cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.7qz7rv
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Occurrence evidence, Living Specimen, Human Observation)",
 "Continent is North America",
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Satan eurystomus Hubbs & Bailey, 1947"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001630-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z9659e
title: Occurrence Download

description: A dataset containing 181304 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Festuca arundinacea Schreb.)",
 "BasisOfRecord is one of (Machine Observation, Human Observation, Observation, Literature Occurrence)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 181304 records from 790 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001625-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28516919
title: Tidal river flooding_submitted to Earth's Future

description: Research Data <br>
DOI: 10.15468/dl.9xgzch
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Lithocarpus paviei (Hickel & A.Camus) A.Camus"
 ]
}

 The dataset includes 6 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001633-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mzwzdn
title: Occurrence Download

description: A dataset containing 438 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Italy",
 "OccurrenceStatus is Present",
 "TaxonKey is Tilia platyphyllos Scop."
 ]
}

 The dataset includes 438 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001635-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bmhghn
title: Occurrence Download

description: A dataset containing 66 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Material sample)",
 "Continent is Asia",
 "Country is Bangladesh",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Macaca mulatta (Zimmermann, 1780)"
 ]
}

 The dataset includes 66 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001676-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28516930
title: Additional file 2 of Molecular evolution of dietary shifts in ladybird beetles (Coleoptera: Coccinellidae): from fungivory to carnivory and herbivory

description: Additional file 2. Table SE1. Information on Coccinellidae and other Coleoptera taxa analyzed in this study. Table SE2: Information on the transcriptomes analyzed in this study. Table SE3: Ortholog groups (OGs) under selection, significant expansions and contractions, clade-specific gene loss, or lineage-specific de novo gene emergence based on our genomic and transcriptomic data. Table SE4: Results of ortholog group (OG) enrichment analysis of differentially expressed genes (DEGs) in six carnivorous ladybird species when treated with different diets. Table SE5: Gene expression in diet- and tissue-specific transcriptomes. Table SE6: Candidate ortholog groups (OG) associated with chemosensation, detoxification, digestion, and immunity.
DOI: 10.6084/m9.figshare.28516930.v1
title: Additional file 2 of Molecular evolution of dietary shifts in ladybird beetles (Coleoptera: Coccinellidae): from fungivory to carnivory and herbivory

description: Additional file 2. Table SE1. Information on Coccinellidae and other Coleoptera taxa analyzed in this study. Table SE2: Information on the transcriptomes analyzed in this study. Table SE3: Ortholog groups (OGs) under selection, significant expansions and contractions, clade-specific gene loss, or lineage-specific de novo gene emergence based on our genomic and transcriptomic data. Table SE4: Results of ortholog group (OG) enrichment analysis of differentially expressed genes (DEGs) in six carnivorous ladybird species when treated with different diets. Table SE5: Gene expression in diet- and tissue-specific transcriptomes. Table SE6: Candidate ortholog groups (OG) associated with chemosensation, detoxification, digestion, and immunity.
DOI: 10.6084/m9.figshare.28516934
title: Additional file 1 of Characterization and chemoproteomic profiling of protein O-GlcNAcylation in SOD1-G93A mouse model

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.28516934.v1
title: Additional file 1 of Characterization and chemoproteomic profiling of protein O-GlcNAcylation in SOD1-G93A mouse model

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.28516937
title: Additional file 2 of Characterization and chemoproteomic profiling of protein O-GlcNAcylation in SOD1-G93A mouse model

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.28516937.v1
title: Additional file 2 of Characterization and chemoproteomic profiling of protein O-GlcNAcylation in SOD1-G93A mouse model

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.28516957
title: Additional file 2 of Global and regional incidence of intrahepatic cholestasis of pregnancy: a systematic review and meta-analysis

description: Additional File 2. Study level data used to produce the results.
DOI: 10.6084/m9.figshare.28516957.v1
title: Additional file 2 of Global and regional incidence of intrahepatic cholestasis of pregnancy: a systematic review and meta-analysis

description: Additional File 2. Study level data used to produce the results.
DOI: 10.6084/m9.figshare.28517008
title: Additional file 1 of Admixture as a source for HLA variation in Neolithic European farming communities

description: Additional file 1. Supplementary Data
DOI: 10.6084/m9.figshare.28517008.v1
title: Additional file 1 of Admixture as a source for HLA variation in Neolithic European farming communities

description: Additional file 1. Supplementary Data
DOI: 10.6084/m9.figshare.28517041
title: Additional file 1 of Non-invasive diagnosis of vulvar dysplasia using cervical methylation markers—a case control study

description: Additional file 1: Table S1 Anonymous patient data and original values
DOI: 10.6084/m9.figshare.28517041.v1
title: Additional file 1 of Non-invasive diagnosis of vulvar dysplasia using cervical methylation markers—a case control study

description: Additional file 1: Table S1 Anonymous patient data and original values
DOI: 10.6084/m9.figshare.28517044
title: Additional file 2 of Non-invasive diagnosis of vulvar dysplasia using cervical methylation markers—a case control study

description: Additional file 2: Table S2 Chi-square tests data of Figs. 1, 4, and 6a
DOI: 10.6084/m9.figshare.28517044.v1
title: Additional file 2 of Non-invasive diagnosis of vulvar dysplasia using cervical methylation markers—a case control study

description: Additional file 2: Table S2 Chi-square tests data of Figs. 1, 4, and 6a
DOI: 10.6084/m9.figshare.28517054
title: Additional file 1 of Shared environments complicate the use of strain-resolved metagenomics to infer microbiome transmission

description: Supplementary Material 1. Supplementary tables: Supplementary Table 1: Read counts and mapping statistics for the human fecal microbiota transplant dataset. Supplementary Table 2: Pairwise comparisons in baboon gut metagenome dataset. Supplementary Table 3: Read counts and mapping statistics for baboon gut metagenome dataset.
DOI: 10.6084/m9.figshare.28517054.v1
title: Additional file 1 of Shared environments complicate the use of strain-resolved metagenomics to infer microbiome transmission

description: Supplementary Material 1. Supplementary tables: Supplementary Table 1: Read counts and mapping statistics for the human fecal microbiota transplant dataset. Supplementary Table 2: Pairwise comparisons in baboon gut metagenome dataset. Supplementary Table 3: Read counts and mapping statistics for baboon gut metagenome dataset.
DOI: 10.6084/m9.figshare.28517056
title: Additional file 3 of Catheter diameter and infection control are important in neonatal continuous kidney replacement therapy: a single-center retrospective study

description: Additional file 3
DOI: 10.6084/m9.figshare.28517056.v1
title: Additional file 3 of Catheter diameter and infection control are important in neonatal continuous kidney replacement therapy: a single-center retrospective study

description: Additional file 3
DOI: 10.6084/m9.figshare.28517074
title: Additional file 1 of Preclinical studies and transcriptome analysis in a model of Parkinson’s disease with dopaminergic ZNF746 expression

description: Additional file 1. Supplementary movie 1. Motor deficit assessment of 3 month old PARIS Tg and control mouse using pole test. Supplementary movie 2. Motor deficit assessment of 2 month old PARIS Tg and control mouse using beam walking test. Supplementary movie 3. L-DOPA rescues motor impairments in PARIS Tg mice. Supplementary movie 4. Nilotinib rescues motor impairments in PARIS Tg mice.
DOI: 10.6084/m9.figshare.28517074.v1
title: Additional file 1 of Preclinical studies and transcriptome analysis in a model of Parkinson’s disease with dopaminergic ZNF746 expression

description: Additional file 1. Supplementary movie 1. Motor deficit assessment of 3 month old PARIS Tg and control mouse using pole test. Supplementary movie 2. Motor deficit assessment of 2 month old PARIS Tg and control mouse using beam walking test. Supplementary movie 3. L-DOPA rescues motor impairments in PARIS Tg mice. Supplementary movie 4. Nilotinib rescues motor impairments in PARIS Tg mice.
DOI: 10.6084/m9.figshare.28517077
title: Additional file 2 of Preclinical studies and transcriptome analysis in a model of Parkinson’s disease with dopaminergic ZNF746 expression

description: Additional file 2. Supplementary table 1. Differentially expressed genes (DEGs) associated with functional annotation and mitochondrial dysfunction. List of mitochondrial dysfunction-associated genes for bubble plot DAVID functional annotation in PARIS Tg, related to Fig. 6D. Supplementary table 2. Differentially expressed genes (DEGs; more than 2× fold alteration) in the midbrains of PARIS Tg mice. List of 2× fold DEGs PARIS-driven transcriptomic alterations in the midbrains of Tg mice, related to Supplementary fig 5B. Supplementary table 3. Cell type proportion. Proportions of each cell type cluster, including major cell types and their subpopulation of neurons, astrocytes, and microglia. Supplementary table 4. Neuron DEG log2FC. List of DEGs in neurons. (Filtration using log2FC &gt;|0.2|) Supplementary table 5. Neuron subpopulation gene expression level. Supplementary table 6. Neuron subpopulation DEG log2FC. List of DEGs in subpopulation of neurons. (Filtration using log2FC; glutamatergic &gt;|0.3|, cholinergic &gt;|0.2|, dopaminergic &gt;|0.12|, GABAergic &gt;|0.2|, and serotonergic &gt;|0.11|). Supplementary table 7. Neuron subpopulation GO ontology. Supplementary table 8. Dopaminergic neuron KEGG analysis. Supplementary table 9. Astrocyte subpopulation DEG log2FC. List of DEGs in subpopulation of astrocytes. (Filtration using log2FC; a0&gt;|0.25|, a1&gt;|0.4|, a2&gt;|0.4|, a3&gt;|0.25|, a4&gt;|0.35|, a5&gt;|0.55|, and a6&gt;|0.4|). Supplementary table 10. Astrocyte subpopulation GO ontology. Supplementary table 11. Microglia subpopulation DEG log2FC. List of DEGs in subpopulation of microglia. (Filtration using log2FC; m0&gt;|0.25|, m1&gt;|0.3|, m2&gt;|0.25|, m3&gt;|0.25|, m4&gt;|0.45|, and m5&gt;|0.85|). Supplementary table 12. Microglia subpopulation GO ontology. Supplementary table 13. Information on number of male and female mice used in each experimental group.
DOI: 10.6084/m9.figshare.28517077.v1
title: Additional file 2 of Preclinical studies and transcriptome analysis in a model of Parkinson’s disease with dopaminergic ZNF746 expression

description: Additional file 2. Supplementary table 1. Differentially expressed genes (DEGs) associated with functional annotation and mitochondrial dysfunction. List of mitochondrial dysfunction-associated genes for bubble plot DAVID functional annotation in PARIS Tg, related to Fig. 6D. Supplementary table 2. Differentially expressed genes (DEGs; more than 2× fold alteration) in the midbrains of PARIS Tg mice. List of 2× fold DEGs PARIS-driven transcriptomic alterations in the midbrains of Tg mice, related to Supplementary fig 5B. Supplementary table 3. Cell type proportion. Proportions of each cell type cluster, including major cell types and their subpopulation of neurons, astrocytes, and microglia. Supplementary table 4. Neuron DEG log2FC. List of DEGs in neurons. (Filtration using log2FC &gt;|0.2|) Supplementary table 5. Neuron subpopulation gene expression level. Supplementary table 6. Neuron subpopulation DEG log2FC. List of DEGs in subpopulation of neurons. (Filtration using log2FC; glutamatergic &gt;|0.3|, cholinergic &gt;|0.2|, dopaminergic &gt;|0.12|, GABAergic &gt;|0.2|, and serotonergic &gt;|0.11|). Supplementary table 7. Neuron subpopulation GO ontology. Supplementary table 8. Dopaminergic neuron KEGG analysis. Supplementary table 9. Astrocyte subpopulation DEG log2FC. List of DEGs in subpopulation of astrocytes. (Filtration using log2FC; a0&gt;|0.25|, a1&gt;|0.4|, a2&gt;|0.4|, a3&gt;|0.25|, a4&gt;|0.35|, a5&gt;|0.55|, and a6&gt;|0.4|). Supplementary table 10. Astrocyte subpopulation GO ontology. Supplementary table 11. Microglia subpopulation DEG log2FC. List of DEGs in subpopulation of microglia. (Filtration using log2FC; m0&gt;|0.25|, m1&gt;|0.3|, m2&gt;|0.25|, m3&gt;|0.25|, m4&gt;|0.45|, and m5&gt;|0.85|). Supplementary table 12. Microglia subpopulation GO ontology. Supplementary table 13. Information on number of male and female mice used in each experimental group.
DOI: 10.6084/m9.figshare.28517107
title: Additional file 2 of Decoding chromosomal instability insights in CRC by integrating omics and patient-derived organoids

description: Supplementary Material 2. Additional File S1. Excel file containing organoids and tissues copy number data.
DOI: 10.6084/m9.figshare.28517107.v1
title: Additional file 2 of Decoding chromosomal instability insights in CRC by integrating omics and patient-derived organoids

description: Supplementary Material 2. Additional File S1. Excel file containing organoids and tissues copy number data.
DOI: 10.6084/m9.figshare.28517110
title: Additional file 3 of Decoding chromosomal instability insights in CRC by integrating omics and patient-derived organoids

description: Supplementary Material 3. Additional File S2. Excel file containing organoids gene signature deriving from transcriptomic analysis used to classify TCGA tissues and differential gene expression analysis.
DOI: 10.6084/m9.figshare.28517110.v1
title: Additional file 3 of Decoding chromosomal instability insights in CRC by integrating omics and patient-derived organoids

description: Supplementary Material 3. Additional File S2. Excel file containing organoids gene signature deriving from transcriptomic analysis used to classify TCGA tissues and differential gene expression analysis.
DOI: 10.6084/m9.figshare.28517113.v1
title: Additional file 4 of Decoding chromosomal instability insights in CRC by integrating omics and patient-derived organoids

description: Supplementary Material 4. Additional File S3. Excel file containing proteomic dataset and full results of integrative and Pearson analysis.
DOI: 10.6084/m9.figshare.28517113
title: Additional file 4 of Decoding chromosomal instability insights in CRC by integrating omics and patient-derived organoids

description: Supplementary Material 4. Additional File S3. Excel file containing proteomic dataset and full results of integrative and Pearson analysis.
DOI: 10.6084/m9.figshare.28517116
title: Additional file 5 of Decoding chromosomal instability insights in CRC by integrating omics and patient-derived organoids

description: Supplementary Material 5. Additional File S4. Excel file containing public databases analysis.
DOI: 10.6084/m9.figshare.28517116.v1
title: Additional file 5 of Decoding chromosomal instability insights in CRC by integrating omics and patient-derived organoids

description: Supplementary Material 5. Additional File S4. Excel file containing public databases analysis.
DOI: 10.6084/m9.figshare.28517143
title: Additional file 2 of Enterocloster clostridioformis protects against Salmonella pathogenesis and modulates epithelial and mucosal immune function

description: Supplementary Material 2: Supplementary tables: Supplementary Table 1: GO term enrichment from caecal epithelial cell RNAseq analyses. Supplementary Table 2: Metadata for RNAseq samples.
DOI: 10.6084/m9.figshare.28517143.v1
title: Additional file 2 of Enterocloster clostridioformis protects against Salmonella pathogenesis and modulates epithelial and mucosal immune function

description: Supplementary Material 2: Supplementary tables: Supplementary Table 1: GO term enrichment from caecal epithelial cell RNAseq analyses. Supplementary Table 2: Metadata for RNAseq samples.
DOI: 10.6084/m9.figshare.28517123
title: Additional file 2 of CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis

description: Additional file 2: Table S1. ATAC-seq peak data summary information from the analysis in CTCF-AID HUDEP-2 cells with IAA treatment vs. without IAA treatment grown in culture under immature conditions for 24 hours.
DOI: 10.6084/m9.figshare.28517123.v1
title: Additional file 2 of CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis

description: Additional file 2: Table S1. ATAC-seq peak data summary information from the analysis in CTCF-AID HUDEP-2 cells with IAA treatment vs. without IAA treatment grown in culture under immature conditions for 24 hours.
DOI: 10.6084/m9.figshare.28517126
title: Additional file 3 of CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis

description: Additional file 3: Table S2. ATAC-seq peak data summary information from the analysis in CTCF-AID HEL cells with IAA treatment vs. without IAA treatment grown in culture under immature conditions for 24 hours.
DOI: 10.6084/m9.figshare.28517126.v1
title: Additional file 3 of CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis

description: Additional file 3: Table S2. ATAC-seq peak data summary information from the analysis in CTCF-AID HEL cells with IAA treatment vs. without IAA treatment grown in culture under immature conditions for 24 hours.
DOI: 10.6084/m9.figshare.28517129
title: Additional file 4 of CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis

description: Additional file 4: Table S3. Enrichment analysis for transcription factors in increased and decreased ATAC-seq peaks, as well as unchanged peaks in CTCF-AID HUDEP-2 cells with IAA treatment vs. without IAA treatment grown in culture under immature conditions for 24 hours. Three separate sheets include decreased vs. unchanged, increased vs. unchanged, and increased vs. decreased, respectively.
DOI: 10.6084/m9.figshare.28517129.v1
title: Additional file 4 of CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis

description: Additional file 4: Table S3. Enrichment analysis for transcription factors in increased and decreased ATAC-seq peaks, as well as unchanged peaks in CTCF-AID HUDEP-2 cells with IAA treatment vs. without IAA treatment grown in culture under immature conditions for 24 hours. Three separate sheets include decreased vs. unchanged, increased vs. unchanged, and increased vs. decreased, respectively.
DOI: 10.6084/m9.figshare.28517132
title: Additional file 5 of CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis

description: Additional file 5: Table S4. GREAT analysis for differential accessibility regionsin CTCF -AID HUDEP-2 and HEL cells with IAA treatment vs. without IAA treatment grown in culture under immature conditions for 24 hours.
DOI: 10.6084/m9.figshare.28517132.v1
title: Additional file 5 of CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis

description: Additional file 5: Table S4. GREAT analysis for differential accessibility regionsin CTCF -AID HUDEP-2 and HEL cells with IAA treatment vs. without IAA treatment grown in culture under immature conditions for 24 hours.
DOI: 10.6084/m9.figshare.28517135
title: Additional file 6 of CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis

description: Additional file 6: Table S5. RNA transcriptome analysis of CTCF-AID HUDEP-2 cells with IAA treatment vs. without IAA treatment grown in culture under immature and mature conditions for 24 hours.
DOI: 10.6084/m9.figshare.28517135.v1
title: Additional file 6 of CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis

description: Additional file 6: Table S5. RNA transcriptome analysis of CTCF-AID HUDEP-2 cells with IAA treatment vs. without IAA treatment grown in culture under immature and mature conditions for 24 hours.
DOI: 10.6084/m9.figshare.28517138
title: Additional file 7 of CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis

description: Additional file 7: Table S6. CTCF ChIP-seq peaks before and after HUDEP-2 erythroid maturation from the public dataset and CTCF ChIP-seq peaks before and after IAA treatment before and after IAA treatment in both HUDEP-2 and HEL cells in the immature state.
DOI: 10.6084/m9.figshare.28517138.v1
title: Additional file 7 of CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis

description: Additional file 7: Table S6. CTCF ChIP-seq peaks before and after HUDEP-2 erythroid maturation from the public dataset and CTCF ChIP-seq peaks before and after IAA treatment before and after IAA treatment in both HUDEP-2 and HEL cells in the immature state.
DOI: 10.6084/m9.figshare.28517144
title: Additional file 8 of CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis

description: Additional file 8: Table S7. RNA transcriptome analysis of CTCF-AID HEL cells with IAA treatment vs. without IAA treatment grown in culture under no hemin and hemin treated conditions for 24 hours.
DOI: 10.6084/m9.figshare.28517144.v1
title: Additional file 8 of CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis

description: Additional file 8: Table S7. RNA transcriptome analysis of CTCF-AID HEL cells with IAA treatment vs. without IAA treatment grown in culture under no hemin and hemin treated conditions for 24 hours.
DOI: 10.6084/m9.figshare.28517147
title: Additional file 9 of CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis

description: Additional file 9: Table S8. Hi-C datasets, and annotated TADs and chromatin loops information in CTCF-AID HEL cells with IAA treatment vs. without IAA treatment grown in culture under no hemin treated conditions for 24 hours.