cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8105441.v1
title: Additional file 5: of Integrated omics-based pathway analyses uncover CYP epoxygenase-associated networks as theranostic targets for metastatic triple negative breast cancer

description: Quantitative proteomic data of eight paired TNBC tumors and adjacent normal tissues using iTRAQ. (XLS 3510 kb)
DOI: 10.6084/m9.figshare.8105429
title: Additional file 4: of Integrated omics-based pathway analyses uncover CYP epoxygenase-associated networks as theranostic targets for metastatic triple negative breast cancer

description: List of nodes related to processes upregulated in CYP epoxyge nase overexpressing TNBC, ERâ /PRâ /HER2+ and ER+/PR+/TPBC samples. (XLS 107 kb)
DOI: 10.6084/m9.figshare.8105435.v1
title: Additional file 1: of Within-sample co-methylation patterns in normal tissues

description: All R scripts for the analysis of this paper. (ZIP 20 kb)
DOI: 10.6084/m9.figshare.8105426
title: MOESM3 of Unraveling essential cellulosomal components of the (Pseudo)Bacteroides cellulosolvens reveals an extensive reservoir of novel catalytic enzymes

description: Additional file 3: Table S2. Differentially expressed proteins represented in Fig.Â 3. A, 166 proteins which showed significantly different intensities between substrates in peak I. B, 245 proteins which showed significantly different intensities between CB and MCC in peak II. LFQ intensities (log2) are shown, where zero intensity values were imputed to 10. Differential proteins were selected with cutoffs of |log2 fold change| â Ľ1 and FDR q-value â ¤0.1. CD, cellobiose; Cl, microcrystalline cellulose.
DOI: 10.6084/m9.figshare.8105426.v1
title: MOESM3 of Unraveling essential cellulosomal components of the (Pseudo)Bacteroides cellulosolvens reveals an extensive reservoir of novel catalytic enzymes

description: Additional file 3: Table S2. Differentially expressed proteins represented in Fig.Â 3. A, 166 proteins which showed significantly different intensities between substrates in peak I. B, 245 proteins which showed significantly different intensities between CB and MCC in peak II. LFQ intensities (log2) are shown, where zero intensity values were imputed to 10. Differential proteins were selected with cutoffs of |log2 fold change| â Ľ1 and FDR q-value â ¤0.1. CD, cellobiose; Cl, microcrystalline cellulose.
DOI: 10.6084/m9.figshare.8105429.v1
title: Additional file 4: of Integrated omics-based pathway analyses uncover CYP epoxygenase-associated networks as theranostic targets for metastatic triple negative breast cancer

description: List of nodes related to processes upregulated in CYP epoxyge nase overexpressing TNBC, ERâ /PRâ /HER2+ and ER+/PR+/TPBC samples. (XLS 107 kb)
DOI: 10.25934/00003508.0
title: Available IPD datapackage for study 'A Randomised, Double-blind, Placebo-controlled Parallel Group Efficacy and Safety Study of BI 1356 (5 mg) Administered Orally Once Daily Over 24 Weeks, With an Open-label Extension to One Year (Placebo Patients Switched to BI 1356), in Type 2 Diabetic Patients With Insufficient Glycaemic Control Despite a Therapy of Metformin in Combination With a Sulphonylurea'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.6084/m9.figshare.8105417
title: MOESM1 of Unraveling essential cellulosomal components of the (Pseudo)Bacteroides cellulosolvens reveals an extensive reservoir of novel catalytic enzymes

description: Additional file 1: Table S1. Label-free LC-MS/MS raw data analysis of cellulosomal fractions. Raw data from MaxQuant analysis of protein intensities before the normalization step. Data were annotated according to the Pseudobacteroides cellulosolvens ATCC 35603 DSM 2993 sequences in UniprotKB.
DOI: 10.6084/m9.figshare.8105420
title: Additional file 3: of Integrated omics-based pathway analyses uncover CYP epoxygenase-associated networks as theranostic targets for metastatic triple negative breast cancer

description: Gene enrichment associations for the tumor specimens in the discovery set with mRNA expression z score of â Ľ2.0 for CYP2J2 and CYP2C9. (XLS 7282 kb)
DOI: 10.25934/00003508.1
title: IPD datapackage for study 'A Randomised, Double-blind, Placebo-controlled Parallel Group Efficacy and Safety Study of BI 1356 (5 mg) Administered Orally Once Daily Over 24 Weeks, With an Open-label Extension to One Year (Placebo Patients Switched to BI 1356), in Type 2 Diabetic Patients With Insufficient Glycaemic Control Despite a Therapy of Metformin in Combination With a Sulphonylurea' and research request: 'Stratification of SGLT2 inhibitor glucose lowering therapy in Type 2 diabetes'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.6084/m9.figshare.8105417.v1
title: MOESM1 of Unraveling essential cellulosomal components of the (Pseudo)Bacteroides cellulosolvens reveals an extensive reservoir of novel catalytic enzymes

description: Additional file 1: Table S1. Label-free LC-MS/MS raw data analysis of cellulosomal fractions. Raw data from MaxQuant analysis of protein intensities before the normalization step. Data were annotated according to the Pseudobacteroides cellulosolvens ATCC 35603 DSM 2993 sequences in UniprotKB.
DOI: 10.6084/m9.figshare.8105420.v1
title: Additional file 3: of Integrated omics-based pathway analyses uncover CYP epoxygenase-associated networks as theranostic targets for metastatic triple negative breast cancer

description: Gene enrichment associations for the tumor specimens in the discovery set with mRNA expression z score of â Ľ2.0 for CYP2J2 and CYP2C9. (XLS 7282 kb)
DOI: 10.6084/m9.figshare.8105405
title: Additional file 5: of Effects of Genetic Background and Environmental Conditions on Texture Properties in a Recombinant Inbred Population of an Inter-Subspecies Cross

description: Table S5. The QTL analysis of amylopectin chain length distribution. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8105408
title: Additional file 6: of Effects of Genetic Background and Environmental Conditions on Texture Properties in a Recombinant Inbred Population of an Inter-Subspecies Cross

description: Table S6. The yield and quality traits of RILs in four areas. (XLSX 143 kb)
DOI: 10.6084/m9.figshare.8105396
title: Additional file 2: of Effects of Genetic Background and Environmental Conditions on Texture Properties in a Recombinant Inbred Population of an Inter-Subspecies Cross

description: Table S2. The quality related genetic background diagnosis of parent lines. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8105399
title: Additional file 3: of Effects of Genetic Background and Environmental Conditions on Texture Properties in a Recombinant Inbred Population of an Inter-Subspecies Cross

description: Table S3. QTL mapping for Texture properties of the RIL population in 2015. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8105402
title: Additional file 4: of Effects of Genetic Background and Environmental Conditions on Texture Properties in a Recombinant Inbred Population of an Inter-Subspecies Cross

description: Figure S1. The fine mapping of dep1. (a) The fine mapping of DEP1 using the data of amylopectin chain length distribution. (b) The sequence comparison of annotated genes in block 19,948. (c) The express preference of annotated genes in block 19,948. (d) The image of DEP1 mutant generated by CRISPR/Cas9 gene editing technology, and the taste score of mutant and WT (Sasanishiki). *, significant at 5% level. (XLSX 1871 kb)
DOI: 10.6084/m9.figshare.8105399.v1
title: Additional file 3: of Effects of Genetic Background and Environmental Conditions on Texture Properties in a Recombinant Inbred Population of an Inter-Subspecies Cross

description: Table S3. QTL mapping for Texture properties of the RIL population in 2015. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8105405.v1
title: Additional file 5: of Effects of Genetic Background and Environmental Conditions on Texture Properties in a Recombinant Inbred Population of an Inter-Subspecies Cross

description: Table S5. The QTL analysis of amylopectin chain length distribution. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8105408.v1
title: Additional file 6: of Effects of Genetic Background and Environmental Conditions on Texture Properties in a Recombinant Inbred Population of an Inter-Subspecies Cross

description: Table S6. The yield and quality traits of RILs in four areas. (XLSX 143 kb)
DOI: 10.6084/m9.figshare.8105402.v1
title: Additional file 4: of Effects of Genetic Background and Environmental Conditions on Texture Properties in a Recombinant Inbred Population of an Inter-Subspecies Cross

description: Figure S1. The fine mapping of dep1. (a) The fine mapping of DEP1 using the data of amylopectin chain length distribution. (b) The sequence comparison of annotated genes in block 19,948. (c) The express preference of annotated genes in block 19,948. (d) The image of DEP1 mutant generated by CRISPR/Cas9 gene editing technology, and the taste score of mutant and WT (Sasanishiki). *, significant at 5% level. (XLSX 1871 kb)
DOI: 10.6084/m9.figshare.8105396.v1
title: Additional file 2: of Effects of Genetic Background and Environmental Conditions on Texture Properties in a Recombinant Inbred Population of an Inter-Subspecies Cross

description: Table S2. The quality related genetic background diagnosis of parent lines. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8105387
title: Additional file 1: of Effects of Genetic Background and Environmental Conditions on Texture Properties in a Recombinant Inbred Population of an Inter-Subspecies Cross

description: Table S1. The sowing, heading and mature date of RILs in four areas. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.8105375
title: Additional file 1: of Critically appraised topic on adverse food reactions of companion animals (7): signalment and cutaneous manifestations of dogs and cats with adverse food reactions

description: Table S1. Summary of articles reporting dogs with cutaneous adverse food reactions. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.8105381
title: Additional file 2: of Critically appraised topic on adverse food reactions of companion animals (7): signalment and cutaneous manifestations of dogs and cats with adverse food reactions

description: Table S2. Summary of articles reporting cats with cutaneous adverse food reactions. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.8105387.v1
title: Additional file 1: of Effects of Genetic Background and Environmental Conditions on Texture Properties in a Recombinant Inbred Population of an Inter-Subspecies Cross

description: Table S1. The sowing, heading and mature date of RILs in four areas. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.8105375.v1
title: Additional file 1: of Critically appraised topic on adverse food reactions of companion animals (7): signalment and cutaneous manifestations of dogs and cats with adverse food reactions

description: Table S1. Summary of articles reporting dogs with cutaneous adverse food reactions. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.8105381.v1
title: Additional file 2: of Critically appraised topic on adverse food reactions of companion animals (7): signalment and cutaneous manifestations of dogs and cats with adverse food reactions

description: Table S2. Summary of articles reporting cats with cutaneous adverse food reactions. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.8105297
title: Additional file 1: of ImageJ SurfCut: a user-friendly pipeline for high-throughput extraction of cell contours from 3D image stacks

description: SurfCut macro. Text file containing the source code of the Fiji macro SurfCut. (TXT 14 kb)
DOI: 10.6084/m9.figshare.8105297.v1
title: Additional file 1: of ImageJ SurfCut: a user-friendly pipeline for high-throughput extraction of cell contours from 3D image stacks

description: SurfCut macro. Text file containing the source code of the Fiji macro SurfCut. (TXT 14 kb)
DOI: 10.6084/m9.figshare.8105267
title: Additional file 4: of Comparative analyses of the variation of the transcriptome and proteome of Rhodobacter sphaeroides throughout growth

description: Proteins showing changed levels at various growth phases and their COG associations. (XLSX 595 kb)
DOI: 10.6084/m9.figshare.8105264
title: Additional file 3: of Comparative analyses of the variation of the transcriptome and proteome of Rhodobacter sphaeroides throughout growth

description: RNAs showing changes in accumulation at various growth phases. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.8105267.v1
title: Additional file 4: of Comparative analyses of the variation of the transcriptome and proteome of Rhodobacter sphaeroides throughout growth

description: Proteins showing changed levels at various growth phases and their COG associations. (XLSX 595 kb)
DOI: 10.6084/m9.figshare.8105264.v1
title: Additional file 3: of Comparative analyses of the variation of the transcriptome and proteome of Rhodobacter sphaeroides throughout growth

description: RNAs showing changes in accumulation at various growth phases. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.8105252
title: Additional file 1: of Comparative analyses of the variation of the transcriptome and proteome of Rhodobacter sphaeroides throughout growth

description: Summary of all changes in transcriptome and proteome. (XLSX 981 kb)
DOI: 10.6084/m9.figshare.8105252.v1
title: Additional file 1: of Comparative analyses of the variation of the transcriptome and proteome of Rhodobacter sphaeroides throughout growth

description: Summary of all changes in transcriptome and proteome. (XLSX 981 kb)
DOI: 10.6084/m9.figshare.8105213
title: Additional file 3: of Transcriptomic and proteomic analyses of genetic factors influencing adductor muscle coloration in QN Orange scallops

description: Table S3. Differentially expressed proteins (DEPs) between the between orange (O) and white adductor muscle (W) samples by the lable free proteomics. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.8105213.v1
title: Additional file 3: of Transcriptomic and proteomic analyses of genetic factors influencing adductor muscle coloration in QN Orange scallops

description: Table S3. Differentially expressed proteins (DEPs) between the between orange (O) and white adductor muscle (W) samples by the lable free proteomics. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.8105189
title: RNA-seq Analysis of Nepenthes ampullaria

description: Sequence, annotation, and analysis files for Nepenthes ampullaria trancriptome analysis
DOI: 10.6084/m9.figshare.8105171
title: 33Grapes.Total.InDel.final.vcf.gz

description: Candidate indel variants detected by analysis of genome resequencing data from 33 grape accessions
DOI: 10.6084/m9.figshare.8105186
title: Treatments administered following castration-resistant prostate cancer diagnosis while investigating the influence of prior treatment on the relationship between prostate-specific antigen kinetics and survival

description: This dataset comprises a single <b>.docx </b>file containing a single table of summary statistics for treatments administered to 295 patients for castration-resistant prostate cancer (CRPC). These treatments were administered as part of study to determine whether prostate-specific antigen (PSA) kinetics may serve as prognosticators regardless of prior local treatment.<br>The same patients were statified in two ways: i) their time to PSA nadir and ii) their time to CRPC progression. Treatments included Docetaxel, androgen receptor-axis targeted (ARAT) agent use, Cabazitaxel, Radium-233, and clinical trials. Data for the number of Docetaxel cycles are presented as median and interquartile range, while all other data are presented as numbers of participants and percentages of the total group.<br>The related study aims to determine the effect of prior local treatment and PSA kinetics during androgen-deprivation therapy (ADT) on the survival of CRPC patients. The authors performed a multicentre retrospective study which included patients who had been diagnosed with CRPC between September 2009 and November 2017, and investigated PSA kinetics during ADT, including percentage PSA decline, PSA nadir level, time to PSA nadir, and time to CRPC progression. Subgroup analysis was performed according to the prior history of local curative treatment.
DOI: 10.6084/m9.figshare.8105159
title: CeRNA network analysis and functional enrichment of salt sensitivity of blood pressure by weighted-gene co-expression analysis

description: p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; text-align: justify; font: 12.0px Times; -webkit-text-stroke: #000000} span.s1 {font-kerning: none} Salt sensitivity of blood pressure (SSBP) is an independent risk factor for cardiovascular disease. The pathogenic mechanisms of SSBP are still uncertain. This study aimed to construct the co-regulatory network of SSBP and data mining strategy based on the competitive endogenous RNA (ceRNA) theory. We used ceRNA microarray to screen for candidate lncRNAs and mRNAs. The WGCNA package and target miRNA and mRNA prediction databases were used to construct the ceRNA co-regulatory network and to discover the pathways related to SSBP. Enrichment and pathway analysis were performed to explore the functions of hub genes in networks.
DOI: 10.6084/m9.figshare.8105171.v1
title: 33Grapes.Total.InDel.final.vcf.gz

description: Candidate indel variants detected by analysis of genome resequencing data from 33 grape accessions
DOI: 10.6084/m9.figshare.8105186.v1
title: Treatments administered following castration-resistant prostate cancer diagnosis while investigating the influence of prior treatment on the relationship between prostate-specific antigen kinetics and survival

description: This dataset comprises a single <b>.docx </b>file containing a single table of summary statistics for treatments administered to 295 patients for castration-resistant prostate cancer (CRPC). These treatments were administered as part of study to determine whether prostate-specific antigen (PSA) kinetics may serve as prognosticators regardless of prior local treatment.<br>The same patients were statified in two ways: i) their time to PSA nadir and ii) their time to CRPC progression. Treatments included Docetaxel, androgen receptor-axis targeted (ARAT) agent use, Cabazitaxel, Radium-233, and clinical trials. Data for the number of Docetaxel cycles are presented as median and interquartile range, while all other data are presented as numbers of participants and percentages of the total group.<br>The related study aims to determine the effect of prior local treatment and PSA kinetics during androgen-deprivation therapy (ADT) on the survival of CRPC patients. The authors performed a multicentre retrospective study which included patients who had been diagnosed with CRPC between September 2009 and November 2017, and investigated PSA kinetics during ADT, including percentage PSA decline, PSA nadir level, time to PSA nadir, and time to CRPC progression. Subgroup analysis was performed according to the prior history of local curative treatment.
DOI: 10.6084/m9.figshare.8105159.v1
title: CeRNA network analysis and functional enrichment of salt sensitivity of blood pressure by weighted-gene co-expression analysis

description: p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; text-align: justify; font: 12.0px Times; -webkit-text-stroke: #000000} span.s1 {font-kerning: none} Salt sensitivity of blood pressure (SSBP) is an independent risk factor for cardiovascular disease. The pathogenic mechanisms of SSBP are still uncertain. This study aimed to construct the co-regulatory network of SSBP and data mining strategy based on the competitive endogenous RNA (ceRNA) theory. We used ceRNA microarray to screen for candidate lncRNAs and mRNAs. The WGCNA package and target miRNA and mRNA prediction databases were used to construct the ceRNA co-regulatory network and to discover the pathways related to SSBP. Enrichment and pathway analysis were performed to explore the functions of hub genes in networks.
DOI: 10.6084/m9.figshare.8105027
title: Full length sequence and classification for circRNAs

description: Here, the full length circRNA sequences and circRNA classification are given for the circRNAs downloaded from circbase, circRNAdb and plantcircbase database.The details for the annotation file and the reference genome are as follows: 1. <b>circbase and circRNAdb</b> The annotation file is downloaded from circRNAdb (http://202.195.183.4:8000/circrnadb/resources.php) and the reference genome hg19 is downloaded from UCSC (http://hgdownload.soe.ucsc.edu/downloads.html#human). 2. <b>Arabidopsis thaliana</b> The reference genome and annotation version TAIR10.38 are downloaded from ftp://ftp.ensemblgenomes.org/pub/plants/release-38/ 3. <b>Poncirus trifoliata </b> The reference genome and annotation version Citrus_clementina_v1.0 are downloaded from https://ftp.ncbi.nih.gov/genomes/refseq/plant 4. <b>Glycine max</b> The reference genome and annotation version Glycine_max_v2.0.38 are downloaded from ftp://ftp.ensemblgenomes.org/pub/plants/release-38/ 5. <b>Gossypium arboreum</b> The reference genome and annotation version Gossypium_arboreum_v1.0 are downloaded from https://ftp.ncbi.nih.gov/genomes/refseq/plant/ 6. <b>Gossypium hirsutum</b> The reference genome and annotation version NBI_Gossypium_hirsutum_v1.1 are downloaded from https://www.cottongen.org/data/download/genome_NBI_AD1 7. <b>Gossypium raimondii</b> The reference genome and annotation version Graimondii_221 are downloaded from ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Graimondii/ 8. <b>Hordeum vulgare</b> The reference genome and annotation version Hv_IBSC_PGSB_v2.38 are downloaded from ftp://ftp.ensemblgenomes.org/pub/plants/release-38/ 9. <b>Oryza sativa</b> The reference genome and annotation version IRGSP-1.0.38 are downloaded from ftp://ftp.ensemblgenomes.org/pub/plants/release-38/ 10. <b>Solanum lycopersicum</b> The reference genome and annotation version SL2.50.38 are downloaded from ftp://ftp.ensemblgenomes.org/pub/plants/release-38/ 11. <b>Solanum tuberosum</b> The reference genome and annotation version SolTub_3.0.38 are downloaded from ftp://ftp.ensemblgenomes.org/pub/plants/release-38/ 12. <b>Triticum aestivum</b> The reference genome and annotation version IWGSC1.0+popseq.29 are downloaded from ftp://ftp.ensemblgenomes.org/pub/plants/release-29/ 13. <b>Zea mays</b> The reference genome and annotation version AGPv4.38 are downloaded from ftp://ftp.ensemblgenomes.org/pub/plants/release-38/
DOI: 10.6084/m9.figshare.8105189.v1
title: RNA-seq Analysis of Nepenthes ampullaria

description: Sequence, annotation, and analysis files for Nepenthes ampullaria trancriptome analysis
DOI: 10.6084/m9.figshare.8105189.v2
title: RNA-seq Analysis of Nepenthes ampullaria

description: Sequence, annotation, and analysis files for Nepenthes ampullaria trancriptome analysis