REdiscoverTE analysis. A. Differential TE expression in exonic region in AT2 cells – RediscoverTE. B. Differential TE expression in intronic region in AT2 cells – RediscoverTE. C. Differential TE expression in intergenic region in AT2 cells– RediscoverTE. D. Summary of all changes obtained by SQuIRE and REdiscoverTE. E. Differential TE expression in intergenic region in AT2 cells- SQuIRE. Only significant TE families are shown. The columns represent the repeat classification, TE expression base mean (baseMean), log2 fold change (log2FoldChange), lfcSE (log fold standard error), stat (Wald statistics; lfc/standard error), p-value, p.adj (BH adjusted p-value).
DOI: 10.6084/m9.figshare.14759762.v1
title: Additional file 5 of The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis

description: Additional file 5: Supplemental Table 2. Summary of the differential analysis of the TE families between the IPF patients and the donors in different cells based on SQuIRE and REdiscoverTE analysis. A. Whole-lung (WL) tissue - SQuIRE, B. Alveolar type II (AT2) cells - SQuIRE. C. Alveolar macrophages (AM) - SQuIRE. D. Whole-lung (WL) tissue - REdiscoverTE, E. Alveolar type II (AT2) cells - REdiscoverTE. F. Alveolar macrophages (AM) - REdiscoverTE. The columns represent the repeat classification, the TE expression base mean (baseMean), log2 fold change (log2FoldChange), lfcSE (log fold standard error), stat (Wald statistics; lfc/standard error), p-value, p.adj (BH adjusted p-value). Only significant upregulated families are shown. G. Summary of all changes in REdiscoverTE analysis.
DOI: 10.6084/m9.figshare.14759759.v1
title: Additional file 4 of The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis

description: Additional file 4: Supplemental Table 1. Summary of the samples used in the bulk RNA-seq and scRNA-seq analyses. Each row represents the sample ID, while the columns indicate the histological types, age, sex, race, smoking history, and phenotype, as reported in the original publication [18]. All the fibrosis samples are grouped and analyzed together, as indicated in the table (analyzed phenotype. HP: hypersensitivity pneumonitis; ILD: interstitial lung disease; IPF: idiopathic pulmonary fibrosis; NA: not available; SSc: systemic sclerosis. An additional sample description can be obtained from the original manuscript.
DOI: 10.6084/m9.figshare.14759744.v1
title: Additional file 10 of The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis

description: Additional file 10: Supplemental Table 7. Summary of the differential analysis of the genes and TEs per individual cell type in the scRNA-seq. Table 5A. Cell number for each subject in each cell type. B. Differentially expressed genes in IPF vs Donor for all cell types. Avg_logFC: Average log fold change; p-value: calculated based on the Wilcoxon rank-sum test; p.adjust: adjusted p-value based on the Bonferroni correction using all the genes in the dataset; pct.1: fraction of the cells that express the gene in IPF patients; pct.2: fraction of the cells that express the gene in donors. C. Differentially expressed TE families in the IPF patient vs. donor samples for the different cell types. D. Differences between the IPF patients and donors represented as correlation between L1 score and TE-related gene expression. A subset of 126 genes identified in RNA bulk seq were tested. A linear model was fitted for each L1 score and the gene pairs. The p-value was calculated using t-test; p.adjust is the Benjamini and Hochberg (BH)-adjusted p-value.
DOI: 10.6084/m9.figshare.14760177
title: S5 Dataset

description: GPR37L1 positive DRG neurons<br>
DOI: 10.6084/m9.figshare.14760177.v1
title: S5 Dataset

description: GPR37L1 positive DRG neurons<br>
DOI: 10.6084/m9.figshare.14759724.v1
title: Additional file 1 of Impact of sociodemographic factors on the consumption of tubers in Brazil

description: Additional file 1.
DOI: 10.6084/m9.figshare.14759718.v1
title: Additional file 9 of Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment

description: Additional file 9: Table S8. Differentially expressed genes in Alzheimer’s disease patients vs. normal controls for each cell type.
DOI: 10.6084/m9.figshare.14759715.v1
title: Additional file 8 of Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment

description: Additional file 8: Table S7. Differentially expressed genes in brain endothelial cells by comparing APOE genotype E3/E3 and E4/E4 in Alzheimer’s disease patients.
DOI: 10.6084/m9.figshare.14759712.v1
title: Additional file 7 of Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment

description: Additional file 7: Table S6. Differentially expressed genes in brain endothelial cells vs. other cell types.
DOI: 10.6084/m9.figshare.14759709.v1
title: Additional file 6 of Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment

description: Additional file 6: Table S5. Raw data and network analysis results of the nodes in Fig. 2b.
DOI: 10.6084/m9.figshare.14759703.v1
title: Additional file 4 of Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment

description: Additional file 4: Table S3. Alzheimer’s disease markers and their expressions.
DOI: 10.6084/m9.figshare.14759700.v1
title: Additional file 3 of Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment

description: Additional file 3: Table S2. Neurological diseases-associated genes/proteins.
DOI: 10.6084/m9.figshare.14759697.v1
title: Additional file 2 of Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment

description: Additional file 2: Table S1. SARS-CoV-2 host factor datasets.
DOI: 10.6084/m9.figshare.14759556.v1
title: Additional file 1 of Expanding the taxonomic range in the fecal metagenome

description: Additional file 1. File containing all scripts and information for benchmarking simulations. This information is also available at the link: https://github.com/theo-allnutt-bioinformatics/Allnutt_etal_2020_expanding_the_taxonomic .
DOI: 10.6084/m9.figshare.14759511.v1
title: Additional file 1 of Duloxetine versus ‘active’ placebo, placebo or no intervention for major depressive disorder; a protocol for a systematic review of randomised clinical trials with meta-analysis and trial sequential analysis

description: Additional file 1:. Table 1. Types of antidepressants.
DOI: 10.6084/m9.figshare.14759507.v1
title: Additional file 3 of Overexpression of DDIT4 and TPTEP1 are associated with metastasis and advanced stages in colorectal cancer patients: a study utilizing bioinformatics prediction and experimental validation

description: Additional file 3: Table S2. Information of miRNA-mRNA network for 11 key genes.
DOI: 10.6084/m9.figshare.14759403.v1
title: Additional file 14 of The Wnt-specific astacin proteinase HAS-7 restricts head organizer formation in Hydra

description: Additional file 14: The individual data values for Figs. 3f and 5f.
DOI: 10.6084/m9.figshare.14759355.v1
title: Additional file 1 of The Patient, Investigator, Nurse, Carer Questionnaire (PINC-Q): a cross-sectional, retrospective, non-interventional study exploring the impact of less frequent medication administration with paliperidone palmitate 3-monthly as maintenance treatment for schizophrenia

description: Additional file 1. Details of Independent Ethics Committees involved in the PINC-Q study. Excel table containing details of Independent Ethics Committees involved in the PINC-Q study.
DOI: 10.6084/m9.figshare.14759906
title: Additional file 9 of Genome-wide association analysis of adaptation to oxygen stress in Nile tilapia (Oreochromis niloticus)

description: Additional file 9: Supplementary Table 3. Information of genome-wide significant and suggestive SNPs in the normoxic environment.
DOI: 10.6084/m9.figshare.14759903
title: Additional file 8 of Genome-wide association analysis of adaptation to oxygen stress in Nile tilapia (Oreochromis niloticus)

description: Additional file 8: Supplementary Table 2. Information of genome-wide significant and suggestive SNPs in the hypoxic environment.
DOI: 10.6084/m9.figshare.14759900
title: Additional file 7 of Genome-wide association analysis of adaptation to oxygen stress in Nile tilapia (Oreochromis niloticus)

description: Additional file 7: Supplementary Table 1. Measurements of dissolved oxygen in the normoxic and hypoxic environments.
DOI: 10.6084/m9.figshare.14759873
title: Additional file 13 of Genome-wide association analysis of adaptation to oxygen stress in Nile tilapia (Oreochromis niloticus)

description: Additional file 13: Supplementary Table 7. Functional enrichment for the whole growth stage across the two environments by meta-analysis.
DOI: 10.6084/m9.figshare.14759870
title: Additional file 12 of Genome-wide association analysis of adaptation to oxygen stress in Nile tilapia (Oreochromis niloticus)

description: Additional file 12: Supplementary Table 6. Functional enrichment for the early stage in the normoxic environment.
DOI: 10.6084/m9.figshare.14759867
title: Additional file 11 of Genome-wide association analysis of adaptation to oxygen stress in Nile tilapia (Oreochromis niloticus)

description: Additional file 11: Supplementary Table 5. Functional enrichment for the early stage in the hypoxic environment.
DOI: 10.6084/m9.figshare.14759864
title: Additional file 10 of Genome-wide association analysis of adaptation to oxygen stress in Nile tilapia (Oreochromis niloticus)

description: Additional file 10: Supplementary Table 4. Information of genome-wide significant SNPs across the two environments by meta-analysis.
DOI: 10.6084/m9.figshare.14759837
title: Additional file 4 of Sex-specific recombination patterns predict parent of origin for recurrent genomic disorders

description: Additional file 4: Table S4. Logistic regression data for 1977 CNVs.
DOI: 10.6084/m9.figshare.14759831
title: Additional file 3 of Sex-specific recombination patterns predict parent of origin for recurrent genomic disorders

description: Additional file 3: Table S2. List of 1268 search results curated from literature search.
DOI: 10.6084/m9.figshare.14759828
title: Additional file 2 of Sex-specific recombination patterns predict parent of origin for recurrent genomic disorders

description: Additional file 2: Table S1. Exclusion/Inclusion statuses and literature search results of genomic disorder loci conducted January 2021.
DOI: 10.6084/m9.figshare.14759820
title: Additional file 1 of Genetic and morphological estimates of androgen exposure predict social deficits in multiple neurodevelopmental disorder cohorts

description: Additional file 1: Table 1. Counts of individuals with reported genetic syndromes in devGenes. Table 2. Parent-report items in devGenes. Reliability for each domain wasassessed using Cronbach's alpha. Table 3. Individual-level data for devGenes participants. The results of ouranalyses may be reproduced using code available at https://research-git.uiowa.edu/michaelson-lab-public/facial-masculinity-2021 . Table 4. Factor loadings for devGenes parent-report items. Table 5. Counts of autosomal genes in GO terms related to androgen signaling and sex differentiation.
DOI: 10.6084/m9.figshare.14759799
title: Additional file 1 of Glycoproteomics identifies HOMER3 as a potentially targetable biomarker triggered by hypoxia and glucose deprivation in bladder cancer

description: Additional file 1.
DOI: 10.6084/m9.figshare.14759783
title: Additional file 1 of Using four decades of FDA orphan drug designations to describe trends in rare disease drug development: substantial growth seen in development of drugs for rare oncologic, neurologic, and pediatric-onset diseases

description: Additional file 1. Data Appendix.
DOI: 10.6084/m9.figshare.14759774
title: Additional file 9 of The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis

description: Additional file 9: Supplemental Table 6. Summary of the linear model test of all the identified TE-gene loci pairs. A. AT2 linear model analysis summary. B. AM linear model analysis summary. The association between the log2-transformed TE expression (independent variable) and the log2-transformed gene expression (dependent variable) was tested using a linear model. Genes, TE locus, distance from the gene and the genomic region of the TE locus are shown. The p value1 represents relationship between gene expression and adjacent TE-locus expression, and the p value2 - represent difference in the regression slopes between the two groups (IPF and donor). The p-value correction was performed using the Benjamini and Hochberg (BH) test and (p.adjust1 and p.adjust2).
DOI: 10.6084/m9.figshare.14759771
title: Additional file 8 of The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis

description: Additional file 8: Supplemental Table 5. Summary of the differential analysis of the TE loci and genes between the IPF patients and the donors in different cells. A. Whole-lung (WL) tissue, B. Alveolar type II (AT2) cells. C. Alveolar macrophages (AM). The columns represent the gene expression base mean (baseMean), log2 fold change (log2FoldChange), lfcSE (log fold standard error), stat (Wald statistics; lfc/standard error), p-value, p.adj (BH adjusted p-value). The plus and minus signs next to the gene names indicate the gene orientation.
DOI: 10.6084/m9.figshare.14759768
title: Additional file 7 of The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis

description: Additional file 7: Supplemental Table 4. Summary of the differential analysis and correlation between the L1HS and their functionally related genes in AT2 cells. A. Manually curated list of genes known to be part of the L1HS defense and antiviral interferon-stimulating genes [25, 39]. B. List of all significant differentially expressed genes in AT2 cells, with functional annotation of L1HS related genes. Only significant genes are shown. The columns represent the gene names, gene expression base mean (baseMean), log2 fold change (log2FoldChange), lfcSE (log fold standard error), stat (Wald statistics; lfc/standard error), p-value, p.adj (BH adjusted p-value). C. Summary of the linear model test of association between the expression of L1HS -related genes and L1HS. The p value1 represents relationship between gene expression and L1HS-locus expression, and the p value2 - represent difference in the regression slopes between the two groups (IPF and donor). The p-value correction was performed using the Benjamini and Hochberg (BH) test and (p.adjust1 and p.adjust2). Model: Gene expression∼L1HS expression + group (IPF/Donor).
DOI: 10.6084/m9.figshare.14759765
title: Additional file 6 of The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis

description: Additional file 6: Supplemental Table 3. Summary of the differential analysis of the TE families between the IPF patients and the donors in AT2 cells based on genomics regions and SQuIRE and REdiscoverTE analysis. A. Differential TE expression in exonic region in AT2 cells – RediscoverTE. B. Differential TE expression in intronic region in AT2 cells – RediscoverTE. C. Differential TE expression in intergenic region in AT2 cells– RediscoverTE. D. Summary of all changes obtained by SQuIRE and REdiscoverTE. E. Differential TE expression in intergenic region in AT2 cells- SQuIRE. Only significant TE families are shown. The columns represent the repeat classification, TE expression base mean (baseMean), log2 fold change (log2FoldChange), lfcSE (log fold standard error), stat (Wald statistics; lfc/standard error), p-value, p.adj (BH adjusted p-value).
DOI: 10.6084/m9.figshare.14759762
title: Additional file 5 of The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis

description: Additional file 5: Supplemental Table 2. Summary of the differential analysis of the TE families between the IPF patients and the donors in different cells based on SQuIRE and REdiscoverTE analysis. A. Whole-lung (WL) tissue - SQuIRE, B. Alveolar type II (AT2) cells - SQuIRE. C. Alveolar macrophages (AM) - SQuIRE. D. Whole-lung (WL) tissue - REdiscoverTE, E. Alveolar type II (AT2) cells - REdiscoverTE. F. Alveolar macrophages (AM) - REdiscoverTE. The columns represent the repeat classification, the TE expression base mean (baseMean), log2 fold change (log2FoldChange), lfcSE (log fold standard error), stat (Wald statistics; lfc/standard error), p-value, p.adj (BH adjusted p-value). Only significant upregulated families are shown. G. Summary of all changes in REdiscoverTE analysis.
DOI: 10.6084/m9.figshare.14759759
title: Additional file 4 of The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis

description: Additional file 4: Supplemental Table 1. Summary of the samples used in the bulk RNA-seq and scRNA-seq analyses. Each row represents the sample ID, while the columns indicate the histological types, age, sex, race, smoking history, and phenotype, as reported in the original publication [18]. All the fibrosis samples are grouped and analyzed together, as indicated in the table (analyzed phenotype. HP: hypersensitivity pneumonitis; ILD: interstitial lung disease; IPF: idiopathic pulmonary fibrosis; NA: not available; SSc: systemic sclerosis. An additional sample description can be obtained from the original manuscript.