cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12858623.v1
title: Additional file 2 of Unraveling the molecular heterogeneity in type 2 diabetes: a potential subtype discovery followed by metabolic modeling

description: Additional file 2. The complete list of differentially expressed genes in each cluster, top-ranked genes with Ensemble ID, perturbed reactions obtained from metabolic modeling in each cluster.
DOI: 10.6084/m9.figshare.12858674.v1
title: Additional file 2 of A novel function of FAF1, which induces dopaminergic neuronal death through cell-to-cell transmission

description: Additional file 1. FAF1 is detected in plasma and CSF according to the CSF Proteome Resource.
DOI: 10.6084/m9.figshare.12858674
title: Additional file 2 of A novel function of FAF1, which induces dopaminergic neuronal death through cell-to-cell transmission

description: Additional file 1. FAF1 is detected in plasma and CSF according to the CSF Proteome Resource.
DOI: 10.6084/m9.figshare.12858699.v1
title: Additional file 1 of Transcriptomic analysis at organ and time scale reveals gene regulatory networks controlling the sulfate starvation response of Solanum lycopersicum

description: Additional file 1: Figure S1. Total leaf area is reduced by sulfate deficiency from 3 weeks after sowing. Figure S2. A) Number of differentially expressed genes by sulfate starvation in roots, leaves or shared by both organs at 2, 3 and 4 weeks after sowing. B) Venn diagrams showing the overlap between early sulfate-regulated genes in roots and late regulated genes in leaves. Figure S3. qPCR validation of RNA-seq data. A) Correlation between relative mRNA levels of qPCR and RNA-seq data on selected transcripts. The list of selected differentially expressed genes by sulfate starvation is shown in Table S3. B) Heatmap comparing the expression patterns of selected genes analyzed by qPCR and RNA-seq. Figure S4. Hierarchical clustering of 52 genes included in the GO term “cellular response to phosphate starvation”, the most enriched GO term of sulfate-responsive orthologous gene families that are found exclusively in tomato plants. Figure S5. Co-expression clusters down-regulatedby sulfate starvation of genes significantly affected by sulfate and time in roots (left) and leaves (right) (q-value 1). On each box, the central mark indicates the median, and the bottom and top edges of the box indicate the 25th and 75th percentiles, respectively. Whisker indicates standard deviation of the expression data of all genes belongs to the cluster. Figure S6. Co-expression clusters up-regulated by sulfate starvation of genes significantly affected by sulfate and time in leaves (q-value 1). On each box, the central mark indicates the median, and the bottom and top edges of the box indicate the 25th and 75th percentiles, respectively. Whisker indicates standard deviation of the expression data of all genes belongs to the cluster. Figure S7. A) Distribution of Cluster 1 genes regulated by sulfate and time in leaves across different categories of the primary metabolism using Mapman4 annotation framework. B) Mapman analysis of sulfate starvation responsive genes in at least one time in leaves. C) Mapman analysis of sulfate starvation responsive genes in at least one time in roots. Figure S8. The root regulatory network. Blue nodes represent TFs and red nodes represent target genes. Figure S9. The leaf regulatory network. Blue nodes represent TFs and red nodes represent target genes. Figure S10. Expression profiles of the phosphate transporter genes Solyc02g088220, Solyc09g066410 and Solyc09g090080 in response to sulfate starvation at 2, 3 and 4 weeks after sowing.
DOI: 10.6084/m9.figshare.12858702.v1
title: Additional file 2 of Transcriptomic analysis at organ and time scale reveals gene regulatory networks controlling the sulfate starvation response of Solanum lycopersicum

description: Additional file 2: Table S1. Normalized RNA-seq data in transcripts per million (TPM) scale. Table S2. Differentially expressed genes between sulfate-starved and control tomato plants at 2, 3 and 4 weeks after sowing. Differential expression analysis was performed in roots and leaves using the sleuth R package (q-value 1). Table S3. List of genes validated by qPCR indicating whether the sulfate regulation was previously reported in Arabidopsis. Table S4. List of Arabidopsis and tomato sulfate-responsive orthologous genes. Table S5. Enriched GO terms for orthologous sulfate-responsive genes in Arabidopsis, tomato, or shared in both species. Table S6. Genes exclusively regulated by sulfate and time in roots. Multifactorial analysis was performed using the sleuth R package (q-value 1 in at least one level of each factor). Table S7. Genes exclusively regulated by sulfate and time in leaves. Multifactorial analysis was performed using the sleuth R package (q-value 1 in at least one level of each factor). Table S8. Enriched GO terms for genes of root clusters. Only significant GO terms (adjusted p-value 1) in this work. Table S16. The primers used in qPCR analysis. (ZIP 17724 kb)
DOI: 10.6084/m9.figshare.12858699
title: Additional file 1 of Transcriptomic analysis at organ and time scale reveals gene regulatory networks controlling the sulfate starvation response of Solanum lycopersicum

description: Additional file 1: Figure S1. Total leaf area is reduced by sulfate deficiency from 3 weeks after sowing. Figure S2. A) Number of differentially expressed genes by sulfate starvation in roots, leaves or shared by both organs at 2, 3 and 4 weeks after sowing. B) Venn diagrams showing the overlap between early sulfate-regulated genes in roots and late regulated genes in leaves. Figure S3. qPCR validation of RNA-seq data. A) Correlation between relative mRNA levels of qPCR and RNA-seq data on selected transcripts. The list of selected differentially expressed genes by sulfate starvation is shown in Table S3. B) Heatmap comparing the expression patterns of selected genes analyzed by qPCR and RNA-seq. Figure S4. Hierarchical clustering of 52 genes included in the GO term “cellular response to phosphate starvation”, the most enriched GO term of sulfate-responsive orthologous gene families that are found exclusively in tomato plants. Figure S5. Co-expression clusters down-regulatedby sulfate starvation of genes significantly affected by sulfate and time in roots (left) and leaves (right) (q-value 1). On each box, the central mark indicates the median, and the bottom and top edges of the box indicate the 25th and 75th percentiles, respectively. Whisker indicates standard deviation of the expression data of all genes belongs to the cluster. Figure S6. Co-expression clusters up-regulated by sulfate starvation of genes significantly affected by sulfate and time in leaves (q-value 1). On each box, the central mark indicates the median, and the bottom and top edges of the box indicate the 25th and 75th percentiles, respectively. Whisker indicates standard deviation of the expression data of all genes belongs to the cluster. Figure S7. A) Distribution of Cluster 1 genes regulated by sulfate and time in leaves across different categories of the primary metabolism using Mapman4 annotation framework. B) Mapman analysis of sulfate starvation responsive genes in at least one time in leaves. C) Mapman analysis of sulfate starvation responsive genes in at least one time in roots. Figure S8. The root regulatory network. Blue nodes represent TFs and red nodes represent target genes. Figure S9. The leaf regulatory network. Blue nodes represent TFs and red nodes represent target genes. Figure S10. Expression profiles of the phosphate transporter genes Solyc02g088220, Solyc09g066410 and Solyc09g090080 in response to sulfate starvation at 2, 3 and 4 weeks after sowing.
DOI: 10.6084/m9.figshare.12858702
title: Additional file 2 of Transcriptomic analysis at organ and time scale reveals gene regulatory networks controlling the sulfate starvation response of Solanum lycopersicum

description: Additional file 2: Table S1. Normalized RNA-seq data in transcripts per million (TPM) scale. Table S2. Differentially expressed genes between sulfate-starved and control tomato plants at 2, 3 and 4 weeks after sowing. Differential expression analysis was performed in roots and leaves using the sleuth R package (q-value 1). Table S3. List of genes validated by qPCR indicating whether the sulfate regulation was previously reported in Arabidopsis. Table S4. List of Arabidopsis and tomato sulfate-responsive orthologous genes. Table S5. Enriched GO terms for orthologous sulfate-responsive genes in Arabidopsis, tomato, or shared in both species. Table S6. Genes exclusively regulated by sulfate and time in roots. Multifactorial analysis was performed using the sleuth R package (q-value 1 in at least one level of each factor). Table S7. Genes exclusively regulated by sulfate and time in leaves. Multifactorial analysis was performed using the sleuth R package (q-value 1 in at least one level of each factor). Table S8. Enriched GO terms for genes of root clusters. Only significant GO terms (adjusted p-value 1) in this work. Table S16. The primers used in qPCR analysis. (ZIP 17724 kb)
DOI: 10.6084/m9.figshare.12858740.v1
title: Additional file 6 of Molecular evidence of IGFBP-3 dependent and independent VD3 action and its nonlinear response on IGFBP-3 induction in prostate cancer cells

description: Additional file 6: Supplementary Fig. 5. Original uncropped images of western blot.
DOI: 10.6084/m9.figshare.12858740
title: Additional file 6 of Molecular evidence of IGFBP-3 dependent and independent VD3 action and its nonlinear response on IGFBP-3 induction in prostate cancer cells

description: Additional file 6: Supplementary Fig. 5. Original uncropped images of western blot.
DOI: 10.6084/m9.figshare.12858758.v1
title: Additional file 4 of Implementation of a national electronic health information system in Gabon: a survey of healthcare providers’ perceptions

description: Additional file 4. Pearson correlations between constructs.
DOI: 10.6084/m9.figshare.12858758
title: Additional file 4 of Implementation of a national electronic health information system in Gabon: a survey of healthcare providers’ perceptions

description: Additional file 4. Pearson correlations between constructs.
DOI: 10.6084/m9.figshare.12858752
title: Additional file 2 of Implementation of a national electronic health information system in Gabon: a survey of healthcare providers’ perceptions

description: Additional file 2. Pearson correlations between items.
DOI: 10.6084/m9.figshare.12858752.v1
title: Additional file 2 of Implementation of a national electronic health information system in Gabon: a survey of healthcare providers’ perceptions

description: Additional file 2. Pearson correlations between items.
DOI: 10.6084/m9.figshare.12858800.v1
title: Additional file 2 of Innate immune response in neuronopathic forms of Gaucher disease confers resistance against viral-induced encephalitis

description: Additional file 2: Table S1. Complete list of the differentially-expressed genes (DEG). RNA-seq data obtained from brains of control, SVNI, CBE, and CBE + SVNI mice 5 DPI. Gene lists were created by criteria based on an absolute linear fold change ≥ 2.0, fdr ≤ 0.05 .
DOI: 10.6084/m9.figshare.12858803.v1
title: Additional file 3 of Innate immune response in neuronopathic forms of Gaucher disease confers resistance against viral-induced encephalitis

description: Additional file 3: Table S2. Gene clusters of differentially-expressed genes (DEG). Values that were used for generation of heat maps of RNA-seq data. The heat maps comparing mRNA obtained from brains of control, SVNI, CBE, and CBE + SVNI mice are represented by lists of 2293 genes that were significantly differentially-expressed (fold change ≥ 2.0, p ≤ 0.05) in at least one of the groups versus control.
DOI: 10.6084/m9.figshare.12858800
title: Additional file 2 of Innate immune response in neuronopathic forms of Gaucher disease confers resistance against viral-induced encephalitis

description: Additional file 2: Table S1. Complete list of the differentially-expressed genes (DEG). RNA-seq data obtained from brains of control, SVNI, CBE, and CBE + SVNI mice 5 DPI. Gene lists were created by criteria based on an absolute linear fold change ≥ 2.0, fdr ≤ 0.05 .
DOI: 10.6084/m9.figshare.12858809
title: Additional file 5 of Innate immune response in neuronopathic forms of Gaucher disease confers resistance against viral-induced encephalitis

description: Additional file 5: Table S4. Gene clusters of myeloid lineage cells and astrocytes-enriched genes. Values that were used for generation of heat maps of RNA-seq data. The heat maps comparing mRNA obtained from brains of control, SVNI, CBE, and CBE + SVNI mice are represented by lists of 68 and 112 genes enriched in astrocytes and myeloid lineage cells, respectively.
DOI: 10.6084/m9.figshare.12858806.v1
title: Additional file 4 of Innate immune response in neuronopathic forms of Gaucher disease confers resistance against viral-induced encephalitis

description: Additional file 4: Table S3. List of significantly enriched GO-Slim Biological Process. Biological processes which were up-regulated in both CBE-treated and SVNI-infected brains are highlighted in yellow.
DOI: 10.6084/m9.figshare.12858809.v1
title: Additional file 5 of Innate immune response in neuronopathic forms of Gaucher disease confers resistance against viral-induced encephalitis

description: Additional file 5: Table S4. Gene clusters of myeloid lineage cells and astrocytes-enriched genes. Values that were used for generation of heat maps of RNA-seq data. The heat maps comparing mRNA obtained from brains of control, SVNI, CBE, and CBE + SVNI mice are represented by lists of 68 and 112 genes enriched in astrocytes and myeloid lineage cells, respectively.
DOI: 10.6084/m9.figshare.12858806
title: Additional file 4 of Innate immune response in neuronopathic forms of Gaucher disease confers resistance against viral-induced encephalitis

description: Additional file 4: Table S3. List of significantly enriched GO-Slim Biological Process. Biological processes which were up-regulated in both CBE-treated and SVNI-infected brains are highlighted in yellow.
DOI: 10.6084/m9.figshare.12858803
title: Additional file 3 of Innate immune response in neuronopathic forms of Gaucher disease confers resistance against viral-induced encephalitis

description: Additional file 3: Table S2. Gene clusters of differentially-expressed genes (DEG). Values that were used for generation of heat maps of RNA-seq data. The heat maps comparing mRNA obtained from brains of control, SVNI, CBE, and CBE + SVNI mice are represented by lists of 2293 genes that were significantly differentially-expressed (fold change ≥ 2.0, p ≤ 0.05) in at least one of the groups versus control.
DOI: 10.6084/m9.figshare.12858828
title: Additional file 6 of Global transcriptomic responses orchestrate difenoconazole resistance in Penicillium spp. causing blue mold of stored apple fruit

description: Additional file 6: Table S2. Transcriptome statistics for each sample observed across all 16 samples.
DOI: 10.6084/m9.figshare.12858822.v1
title: Additional file 4 of Global transcriptomic responses orchestrate difenoconazole resistance in Penicillium spp. causing blue mold of stored apple fruit

description: Additional file 4: Table S1. Penicillium spp. genome statistics used in phylogenomic tree construction.
DOI: 10.6084/m9.figshare.12858822
title: Additional file 4 of Global transcriptomic responses orchestrate difenoconazole resistance in Penicillium spp. causing blue mold of stored apple fruit

description: Additional file 4: Table S1. Penicillium spp. genome statistics used in phylogenomic tree construction.
DOI: 10.6084/m9.figshare.12858828.v1
title: Additional file 6 of Global transcriptomic responses orchestrate difenoconazole resistance in Penicillium spp. causing blue mold of stored apple fruit

description: Additional file 6: Table S2. Transcriptome statistics for each sample observed across all 16 samples.
DOI: 10.6084/m9.figshare.12858936.v1
title: Additional file 2 of Sphingomyelin(d35:1) as a novel predictor for lung adenocarcinoma recurrence after a radical surgery: a case-control study

description: Additional file 2. The full list of identified 2595 lipid species.
DOI: 10.6084/m9.figshare.12858936
title: Additional file 2 of Sphingomyelin(d35:1) as a novel predictor for lung adenocarcinoma recurrence after a radical surgery: a case-control study

description: Additional file 2. The full list of identified 2595 lipid species.
DOI: 10.6084/m9.figshare.12858969.v1
title: Additional file 7 of Whole exome sequencing revealed a novel homozygous variant in the DGKE catalytic domain: a case report of familial hemolytic uremic syndrome

description: Additional file 7: Table S7. A large region of homozygsity on chromosome 17 around the detected variant.
DOI: 10.6084/m9.figshare.12858969
title: Additional file 7 of Whole exome sequencing revealed a novel homozygous variant in the DGKE catalytic domain: a case report of familial hemolytic uremic syndrome

description: Additional file 7: Table S7. A large region of homozygsity on chromosome 17 around the detected variant.
DOI: 10.6084/m9.figshare.12858975.v1
title: Additional file 1 of Investigation of the genetic variation in ACE2 on the structural recognition by the novel coronavirus (SARS-CoV-2)

description: Additional file 1. A total of 251 non-silent genetic variants in ACE2 genes were characterized after removing those with low quality control, or had a AF = 0.
DOI: 10.6084/m9.figshare.12858975
title: Additional file 1 of Investigation of the genetic variation in ACE2 on the structural recognition by the novel coronavirus (SARS-CoV-2)

description: Additional file 1. A total of 251 non-silent genetic variants in ACE2 genes were characterized after removing those with low quality control, or had a AF = 0.
DOI: 10.6084/m9.figshare.12859002.v1
title: Additional file 4 of The GAMYB gene in rye: sequence, polymorphisms, map location, allele-specific markers, and relationship with α-amylase activity

description: Additional file 4 1: The genetic map of chromosome 3R with ScGAMYB of three rye mapping populations: BSR-F2, RIL-K, and RIL-L. 2: The segregations of markers from chromosome 3R in rye mapping population BSR-F2. 3: The segregations of markers from chromosome 3R in rye mapping population RIL-K. 4: The segregations of markers from chromosome 3R in rye mapping population RIL-L.
DOI: 10.6084/m9.figshare.12858993.v1
title: Additional file 1 of The GAMYB gene in rye: sequence, polymorphisms, map location, allele-specific markers, and relationship with α-amylase activity

description: Additional file 1 The characteristic and annotation data of the contig c81081 (ScGAMYB transcript).
DOI: 10.6084/m9.figshare.12859008.v1
title: Additional file 1 of Investigation of mechanisms underlying chaotic genetic patchiness in the intertidal marbled crab Pachygrapsus marmoratus (Brachyura: Grapsidae) across the Ligurian Sea

description: Additional file 1. Dataset supporting the conclusions of this article (text file formatted as Genepop input).
DOI: 10.6084/m9.figshare.12859002
title: Additional file 4 of The GAMYB gene in rye: sequence, polymorphisms, map location, allele-specific markers, and relationship with α-amylase activity

description: Additional file 4 1: The genetic map of chromosome 3R with ScGAMYB of three rye mapping populations: BSR-F2, RIL-K, and RIL-L. 2: The segregations of markers from chromosome 3R in rye mapping population BSR-F2. 3: The segregations of markers from chromosome 3R in rye mapping population RIL-K. 4: The segregations of markers from chromosome 3R in rye mapping population RIL-L.
DOI: 10.6084/m9.figshare.12859005.v1
title: Additional file 5 of The GAMYB gene in rye: sequence, polymorphisms, map location, allele-specific markers, and relationship with α-amylase activity

description: Additional file 5. Alpha-amylase activity in rye mapping population RIL-L.
DOI: 10.6084/m9.figshare.12859005
title: Additional file 5 of The GAMYB gene in rye: sequence, polymorphisms, map location, allele-specific markers, and relationship with α-amylase activity

description: Additional file 5. Alpha-amylase activity in rye mapping population RIL-L.
DOI: 10.6084/m9.figshare.12859008
title: Additional file 1 of Investigation of mechanisms underlying chaotic genetic patchiness in the intertidal marbled crab Pachygrapsus marmoratus (Brachyura: Grapsidae) across the Ligurian Sea

description: Additional file 1. Dataset supporting the conclusions of this article (text file formatted as Genepop input).
DOI: 10.6084/m9.figshare.12858993
title: Additional file 1 of The GAMYB gene in rye: sequence, polymorphisms, map location, allele-specific markers, and relationship with α-amylase activity

description: Additional file 1 The characteristic and annotation data of the contig c81081 (ScGAMYB transcript).
DOI: 10.11577/1650020
title: Advances in long-wavelength native phasing at X-ray free-electron lasers

description: Diffraction images of the A2A data set at 4.57 keV
DOI: 10.11577/1650021
title: Advances in long-wavelength native phasing at X-ray free-electron lasers

description: Diffraction images of the thaumatin data set at 4.57 keV.
DOI: 10.11577/1650022
title: Advances in long-wavelength native phasing at X-ray free-electron lasers

description: Diffraction images of the thaumatin data set at 6.06 keV.
DOI: 10.5281/zenodo.3726665
title: Governance networks around grasslands with contrasting management history

description: Dataset article Governance networks around grasslands with contrasting management history.
DOI: 10.5281/zenodo.3726664
title: Governance networks around grasslands with contrasting management history

description: Dataset article Governance networks around grasslands with contrasting management history.
DOI: 10.4225/08/5758ccc862ad5
title: Topographic Position Index derived from 1" SRTM DEM-S

description: Topographic Position Index (TPI) is a topographic position classification identifying upper, middle and lower parts of the landscape. This dataset includes a mask that identifies where topographic position cannot be reliably derived in low relief areas. The TPI product was derived from Smoothed Digital Elevation Model (DEM-S; ANZCW0703014016), which was derived from the 1 arc-second resolution SRTM data acquired by NASA in February 2000. A masked version of the TPI product was derived using the slope relief classification product. The TPI data are available at 1 arc-second and 3 arc-second resolution. The 3 arc-second resolution dataset was generated from the 1 arc-second TPI product and masked by the 3” water and ocean mask datasets.