cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3611162_d5
title: Additional file 10: Table S10. of Transcriptomic analysis of differentially expressed genes in the floral transition of the summer flowering chrysanthemum

description: Genes differentially transcribed in the comparison in the comparison L2 vs S2. Criteria as given in Additional file 4: Table S4. (XLS 1772Â kb)
DOI: 10.6084/m9.figshare.c.3611162_d4
title: Additional file 4: Table S4. of Transcriptomic analysis of differentially expressed genes in the floral transition of the summer flowering chrysanthemum

description: Genes differentially transcribed in the comparison CK vs S1. The criteria applied for assigning significance were: P-value
DOI: 10.6084/m9.figshare.c.3611150_d6
title: Additional file 3: of Integrated analysis of mRNA, microRNA and protein in systemic lupus erythematosus-specific induced pluripotent stem cells from urine

description: Table S3. Up-regulation of differentially expressed proteins. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3611162_d3
title: Additional file 11: Table S11. of Transcriptomic analysis of differentially expressed genes in the floral transition of the summer flowering chrysanthemum

description: Differential transcription genes involved in the photoperiod pathway in the comparisons L1 vs S1 and L2 vs S2. (XLS 52Â kb)
DOI: 10.15468/dl.vkfxfx
title: Occurrence Download

description: A dataset containing 820 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "DatasetKey is iNaturalist Research-grade Observations",
 "Geometry POLYGON((-120.653 34.373,-119.44 34.373,-119.44 35.114,-120.653 35.114,-120.653 34.373))",
 "TaxonKey is one of (Tamarix ramosissima Ledeb., Bromus tectorum L., Brassica nigra (L.) Andrz., Carduus pycnocephalus L., Centaurea melitensis L., Centaurea solstitialis L., Cirsium vulgare (Savi) Petr., Spartium junceum var. plenum Weston)"
 ]
}

 The dataset includes 820 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032631-241126133413365/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.c.3610958_d9
title: Additional file 4: Table S2. of Mapping the landscape of metabolic goals of a cell

description: shows non-zero minimal/maximal optimization coefficients computed by objective variability analysis (OVA) for each reaction from simulated succinate-limited E. coli fluxes. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3610958_d8
title: Additional file 5: Table S3. of Mapping the landscape of metabolic goals of a cell

description: shows non-zero minimal/maximal optimization coefficients computed by objective variability analysis (OVA) for each reaction from simulated glycerol-limited E. coli fluxes. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3610958_d6
title: Additional file 2: Table S7. of Mapping the landscape of metabolic goals of a cell

description: shows invFBA results from L1 and L0 norm regularization of simulated E. coli data under different growth conditions (with growth flux maximization as the objective). (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3610952_d6
title: Additional file 8: Table S6. of Large-scale identification of wheat genes resistant to cereal cyst nematode Heterodera avenae using comparative transcriptomic analysis

description: KEGG enrichment analysis of the rescued genes exhibiting uncoordinated expression profiles. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.c.3610958_d5
title: Additional file 3: Table S1. of Mapping the landscape of metabolic goals of a cell

description: shows non-zero minimal/maximal optimization coefficients computed by objective variability analysis (OVA) for each reaction from simulated glucose-limited E. coli fluxes. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3610958_d3
title: Additional file 6: Table S8. of Mapping the landscape of metabolic goals of a cell

description: shows invFBA results from L1 and L0 regularization of simulated E. coli data under different growth conditions (with maximization of ATP synthase as the objective). (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3610952_d5
title: Additional file 6: Table S4. of Large-scale identification of wheat genes resistant to cereal cyst nematode Heterodera avenae using comparative transcriptomic analysis

description: Identification of ROS-producing genes and primers used for qRT-PCR assay. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3610958_d2
title: Additional file 7: Table S9. of Mapping the landscape of metabolic goals of a cell

description: shows invFBA results from L1 and L0 regularization of simulated E. coli data under glucose minimal medium (with minimization of glucose uptake as the objective). (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3610952_d4
title: Additional file 7: Table S5. of Large-scale identification of wheat genes resistant to cereal cyst nematode Heterodera avenae using comparative transcriptomic analysis

description: Additional rescued candidate resistance genes. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3610958_d1
title: Additional file 10: Table S6. of Mapping the landscape of metabolic goals of a cell

description: shows maximal optimization coefficients computed by objective variability analysis (OVA) for each reaction from fluxes measured in 11 evolved E. coli strains. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3610925_d1
title: Additional file 3: Table S3. of Characterization of genome-wide H3K27ac profiles reveals a distinct PM2.5-associated histone modification signature

description: Complete list of differentially modified H3K27ac loci. (XLSX 69 kb)
DOI: 10.6084/m9.figshare.c.3610925_d2
title: Additional file 4: Table S4. of Characterization of genome-wide H3K27ac profiles reveals a distinct PM2.5-associated histone modification signature

description: Complete list of functional annotations. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.c.3610535_d1
title: Additional file 2: Tables S1â  S9. of Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures

description: Supplementary tables. (XLSX 3868 kb)
DOI: 10.6084/m9.figshare.c.3610523_d2
title: Additional file 2: of Identification and characterization of a high kernel weight mutant induced by gamma radiation in wheat (Triticum aestivum L.)

description: The sequence of Xbarc239. (TXT 1Â kb)
DOI: 10.6084/m9.figshare.c.3610523_d1
title: Additional file 1: of Identification and characterization of a high kernel weight mutant induced by gamma radiation in wheat (Triticum aestivum L.)

description: The data of genotype and phenotype. (XLSX 100Â kb)
DOI: 10.6084/m9.figshare.c.3610499_d1
title: Additional file 1: Table S1. of Genetic basis of maize kernel starch content revealed by high-density single nucleotide polymorphism markers in a recombinant inbred line population

description: Summary of SNPs polymorphic between two parents in the CI7/K22 RIL population. Table S2 Summary of the bin and genetic linkage maps in the CI7/K22 RIL population. Table S3 List of genes within the genomic region spanning the single bin at the QTL peak. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.c.3610379_d6
title: Additional file 7: Table S5. of Comparative proteomics reveals that central metabolism changes are associated with resistance against Sporisorium scitamineum in sugarcane

description: List of upregulated proteins identified and quantified by the iTRAQ analysis in RT/RCK. (XLS 263 kb)
DOI: 10.6084/m9.figshare.c.3610379_d5
title: Additional file 8: Table S6. of Comparative proteomics reveals that central metabolism changes are associated with resistance against Sporisorium scitamineum in sugarcane

description: List of downregulated proteins identified and quantified by the iTRAQ analysis in RT/RCK. (XLS 171 kb)
DOI: 10.6084/m9.figshare.c.3609995_d4
title: Additional file 8: of A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with Orange allelic variation and fruit Î˛-carotene accumulation in melon fruit

description: Table S7. RNA-sequencing statsitics. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.c.3609980_d8
title: Additional file 9: of Dissecting the biological relationship between TCGA miRNA and mRNA sequencing data using MMiRNA-Viewer

description: Comparison of correlation coefficient values between MMiRNA-Viewer and CrossHub (XLSX 156 kb)
DOI: 10.6084/m9.figshare.c.3609995_d3
title: Additional file 5: Table S4. of A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with Orange allelic variation and fruit Î˛-carotene accumulation in melon fruit

description: List of 79, 805, 37 and 122 genes that were differentially expressed at 10, 20, 30 DAA, and the mature stage, respectively. (XLSX 162Â kb)
DOI: 10.6084/m9.figshare.c.3609980_d6
title: Additional file 8: of Dissecting the biological relationship between TCGA miRNA and mRNA sequencing data using MMiRNA-Viewer

description: The Genes and their associated GO terms for the top 5Â % expression correlation coefficient of different levels at Normal High (NH), Normal Low (NL), Tumor High (TH), Tumor Low (TL) genes of eight cancers. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.c.3609995_d2
title: Additional file 7: Table S6. of A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with Orange allelic variation and fruit Î˛-carotene accumulation in melon fruit

description: DEGs at different fruit developmental stages categorized into functional groups using MapMan. (XLSX 4378Â kb)
DOI: 10.6084/m9.figshare.c.3609980_d5
title: Additional file 2: of Dissecting the biological relationship between TCGA miRNA and mRNA sequencing data using MMiRNA-Viewer

description: 238 miRNA and mRNA pairs (both tumor and normal types) which met the cutoff criteria of inverse correlation and opposite fold change values and FDRâ
DOI: 10.6084/m9.figshare.c.3609995_d1
title: Additional file 2: of A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with Orange allelic variation and fruit Î˛-carotene accumulation in melon fruit

description: Table S1. List of primers. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3609980_d3
title: Additional file 3: of Dissecting the biological relationship between TCGA miRNA and mRNA sequencing data using MMiRNA-Viewer

description: Statistics of the presence in eight cancer types for 238 miRNA and mRNA pairs (both tumor and normal types) which met the cutoff criteria of inverse correlation and opposite fold change values and FDRâ
DOI: 10.6084/m9.figshare.c.3609980_d4
title: Additional file 5: of Dissecting the biological relationship between TCGA miRNA and mRNA sequencing data using MMiRNA-Viewer

description: The centrality scores of genes and miRNAs based on various matrix measurement for the largest connected component of eight cancer types. This file contains results for the largest cluster for all seven other cancers and the second largest cluster for LUSC. (XLSX 886 kb)
DOI: 10.6084/m9.figshare.c.3609980_d2
title: Additional file 1: of Dissecting the biological relationship between TCGA miRNA and mRNA sequencing data using MMiRNA-Viewer

description: 14,505 total miRNA and mRNA pairs (both tumor and normal types) which met the statistical cutoff criteria (inverse correlation values and FDRâ
DOI: 10.6084/m9.figshare.c.3609980_d1
title: Additional file 6: of Dissecting the biological relationship between TCGA miRNA and mRNA sequencing data using MMiRNA-Viewer

description: Cancer association results for 238 pairs which are reported to have opposite FC values between mRNAs and miRNAs and inverse correlations between tumor and normal samples. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.c.3609290_d9
title: Additional file 2: Table S1–S28. of The Sinocyclocheilus cavefish genome provides insights into cave adaptation

description: The supplementary data and statistics, including the information of genome sequencing and assembly (Table S1–S9), genome annotation (Table S10–S17), evolutionary analyses (Table S18–S24), and cave adaption analysis (Table S25–S28). (XLSX 134 kb)
DOI: 10.6084/m9.figshare.c.3609290_d4
title: Additional file 8: Table S29. of The Sinocyclocheilus cavefish genome provides insights into cave adaptation

description: The results of gene family contraction and expansion. (XLSX 75 kb)
DOI: 10.6084/m9.figshare.c.3609290_d1
title: Additional file 10: Table S30. of The Sinocyclocheilus cavefish genome provides insights into cave adaptation

description: The Sinocyclocheilus positive selection gene (PSG) list. (XLSX 153 kb)
DOI: 10.48610/614d78d
title: Reaction zones P fertiliser data

description: Processed data to accompany submitted manuscript file as per journal requirements. This file contains processed P K-edge X-ray adsorption near edge structure as Athena Project files, and the results of linear combination fitting as an excel spreadsheet. Raw data from the incubation experiment is provided in an excel spreadsheet. P32 isotopically exchangeable P results and processed data are provided as an excel spreadsheet. micro-X-ray fluorescence traverse data is provided as an excel spreadsheet.
DOI: 10.6084/m9.figshare.c.3608738_d1
title: Additional file 1 of Predicting drug side effects by multi-label learning and ensemble learning

description: Datasets and source codes. (ZIP 13491Â kb)
DOI: 10.6084/m9.figshare.c.3608669_d4
title: Additional file 2: of Microarray profiling shows distinct differences between primary tumors and commonly used preclinical models in hepatocellular carcinoma

description: Expression profiling data of explant 261004. (XLS 110 kb)
DOI: 10.6084/m9.figshare.c.3608669_d3
title: Additional file 3: of Microarray profiling shows distinct differences between primary tumors and commonly used preclinical models in hepatocellular carcinoma

description: Expression profiling data of explant 01-0207. (XLS 38 kb)
DOI: 10.6084/m9.figshare.c.3608669_d2
title: Additional file 4: of Microarray profiling shows distinct differences between primary tumors and commonly used preclinical models in hepatocellular carcinoma

description: Expression profiling data of explant HEP G2. (XLS 2175 kb)
DOI: 10.6084/m9.figshare.c.3608633_d5
title: Additional file 1: of Selecting SNPs informative for African, American Indian and European Ancestry: application to the Family Investigation of Nephropathy and Diabetes (FIND)

description: RCWilliamsContrastEU_AI450AIMs. (XLSX 60 kb)
DOI: 10.6084/m9.figshare.c.3608633_d3
title: Additional file 2: of Selecting SNPs informative for African, American Indian and European Ancestry: application to the Family Investigation of Nephropathy and Diabetes (FIND)

description: RCWilliamsContrastEU_AF450AIMs. (XLSX 60 kb)
DOI: 10.6084/m9.figshare.c.3608633_d4
title: Additional file 3: of Selecting SNPs informative for African, American Indian and European Ancestry: application to the Family Investigation of Nephropathy and Diabetes (FIND)

description: RCWilliamsContrastAI_AF400AIMS. (XLSX 55 kb)
DOI: 10.6084/m9.figshare.c.3608633_d2
title: Additional file 6: of Selecting SNPs informative for African, American Indian and European Ancestry: application to the Family Investigation of Nephropathy and Diabetes (FIND)

description: RCWilliamsBalanced975AIMs. (XLSX 120 kb)
DOI: 10.6084/m9.figshare.c.3608192_d1
title: Additional file 1: of Platelet to lymphocyte ratio as an independent prognostic indicator for prostate cancer patients receiving androgen deprivation therapy

description: Original data of 290 prostate cancer patients receiving androgen deprivation therapy. (XLS 70 kb)
DOI: 10.6084/m9.figshare.c.3608153_d6
title: Additional file 3: Table S3. of High concentrations of atmospheric ammonia induce alterations of gene expression in the breast muscle of broilers (Gallus gallus) based on RNA-Seq

description: Genes expressed in the breast muscle tissues of broilers are identified using sequencing. (XLSX 2831 kb)
DOI: 10.6084/m9.figshare.c.3608153_d1
title: Additional file 5: Table S4. of High concentrations of atmospheric ammonia induce alterations of gene expression in the breast muscle of broilers (Gallus gallus) based on RNA-Seq

description: Differentially expressed genes in chickens between control and treatment groups. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.c.3608069_d7
title: Additional file 2: of An epigenetic clock for gestational age at birth based on blood methylation data

description: CpG sites and corresponding genes used to predict DNAm age. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.c.3608069_d8
title: Additional file 3: of An epigenetic clock for gestational age at birth based on blood methylation data

description: CpG sites and coefficients used to predict DNAm age. (CSV 3 kb)
DOI: 10.6084/m9.figshare.c.3608096_d3
title: Additional file 2: of Dynamic modulation of phosphoprotein expression in ovarian cancer xenograft models

description: Assessment of biological replicate concordance. Number of replicates for all tested conditions (xenograft/treatment/day) is shown. Correlation coefficients were calculated for all possible pairs of biological replicates and averaged (mean replicate r) using expression values from all detected proteins within each condition. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.c.3608069_d6
title: Additional file 8: of An epigenetic clock for gestational age at birth based on blood methylation data

description: Relevant data from PROGRESS cohort. (CSV 282 kb)
DOI: 10.6084/m9.figshare.c.3608096_d2
title: Additional file 1: of Dynamic modulation of phosphoprotein expression in ovarian cancer xenograft models

description: Protein expression matrix. Protein expression matrix of raw data of 49 proteins/phosphoproteins assayed in 166 xenograft samples of the dataset. (XLSX 224 kb)
DOI: 10.6084/m9.figshare.c.3607640_d1
title: Additional file 1: Table S1. of Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in Brachypodium distachyon

description: The primers used in RT-PCR analysis. Table S2. Summary of functional domains presented in the BdAP2/ERF proteins. Table S3. Detail information of motifs identified in BdAP2/ERF proteins. Table S4. Characteristics of cis-regulatory elements in the promoter region of BdAP2/ERF genes. Table S5. Annotations of 278 putative cis-acting regulatory DNA elements identified in 141 BdERF genes in B. distachyon by PLACE. Table S6. List of putative miRNAs targeted BdAP2/ERF predicted by psRNATarget tool. Table S7. The Ka/Ks ratios and estimated divergence time for tandemly duplicated BdAP2/ERF genes. Table S8. The Ka/Ks ratios and estimated divergence time for segmentally duplicated BdAP2/ERF genes. Table S9. The Ka/Ks ratios and estimated divergence time for orthologous BdAP2/ERF proteins between B. distachyon and rice. Table S10. The Ka/Ks ratios and estimated divergence time for orthologous BdAP2/ERF proteins between B. distachyon and maize. Table S11. The Ka/Ks ratios and estimated divergence time for orthologous BdAP2/ERF proteins between B. distachyon and sorghum. Table S12. Detail information of network of BdAP2/ERF with other genes. Table S13. Detail information of alternative splicing variants. (XLSX 412 kb)
DOI: 10.6084/m9.figshare.c.3607610_d8
title: Additional file 6: of Transcriptome adaptation of the bovine mammary gland to diets rich in unsaturated fatty acids shows greater impact of linseed oil over safflower oil on gene expression and metabolic pathways

description: a-d: Differentially expressed genes between cows on control diet and the same cows supplemented with 5Â % safflower oil for 28Â days (day-14 vs day+28 and day+7 vs day+28). (XLSX 41Â kb)
DOI: 10.6084/m9.figshare.c.3607610_d7
title: Additional file 5: of Transcriptome adaptation of the bovine mammary gland to diets rich in unsaturated fatty acids shows greater impact of linseed oil over safflower oil on gene expression and metabolic pathways

description: a-e: Differentially expressed genes between cows on control diet and the same cows supplemented with 5Â % linseed oil for 28Â days (day-14 vs day+28, day-14 vs day+7 and day+7 vs day+28). (XLSX 149Â kb)
DOI: 10.6084/m9.figshare.c.3607610_d6
title: Additional file 11: of Transcriptome adaptation of the bovine mammary gland to diets rich in unsaturated fatty acids shows greater impact of linseed oil over safflower oil on gene expression and metabolic pathways

description: a-b: Several functions of lipid metabolism were affected by genes differentially expressed when cows were fed diets supplemented with 5%linseed oil (a) or 5Â % safflower oil (b) for 4Â weeks as compared to same cows on a control diet. (XLS 50Â kb)
DOI: 10.6084/m9.figshare.c.3607610_d4
title: Additional file 7: of Transcriptome adaptation of the bovine mammary gland to diets rich in unsaturated fatty acids shows greater impact of linseed oil over safflower oil on gene expression and metabolic pathways

description: Differentially expressed genes in the solute carrier super gene family. (XLSX 24Â kb)
DOI: 10.6084/m9.figshare.c.3607610_d3
title: Additional file 3: of Transcriptome adaptation of the bovine mammary gland to diets rich in unsaturated fatty acids shows greater impact of linseed oil over safflower oil on gene expression and metabolic pathways

description: Reads and mapping statistics according to treatment. (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.c.3607529_d5
title: Additional file 5: Table S8-S9. of Genome-wide identification of copy number variations between two chicken lines that differ in genetic resistance to Marekâ  s disease

description: GO and KEGG pathway analysis of genes affected by resistant-specific CNVRs (Table S8) and susceptible-specific CNVRs (Table S9). (XLSX 27 kb)
DOI: 10.6084/m9.figshare.c.3607529_d4
title: Additional file 1: Table S1. of Genome-wide identification of copy number variations between two chicken lines that differ in genetic resistance to Marek’s disease

description: Summary of identified CNVs and CNVRs in the two chicken lines. For CNVs reported by CNVnator, the copy number denoted the absolute copy number estimated by CNVnator, and for those predicted by Pindel, the absolute copy number was not available and represented by ratio of the total number of uniquely mapped reads in the population supporting the CNV to that supporting the reference. Besides, Pindel can detected some not pure deletions (some fragments are inserted in the deletion region), and the inserted fragments were listed in the “Note” column. (XLSX 1591 kb)
DOI: 10.6084/m9.figshare.c.3607157_d13
title: Additional file 13: Table S9. of Genetic variation and association mapping for 12 agronomic traits in indica rice

description: Summary of the 16 loci detected in two environments and the 423 candidate genes. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.c.3607157_d11
title: Additional file 6: Table S5. of Genetic variation and association mapping for 12 agronomic traits in indica rice

description: Subpopulations and genetic components of 469 indica accessions. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.c.3607157_d9
title: Additional file 11:Table S8. of Genetic variation and association mapping for 12 agronomic traits in indica rice

description: Summary of 298 significant peak SNPs, including known genes (or QTLs) and new candidate genes. (XLSX 109 kb)
DOI: 10.6084/m9.figshare.c.3607157_d8
title: Additional file 3: Table S2. of Genetic variation and association mapping for 12 agronomic traits in indica rice

description: Information on the 4,136 SNPs. (XLSX 567 kb)
DOI: 10.6084/m9.figshare.c.3607157_d6
title: Additional file 10: Table S7. of Genetic variation and association mapping for 12 agronomic traits in indica rice

description: Phenotypic data for 12 traits in Lingshui and Hangzhou. (XLSX 116 kb)
DOI: 10.6084/m9.figshare.c.3607157_d7
title: Additional file 1: Table S1. of Genetic variation and association mapping for 12 agronomic traits in indica rice

description: Origination and classification of 523 germplasm accessions. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.c.3607157_d3
title: Additional file 5: Table S4. of Genetic variation and association mapping for 12 agronomic traits in indica rice

description: Summary of primers used for quantitative real-time PCR. (XLSX 15 kb)