cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10034402.v1
title: Additional file 3: of Differential proteomic comparison of breast cancer secretome using a quantitative paired analysis workflow

description: Table S3. Functional analysis of differentially abundant proteins (NAF samples from breast cancer patients). a) Cancer_vs_Nondiseased: Reactome pathways categorization of the proteins found as differentially abundant after paired comparison of NAF samples from breast cancer patients; b) ERpos_vs_Nondiseased: Reactome pathways categorization for differentially abundant proteins according to the paired comparison of NAF samples from ERpos breast cancer patients. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.10034405.v1
title: Additional file 4: of Differential proteomic comparison of breast cancer secretome using a quantitative paired analysis workflow

description: Table S4. Summary result of protein and peptide identifications (NAF samples from ERpos breast cancer patients). a) Protein Report: List of all 873 proteins statistically evaluated after paired comparisons of NAF samples from ERpos breast cancer patients; b) Peptide Report: List of all 873 proteins and the respective peptides statistically evaluated according to the paired comparisons of NAF samples from ERpos breast cancer patients. (XLSX 639 kb)
DOI: 10.6084/m9.figshare.10034396.v1
title: Additional file 1: of Differential proteomic comparison of breast cancer secretome using a quantitative paired analysis workflow

description: Table S1. Result summary of the protein and peptide identifications from the NAF samples from breast cancer patients. a) Protein Report: List of all 1227 proteins statistically evaluated after paired comparisons of NAF samples from breast cancer patients; b) Peptide Report: List of all 1227 proteins and the respective peptides statistically evaluated after paired comparisons of NAF samples from breast cancer patients. (XLSX 1245 kb)
DOI: 10.6084/m9.figshare.10034399.v1
title: Additional file 2: of Differential proteomic comparison of breast cancer secretome using a quantitative paired analysis workflow

description: Table S2. Result summary of protein and peptide identifications (NAF samples from control women). a) Protein Report: Complete list of 578 proteins statistically evaluated after paired comparisons of non diseased breast NAF samples from control women; b) Peptide Report: Complete list of 578 proteins and the respective peptides statistically evaluated after paired comparisons of non diseased breast NAF samples from control women. (XLSX 364 kb)
DOI: 10.6084/m9.figshare.10034411.v1
title: Additional file 5: of Differential proteomic comparison of breast cancer secretome using a quantitative paired analysis workflow

description: Table S5. Summary result of the proteins monitored by SRM (NAF samples from breast cancer patients). a) Protein Report: List of the 9 proteins monitored by SRM and statistically evaluated after paired comparisons of NAF samples from breast cancer patients; b) Peptide Report: List of the 9 proteins and the respective peptides monitored by SRM and statistically evaluated according to the paired comparisons of NAF samples from breast cancer patients. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.10034354
title: Additional file 1: of HseSUMO: Sumoylation site prediction using half-sphere exposures of amino acids residues

description: Supplementary Table S1. Prediction of protein sequences by predictors (XLS 58 kb)
DOI: 10.6084/m9.figshare.10034345
title: Additional file 1: of Androgen receptor expression is required to ensure development of adult Leydig cells and to prevent development of steroidogenic cells with adrenal characteristics in the mouse testis

description: Raw data from figures and tables. Primary raw data from Figure S1-S5 and from Table S1. (XLS 73 kb)
DOI: 10.6084/m9.figshare.10034354.v1
title: Additional file 1: of HseSUMO: Sumoylation site prediction using half-sphere exposures of amino acids residues

description: Supplementary Table S1. Prediction of protein sequences by predictors (XLS 58 kb)
DOI: 10.6084/m9.figshare.10034342
title: Additional file 1: of Evolutionary conservation of MLO gene promoter signatures

description: Table S1. List of 316 candidate CREs in the putative promoter regions of MLOs characterized by Iovieno et al., (2016). Table S2. Functional annotation of CREs in MLO-PPRs. The classification is based on the molecular function and the biological processes of the genes containing CREs. Table S3. List of enriched-CREs identified for each phylogenetic clade. Table S4. List of enriched motifs identified in the putative promoter regions (PPRs) of MLO genes upregulated during the interaction with PM fungi and/or belonging to the phylogenetic clade V. Table S5. Gene-specific primers used in this study for gene-expression analysis and their amplification efficiency. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.10034345.v1
title: Additional file 1: of Androgen receptor expression is required to ensure development of adult Leydig cells and to prevent development of steroidogenic cells with adrenal characteristics in the mouse testis

description: Raw data from figures and tables. Primary raw data from Figure S1-S5 and from Table S1. (XLS 73 kb)
DOI: 10.6084/m9.figshare.10034327
title: Additional file 1: of Fabrication of polydimethylsiloxane nanofluidic chips under AFM tip-based nanomilling process

description: Figure S1. Schematic diagram of homemade alignment system. Figure S2. Schematic illustrations of alignment procedures during bonding process. Figure S3. Relationship between scratching circle diameter and driving voltage. Figure S4. Typical AFM images of the machined nanochannel with different machining parameters. Figure S5. Relationship between wall size and transfer parameters (various weight ratio of PDMS) during first transfer process, where the channel molds were fabricated with single scratching approach: (a) Wall height, (b) Wall width. Figure S6. Typical AFM image (left) and corresponding cross-section (right) of the wall obtained from nanochannel I at a PDMS weight ratio of 5:1 during first transfer. Figure S7. Relationship between wall size and transfer parameters (various weight ratio of PDMS) during first transfer process, where the channel molds were fabricated with a normal load of 17 ÎźN and a frequency of 100 Hz: (a) Wall height, (b) Wall width. Figure S8. Typical AFM image (left) and corresponding cross-section (right) of the wall obtained from nanochannel II at a weight ratio of 5:1 during first transfer. Figure S9. Relationship between nanochannel size and transfer parameters (various weight ratio of PDMS) during second transfer, where the channel molds were fabricated with single scratching approach: (a) Nanochannel depth, (b) Nanochannel width. Figure S10. Typical AFM image (left) and corresponding cross-section (right) of the nanochannel obtained from wall I at a weight ratio of 10:1 during second transfer. Figure S11. Relationship between nanochannel size and transfer parameters (various weight ratio of PDMS) during second transfer, where the channel molds were fabricated with a normal load of 17 ÎźN and a frequency of 100 Hz: (a) Nanochannel depth, (b) Nanochannel width. Figure S12. Typical AFM image (left) and corresponding cross-section (right) of the nanochannel obtained from wall II at a weight ratio of 10:1 during second transfer. (ZIP 16617 kb)
DOI: 10.6084/m9.figshare.10034327.v1
title: Additional file 1: of Fabrication of polydimethylsiloxane nanofluidic chips under AFM tip-based nanomilling process

description: Figure S1. Schematic diagram of homemade alignment system. Figure S2. Schematic illustrations of alignment procedures during bonding process. Figure S3. Relationship between scratching circle diameter and driving voltage. Figure S4. Typical AFM images of the machined nanochannel with different machining parameters. Figure S5. Relationship between wall size and transfer parameters (various weight ratio of PDMS) during first transfer process, where the channel molds were fabricated with single scratching approach: (a) Wall height, (b) Wall width. Figure S6. Typical AFM image (left) and corresponding cross-section (right) of the wall obtained from nanochannel I at a PDMS weight ratio of 5:1 during first transfer. Figure S7. Relationship between wall size and transfer parameters (various weight ratio of PDMS) during first transfer process, where the channel molds were fabricated with a normal load of 17 ÎźN and a frequency of 100 Hz: (a) Wall height, (b) Wall width. Figure S8. Typical AFM image (left) and corresponding cross-section (right) of the wall obtained from nanochannel II at a weight ratio of 5:1 during first transfer. Figure S9. Relationship between nanochannel size and transfer parameters (various weight ratio of PDMS) during second transfer, where the channel molds were fabricated with single scratching approach: (a) Nanochannel depth, (b) Nanochannel width. Figure S10. Typical AFM image (left) and corresponding cross-section (right) of the nanochannel obtained from wall I at a weight ratio of 10:1 during second transfer. Figure S11. Relationship between nanochannel size and transfer parameters (various weight ratio of PDMS) during second transfer, where the channel molds were fabricated with a normal load of 17 ÎźN and a frequency of 100 Hz: (a) Nanochannel depth, (b) Nanochannel width. Figure S12. Typical AFM image (left) and corresponding cross-section (right) of the nanochannel obtained from wall II at a weight ratio of 10:1 during second transfer. (ZIP 16617 kb)
DOI: 10.6084/m9.figshare.10034342.v1
title: Additional file 1: of Evolutionary conservation of MLO gene promoter signatures

description: Table S1. List of 316 candidate CREs in the putative promoter regions of MLOs characterized by Iovieno et al., (2016). Table S2. Functional annotation of CREs in MLO-PPRs. The classification is based on the molecular function and the biological processes of the genes containing CREs. Table S3. List of enriched-CREs identified for each phylogenetic clade. Table S4. List of enriched motifs identified in the putative promoter regions (PPRs) of MLO genes upregulated during the interaction with PM fungi and/or belonging to the phylogenetic clade V. Table S5. Gene-specific primers used in this study for gene-expression analysis and their amplification efficiency. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.10034309
title: Additional file 1: of Religiosity and sexual abstinence among Nigerian youths: does parent religion matter?

description: Protective Sexual Behaviour. (XLSX 52 kb)
DOI: 10.6084/m9.figshare.10034303
title: Additional file 5 of Integration of transcriptomic data in a genome-scale metabolic model to investigate the link between obesity and breast cancer

description: Enrichment analysis of top 50 rewired nodes of tp4 and tp5 central reference gene-based networks, obtained by the union and comparison between lean and obese networks. The list of the rewired genes and the relative Dn-scores is also provided. (XLSX 17.6 kb)
DOI: 10.6084/m9.figshare.10034309.v1
title: Additional file 1: of Religiosity and sexual abstinence among Nigerian youths: does parent religion matter?

description: Protective Sexual Behaviour. (XLSX 52 kb)
DOI: 10.6084/m9.figshare.10034294
title: Additional file 2 of Integration of transcriptomic data in a genome-scale metabolic model to investigate the link between obesity and breast cancer

description: R scripts and the relative input files to create the reaction-based graphs. (ZIP 368 kb)
DOI: 10.6084/m9.figshare.10034300
title: Additional file 4 of Integration of transcriptomic data in a genome-scale metabolic model to investigate the link between obesity and breast cancer

description: Top 20 rewired nodes of tp4 and tp5 central reference networks, obtained by the union and comparison between lean and obese networks. The table contains for each HMR code, the equation, the subsystem and the associated genes. (XLSX 52.9 kb)
DOI: 10.6084/m9.figshare.10034291
title: Additional file 1 of Integration of transcriptomic data in a genome-scale metabolic model to investigate the link between obesity and breast cancer

description: Matlab code and the relative expression input files to simulate the metabolic model by integrating gene expression data. (ZIP 367 kb)
DOI: 10.6084/m9.figshare.10034297
title: Additional file 3 of Integration of transcriptomic data in a genome-scale metabolic model to investigate the link between obesity and breast cancer

description: Tables of the flux rates output having either opposite direction or same direction with abs(log 2FC) â Ľâ 1 in lean and obese metabolic network. For each table of fluxes, we also provided the table with the expression values (mean and SD) of the associated genes. (XLSX 304 kb)
DOI: 10.6084/m9.figshare.10034303.v1
title: Additional file 5 of Integration of transcriptomic data in a genome-scale metabolic model to investigate the link between obesity and breast cancer

description: Enrichment analysis of top 50 rewired nodes of tp4 and tp5 central reference gene-based networks, obtained by the union and comparison between lean and obese networks. The list of the rewired genes and the relative Dn-scores is also provided. (XLSX 17.6 kb)
DOI: 10.6084/m9.figshare.10034294.v1
title: Additional file 2 of Integration of transcriptomic data in a genome-scale metabolic model to investigate the link between obesity and breast cancer

description: R scripts and the relative input files to create the reaction-based graphs. (ZIP 368 kb)
DOI: 10.6084/m9.figshare.10034297.v1
title: Additional file 3 of Integration of transcriptomic data in a genome-scale metabolic model to investigate the link between obesity and breast cancer

description: Tables of the flux rates output having either opposite direction or same direction with abs(log 2FC) â Ľâ 1 in lean and obese metabolic network. For each table of fluxes, we also provided the table with the expression values (mean and SD) of the associated genes. (XLSX 304 kb)
DOI: 10.6084/m9.figshare.10034300.v1
title: Additional file 4 of Integration of transcriptomic data in a genome-scale metabolic model to investigate the link between obesity and breast cancer

description: Top 20 rewired nodes of tp4 and tp5 central reference networks, obtained by the union and comparison between lean and obese networks. The table contains for each HMR code, the equation, the subsystem and the associated genes. (XLSX 52.9 kb)
DOI: 10.6084/m9.figshare.10034291.v1
title: Additional file 1 of Integration of transcriptomic data in a genome-scale metabolic model to investigate the link between obesity and breast cancer

description: Matlab code and the relative expression input files to simulate the metabolic model by integrating gene expression data. (ZIP 367 kb)
DOI: 10.6084/m9.figshare.10034228
title: Additional file 2: of Understanding patient engagement in health system decision-making: a co-designed scoping review

description: Data-charting (extraction) sheet. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.10034228.v1
title: Additional file 2: of Understanding patient engagement in health system decision-making: a co-designed scoping review

description: Data-charting (extraction) sheet. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.10034186
title: Additional file 1: of Sugar-sweetened beverage affordability and the prevalence of overweight and obesity in a cross section of countries

description: Including the following Tables and Figures: Table S1. Source and short description of each variable. Table S2. Raw data (full dataset, with 183 countries). Figure S1. Sugar-sweetened beverage consumption and the prevalence of overweight. Figure S2. Sugar-sweetened beverage affordability and the prevalence of overweight. (XLS 173 kb)
DOI: 10.6084/m9.figshare.10034186.v1
title: Additional file 1: of Sugar-sweetened beverage affordability and the prevalence of overweight and obesity in a cross section of countries

description: Including the following Tables and Figures: Table S1. Source and short description of each variable. Table S2. Raw data (full dataset, with 183 countries). Figure S1. Sugar-sweetened beverage consumption and the prevalence of overweight. Figure S2. Sugar-sweetened beverage affordability and the prevalence of overweight. (XLS 173 kb)
DOI: 10.6084/m9.figshare.10034171
title: Additional file 1 of From trash to treasure: detecting unexpected contamination in unmapped NGS data

description: This Excel file includes several sheets containing all the details on the data used for the accuracy assessment and the comparison with other tools, and the obtained results. (XLSX 139 kb)
DOI: 10.6084/m9.figshare.10034171.v1
title: Additional file 1 of From trash to treasure: detecting unexpected contamination in unmapped NGS data

description: This Excel file includes several sheets containing all the details on the data used for the accuracy assessment and the comparison with other tools, and the obtained results. (XLSX 139 kb)
DOI: 10.6084/m9.figshare.10034138
title: Additional file 8: of Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer

description: Crosstalks_network. Network of crosstalks based on shared proteins between modules of ACSN and subsystems of ReconMap 2.0 in TXT format. This file contains Source nodes, Target nodes, Interaction type and the number of intersection proteins corresponding to each edge. The file was used for visualisation of the crosstalks in Fig. 4 (available at https://navicell.curie.fr/pages/maps_ReconMap 2.html ). (TXT 9 kb)
DOI: 10.6084/m9.figshare.10034138.v1
title: Additional file 8: of Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer

description: Crosstalks_network. Network of crosstalks based on shared proteins between modules of ACSN and subsystems of ReconMap 2.0 in TXT format. This file contains Source nodes, Target nodes, Interaction type and the number of intersection proteins corresponding to each edge. The file was used for visualisation of the crosstalks in Fig. 4 (available at https://navicell.curie.fr/pages/maps_ReconMap 2.html ). (TXT 9 kb)
DOI: 10.6084/m9.figshare.10034126
title: Additional file 4: of Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer

description: ReconMap2 GMT. Gene sets composing ReconMap 2.0 subsystems (available at https://navicell.curie.fr/pages/maps_ReconMap 2.html ). (GMT 21 kb)
DOI: 10.6084/m9.figshare.10034126.v1
title: Additional file 4: of Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer

description: ReconMap2 GMT. Gene sets composing ReconMap 2.0 subsystems (available at https://navicell.curie.fr/pages/maps_ReconMap 2.html ). (GMT 21 kb)
DOI: 10.6084/m9.figshare.10034123
title: Additional file 3: of Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer

description: ACSN GMT. Gene sets composing ACSN modules (available at https://navicell.curie.fr/pages/maps_ReconMap 2.html ). (GMT 31 kb)
DOI: 10.6084/m9.figshare.10034117
title: Additional file 1: of Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer

description: List of common proteins. List of the 252 proteins found in common between ACSN and ReconMapÂ 2.0 maps (available at https://navicell.curie.fr/pages/maps_ReconMap 2.html ). (TXT 1 kb)
DOI: 10.6084/m9.figshare.10034123.v1
title: Additional file 3: of Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer

description: ACSN GMT. Gene sets composing ACSN modules (available at https://navicell.curie.fr/pages/maps_ReconMap 2.html ). (GMT 31 kb)
DOI: 10.6084/m9.figshare.10034117.v1
title: Additional file 1: of Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer

description: List of common proteins. List of the 252 proteins found in common between ACSN and ReconMapÂ 2.0 maps (available at https://navicell.curie.fr/pages/maps_ReconMap 2.html ). (TXT 1 kb)
DOI: 10.6084/m9.figshare.10034087
title: Additional file 1 of Sequence imputation from low density single nucleotide polymorphism panel in a black poplar breeding population

description: Sequencing, pedigree and reference information’s of each reference individuals. (CSV 4.33 kb)
DOI: 10.6084/m9.figshare.10034087.v1
title: Additional file 1 of Sequence imputation from low density single nucleotide polymorphism panel in a black poplar breeding population

description: Sequencing, pedigree and reference information’s of each reference individuals. (CSV 4.33 kb)
DOI: 10.6084/m9.figshare.10034006
title: Additional file 3: of SQUAT: a Sequencing Quality Assessment Tool for data quality assessments of genome assemblies

description: Post-assembly reports of the datasets used in Table 4. (ZIP 3120 kb)
DOI: 10.6084/m9.figshare.10034000
title: Additional file 1: of SQUAT: a Sequencing Quality Assessment Tool for data quality assessments of genome assemblies

description: Pre-assembly reports of the datasets used in Table 3. (ZIP 46 kb)
DOI: 10.6084/m9.figshare.10034000.v1
title: Additional file 1: of SQUAT: a Sequencing Quality Assessment Tool for data quality assessments of genome assemblies

description: Pre-assembly reports of the datasets used in Table 3. (ZIP 46 kb)
DOI: 10.6084/m9.figshare.10034006.v1
title: Additional file 3: of SQUAT: a Sequencing Quality Assessment Tool for data quality assessments of genome assemblies

description: Post-assembly reports of the datasets used in Table 4. (ZIP 3120 kb)
DOI: 10.6084/m9.figshare.10033988
title: Additional file 4: of BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing

description: R script used to generate the simulated dataset with powsimR package [28]. (R 6 kb)
DOI: 10.6084/m9.figshare.10033982
title: Additional file 2: of BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing

description: Table S1. List of publications referencing the Soumillon et al. 2014 study in the context of bulk RNA profiling using the SCRB-seq protocol. Table S2. List of LCL samples from the GBR population in the 1000 Genome Project. Table S3. The detailed cost structure of the BRB-seq protocol. Table S4. List of samples used in the manuscript. Table S5. List of primers used RT-qPCR. Table S6. BRB-seq barcoded oligo-dT primers (BU3). Table S7. Primers used for BRB-seq library preparation. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.10033988.v1
title: Additional file 4: of BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing

description: R script used to generate the simulated dataset with powsimR package [28]. (R 6 kb)
DOI: 10.6084/m9.figshare.10033982.v1
title: Additional file 2: of BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing

description: Table S1. List of publications referencing the Soumillon et al. 2014 study in the context of bulk RNA profiling using the SCRB-seq protocol. Table S2. List of LCL samples from the GBR population in the 1000 Genome Project. Table S3. The detailed cost structure of the BRB-seq protocol. Table S4. List of samples used in the manuscript. Table S5. List of primers used RT-qPCR. Table S6. BRB-seq barcoded oligo-dT primers (BU3). Table S7. Primers used for BRB-seq library preparation. (XLSX 34 kb)