cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3604973_d4.v1
title: Additional file 3: Figure S3. of ANLN is a prognostic biomarker independent of Ki-67 and essential for cell cycle progression in primary breast cancer

description: A. Association of ANLN expression with cell cycle arrest in SKBR3 cells. Flow cytometry-generated data showed that ANLN depletion lead to a significant accumulation of cells in the G2/M phase of the cell cycle 3 days after siRNA knockdown in SKBR3 cells. This accumulation was clearly visible but not statistically significant 5 days after ANLN siRNA knockdown. B. Association of ANLN expression with cell cycle arrest in T47D cells. Flow cytometry-generated data showed that ANLN depletion lead to a significant accumulation of cells in the G2/M phase of the cell cycle 3 days after siRNA knockdown in T47D cells. This accumulation was clearly visible but not statistically significant 5 days after ANLN siRNA knockdown. (ZIP 146 kb)
DOI: 10.6084/m9.figshare.c.3604958_d5.v1
title: Additional file 1: of Intestinal microbial communities associated with acute enteric infections and disease recovery

description: The richness and diversity estimates for intestinal communities from otherwise healthy individuals without enteric infections. (XLSX 22Â kb)
DOI: 10.6084/m9.figshare.c.3605030_d3.v1
title: Additional file 8: Table S4. of Comparative transcriptome analysis revealing dormant conidia and germination associated genes in Aspergillus species: an essential role for AtfA in conidial dormancy

description: List of primers used in this study. (XLSX 51Â kb)
DOI: 10.6084/m9.figshare.c.3605042_d2.v1
title: Additional file 4: of ClinQC: a tool for quality control and cleaning of Sanger and NGS data in clinical research

description: Adapter-Primer file (optional input file) to perform adapters and PCR primers trimming. (TXT 1 kb)
DOI: 10.6084/m9.figshare.c.3605021_d5.v1
title: Additional file 7: of Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat

description: Clustering and functional annotation results of differentially expressed genes. (XLSX 15048 kb)
DOI: 10.6084/m9.figshare.c.3605030_d4.v1
title: Additional file 2: Table S1A. of Comparative transcriptome analysis revealing dormant conidia and germination associated genes in Aspergillus species: an essential role for AtfA in conidial dormancy

description: GO terms that were enriched in CAGs. (XLSX 11Â kb)
DOI: 10.15468/dl.84822f
title: Occurrence Download

description: A dataset containing 3528 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "Country is one of (Spain, Portugal)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is one of (May, June, July, April)",
 "PublishingOrg is one of (28eb1a3f-1c15-4a95-931a-4af90ecb574d, ada19a05-4216-44c7-aa4f-6e7177bcb0ac, 6b8da9ca-0648-4df3-9f0a-d43ab20a9412, c8d737e0-2ff8-42e8-b8fc-6b805d26fc5f)",
 "TaxonKey is Sturnus vulgaris Linnaeus, 1758",
 "Year 2000-2024"
 ]
}

 The dataset includes 3528 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037527-241126133413365/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.3605042_d4.v1
title: Additional file 1: of ClinQC: a tool for quality control and cleaning of Sanger and NGS data in clinical research

description: ClinQCOptions_Sanger file to specify all input files and parameters for Sanger sequencing data analysis. (TXT 3 kb)
DOI: 10.6084/m9.figshare.c.3605042_d5.v1
title: Additional file 2: of ClinQC: a tool for quality control and cleaning of Sanger and NGS data in clinical research

description: ClinQCOptions_NGS file to specify all input files and parameters for Sanger sequencing data analysis. (TXT 2 kb)
DOI: 10.6084/m9.figshare.c.3605030_d5.v1
title: Additional file 4: Table S2. of Comparative transcriptome analysis revealing dormant conidia and germination associated genes in Aspergillus species: an essential role for AtfA in conidial dormancy

description: List of A. fumigatus allergen-related genes and their FPKM values. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3605105_d1.v1
title: Additional file 1: of Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda)

description: Putative primer pairs for the class I and class II SSRs in the coding regions of Norway spruce (Picea abies ) and Loblolly pine ( Pinus taeda ). (XLSX 4157 kb)
DOI: 10.60656/b821b43138994183
title: Custom collection of ice water content data from Bucharest, Chilbolton, Galați, Granada, Hyytiälä, and 10 other sites between 1 and 31 Aug 2023
DOI: 10.6084/m9.figshare.c.3605171_d3.v1
title: Additional file 3: Table S1. of Genome-wide studies reveal novel and distinct biological pathways regulated by SIN3 isoforms

description: Detailed information on peaks identified by ChIP-seq analysis. This table is related to Figs.Â 2 and 3 (XLSX 823Â kb)
DOI: 10.6084/m9.figshare.c.3605153_d7.v1
title: Additional file 24: Table S16. of Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1

description: Identification of genes whose expression is strongly correlated to that of both pfcrt and pfmr1. PCC were estimated from 110 pairwise comparisons of 11 transcriptome data sets. (A) List of genes organized by functional categories whose expression is highly correlated (PCC &gt;0.7) to that of both pfcrt and pfmdr1. *Indicates genes with confidence, as found when using PCC computed from 55 unidirectional pairwise comparisons of the 11 transcriptome data sets. (B) List of genes organized by functional categories whose expression is highly anti-correlated (PCC
DOI: 10.6084/m9.figshare.c.3605171_d4.v1
title: Additional file 10: Table S4. of Genome-wide studies reveal novel and distinct biological pathways regulated by SIN3 isoforms

description: Differential gene expression analysis upon overexpression of SIN3 187HA as determined by Cuffdiff. This table is related Figs.Â 5 and 6 (XLSX 1669Â kb)
DOI: 10.6084/m9.figshare.27187143
title: Flow hydrograph shape metrics.xlsx

description: A worked example of the flow hydrograph shape metrics database for use in time-series flood hydrology analysis.<br>Please see https://www.protocols.io/edit/hydrograph-extraction-and-metrics-calculation-work-c5yay7se
DOI: 10.6084/m9.figshare.c.3605171_d5.v1
title: Additional file 12: Table S5. of Genome-wide studies reveal novel and distinct biological pathways regulated by SIN3 isoforms

description: Table listing the primers used in this study (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3605171_d6.v1
title: Additional file 5: Table S2. of Genome-wide studies reveal novel and distinct biological pathways regulated by SIN3 isoforms

description: Detailed annotation of ChIP-seq peaks for SIN3 187HA (SIN3 187HA ceas) or SIN3 220HA (SIN3 220HA ceas) as determined by the cis-regulatory enrichment annotation (CEAS) system. This table is related to Fig.Â 2 (XLSX 4014Â kb)
DOI: 10.6084/m9.figshare.28001450.v13
title: GBM-Reservoir: Dataset and Segmentations

description: In this repository, we present a brain tumor database collection comprising 23,049 samples, with each sample including four different types of MRI brain scans: FLAIR, T1, T1ce, and T2. Additionally, two segmentation masks (ground truth) are provided for each sample. The first mask is the raw output from the registration process, while the second is a post-processed version of the first, designed to simplify interpretation and optimize it for network training. These samples have been acquired via registration process of 438 samples available at the moment of registration from the original dataset provided by the BraTS 2022 Challenge. Registering each pair of existing brain scans results in two additional scans that retain a similar brain shape while featuring varying tumor locations. Consequently, by registering all possible pairs, a dataset originally consisting of n samples can be expanded to n<sup>2</sup> samples. The original dataset was collected from different institutions under standard clinical conditions, but with different equipment and imaging protocols. As a result, the image quality is heterogeneous, reflecting the diversity of clinical practices across institutions. This dataset can be utilized for various tasks, such as developing fully automated segmentation algorithms for new, unseen brain tumor cases, particularly through deep learning-based approaches, since ground truth is provided for each sample.
DOI: 10.6084/m9.figshare.c.3605153_d11.v1
title: Additional file 8: Table S4. of Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1

description: Values for gene expression fold differences between strains in the 7G8 data set for genes on chromosome 2. The boxed area corresponds to the region on chromosome 2 containing genes with a significant fold change (values &lt;0.6). (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3605153_d12.v1
title: Additional file 5: Table S2. of Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1

description: List of genes within the pfmdr1-containing amplicon with associated fold change between FCB and both FCB pfmdr1_3â ˛KD and 106/1, as measured by microarrays. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3605171_d8.v1
title: Additional file 9: Table S3. of Genome-wide studies reveal novel and distinct biological pathways regulated by SIN3 isoforms

description: Detailed information of the GO analysis performed on genes directly regulated by SIN3 isoforms. This table is related to Figs.Â 4 and 6 (XLSX 140Â kb)
DOI: 10.6084/m9.figshare.c.3605189_d1.v1
title: Additional file 2: of Sexually antagonistic selection on genetic variation underlying both male and female same-sex sexual behavior

description: Data: Locomotor activity & Same-Sex Mounting, Lifetime Reproductive Success, Male Perception Error. (ZIP 6Â kb)
DOI: 10.6084/m9.figshare.c.3605153_d24.v1
title: Additional file 11: Table S6 of Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1

description: Genes (A-D) and gene sets (E-H) differentially expressed in the pfmdr1 data set. For each pairwise comparison, we listed genes with significant differential expression, i.e. with a fold change greater than 1.5 and a normalized fold change two standard deviations above the median values and genes with a fold change lower than 0.6 and a normalized fold change three standard deviations below the median value, which generally represented the quasi-totality of genes with a fold change below 0.6. Normalization was performed using the average fold change computed across a background pool of 11 transcriptome data sets as a scaling factor. This normalization allowed us to identify and filter out most of the hypervariable genes (e.g. var, rifin, stevor, phist, and hyp). Antigenically variant genes not detected by automatic filtering were manually removed. We listed the gene sets with significant differential expression (based on the mean rank of enrichment score &gt;0.9 (significantly enriched) or &lt;0.1 (significantly impoverished)) that are found in both FCB vs. FCB pfmdr1_3â ˛KD and FCB vs. 106/1 pairwise comparisons. (XLSX 65 kb)
DOI: 10.6084/m9.figshare.c.3605213_d1.v1
title: Additional file 3: of Encyclopedia of bacterial gene circuits whose presence or absence correlate with pathogenicity – a large-scale system analysis of decoded bacterial genomes

description: Bacterial strain orthology logic array indicating the presence of given orthologs (7194 of them) in the 2527 bacterial strain genomes considered in this study. (RAR 1397 kb)
DOI: 10.6084/m9.figshare.c.3605153_d26.v1
title: Additional file 10: Table S5. of Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1

description: Assessment of a possible time shift in gene expression between parasite lines. We examined the data to assess whether some genes displayed a shifted timing of expression between parasite strains. By comparing peaks of expression for each gene in each pairwise comparison, we determined the number of genes whose peak of expression was shifted of a determined number of hours. 0 corresponds to a shift of less than 1 h, one corresponds to a shift of at least 1 h but less than two hours, etc. Therefore, two genes cannot be more than 24 h apart of each other in either direction. We observed that more than 70 % of all genes peaked within the same 8-hour window in the pfmdr1 dataset (Table S5A) while about 80 % of the genes peaked within the same 5-hour window in the pfcrt dataset (Table S5B). (XLSX 44 kb)
DOI: 10.6084/m9.figshare.c.3605153_d27.v1
title: Additional file 16: Table S10. of Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1

description: List of genes with significant differential expression between 7G8 and 7G8 pfcrt_CTL in a stage-specific manner. Genes with significantly higher expression displayed absolute fold changes &gt;1.5 and normalized fold changes values two standard deviations above the median normalized fold change value. Genes with significantly lower expression had absolute fold change values lower than 0.6 and a normalized fold change three standard deviations below the median value. Fold change for each gene at the designated stage is indicated. (XLSX 55 kb)
DOI: 10.6084/m9.figshare.c.3605213_d3.v1
title: Additional file 2: of Encyclopedia of bacterial gene circuits whose presence or absence correlate with pathogenicity – a large-scale system analysis of decoded bacterial genomes

description: List of 1578 decoded bacterial genomes present in the KEGG web platform with no present citation implicating them as pathogenic. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.c.3605213_d2.v1
title: Additional file 4: of Encyclopedia of bacterial gene circuits whose presence or absence correlate with pathogenicity – a large-scale system analysis of decoded bacterial genomes

description: List of 7194 orthologs ordered according to pathogen association score PA. The orthologs shaded in pink represent ones present in VFDB. (XLSX 570 kb)
DOI: 10.6084/m9.figshare.c.3605213_d4.v1
title: Additional file 1: of Encyclopedia of bacterial gene circuits whose presence or absence correlate with pathogenicity – a large-scale system analysis of decoded bacterial genomes

description: List of 949 decoded bacterial genomes present in the KEGG web platform deemed as pathogenic along with literature citations for pathogenicity and antibiotic resistance phenotype. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.c.3605216_d1.v1
title: Additional file 1: Figure S1. of Transcriptome analysis of sweet orange trees infected with â  Candidatus Liberibacter asiaticusâ   and two strains of Citrus Tristeza Virus

description: Summary of reads from Citrus sinensis infected with CTV-B2, CTV-B6 and CaLas-B232 and the mock-inoculated control (H). Reads were obtained through paired-end RNA sequencing and mapped to the C. sinensis genome. Figure S2. Differentially expressed transcripts in diseased compared to healthy C. sinensis. Transcripts were up- or down-regulated in response to infection by CTV-B2, CTV-B6 and CaLas-B232. Figure S3. Melt curves of gene products assayed by RT-qPCR demonstrate specificity and reproducibility of the qPCR reactions. Gene targets are described in Table S11. Figure S4. Summary of differentially expressed transcripts based on functional categorization by Mapman. A. cell wall modification and cell organization; B. transcription factors; C. transporters; D. hormone metabolism; E. secondary metabolism; F. signaling; G. disease resistance proteins; H. proteolysis; I. development. Figure S5. Leaves that were sampled for RNA-seq. A, healthy; B, CTV-B2 positive; C, CTV-B6 positive; D, CaLas-B232 positive. Table S1. Differentially expressed transcripts of genes with unknown functions in response to CTV-B2, CTV-B6 and CaLas-B232. Table S2. GO categorization of genes that were differentially expressed in response to CTV-B2, CTV-B6 and CaLas-B232. Table S3. GO categorization of genes that were differentially expressed in response to CTV-B2, CTV-B6 but not CaLas-B232. Table S4. GO categorization of genes that responded to CTV-B2 and CaLas-B232 but not CTV-B6. Table S5. GO categorization of genes that responded to CTV-B6 and CaLas-B232 but not CTV-B2. Table S6. GO categorization of genes that responded only to CTV-B2. Table S7. GO categorization of genes that responded only to CTV-B6. Table S8. GO categorization of genes that responded only to CaLas-B232. Table S9. Complete set of differentially expressed transcripts in response to the three pathogens. Table S10. Estimates of changes in gene expression (fold change) by RT-qPCR and Gfold. Table S11. Primers used for qRT-PCR validation of differentially expressed transcripts identified by Gfold. (ZIP 1765 kb)
DOI: 10.6084/m9.figshare.c.3605300_d1.v1
title: Additional file 2: Table S1. of Effects of new motorway infrastructure on active travel in the local population: a retrospective repeat cross-sectional study in Glasgow, Scotland

description: Sensitivity analysis of RR of journey stages being made by active means. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3605300_d2.v1
title: Additional file 1: Table S2. of Effects of new motorway infrastructure on active travel in the local population: a retrospective repeat cross-sectional study in Glasgow, Scotland

description: Description of Dichotomised variables from SHS. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3605309_d1.v1
title: Additional file 5: Table S4. of Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome

description: Tribe-MCL gene families and annotations for all 15 species used. (CSV 1210 kb)
DOI: 10.6084/m9.figshare.c.3605315_d1.v1
title: Additional file 1: of MutSpec: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes

description: Example of Excel file generated by MutSpec-Stat tool. The data in this file correspond to the example analysis of OSCC described herein. (XLS 37674Â kb)
DOI: 10.6084/m9.figshare.c.3605327_d1.v1
title: Additional file 8: of Amnion as a surrogate tissue reporter of the effects of maternal preeclampsia on the fetus

description: Supporting Tables. (XLSX 15.7 MB)
DOI: 10.6084/m9.figshare.c.3605318_d2.v1
title: Additional file 2: Table S1. of Epidermal growth factor signals regulate dihydropyrimidine dehydrogenase expression in EGFR-mutated non-small-cell lung cancer

description: Effects of 5-FU, gefitinib, and mithramycin A on cell proliferation in NSCLC cell lines. Cells were incubated with various concentrations of 5-FU for 72Â h, and cell viability was examined by WST-1 assay. The IC50 values of these drugs were calculated for each cell line. Cell viability of the control group (DMSO) was set at 100Â %. Values are means from three samples from one representative experiment. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3605309_d9.v1
title: Additional file 3: Table S3. of Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome

description: Predicted species distribution for non-pine origin sequences removed from the Pinus patula v1.0 transcriptome. (TSV 7 kb)
DOI: 10.6084/m9.figshare.c.3605345_d2.v1
title: Additional file 2: of mAPKL: R/ Bioconductor package for detecting gene exemplars and revealing their characteristics

description: Package â  mAPKLData_1.0.0.tar.gzâ   including microarray data and documentation. (GZ 9281 kb)
DOI: 10.6084/m9.figshare.c.3605363_d1.v1
title: Additional file 1: Table S2. of The Nipponbare genome and the next-generation of rice genomics research in Japan

description: Rice varieties and landraces with whole-genome short-read sequences submitted by Japanese research organizations in the NCBI database. (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.c.3605327_d7.v1
title: Additional file 7: of Amnion as a surrogate tissue reporter of the effects of maternal preeclampsia on the fetus

description: Codes used in this study. (TXT 66.7 kb)
DOI: 10.6084/m9.figshare.c.3605363_d2.v1
title: Additional file 2: Table S1. of The Nipponbare genome and the next-generation of rice genomics research in Japan

description: Rice genes reported by Japanese researchers in various scientific journals in 2005–2014. Literatures were searched and obtained from PubMed with ‘rice’ and ‘Oryza’ as keywords in either the title or abstract, and further selected by natural language processing and manual curation. The data can be accessed from Oryzabase ( http://shigen.nig.ac.jp/rice/oryzabase/download/reference ). (XLSX 215 kb)
DOI: 10.6084/m9.figshare.c.3605375_d1.v1
title: Additional file 5: of Genome-wide binding analysis of the transcriptional regulator TrmBL1 in Pyrococcus furiosus

description: Functional annotation of genes of the TrmBL1 regulon. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.c.3605399_d2.v1
title: Additional file 3: Table S2. of High-performance web services for querying gene and variant annotation

description: The variant-specific annotation fields available from MyVariant.info. (XLS 58 kb)
DOI: 10.15468/dl.g3vxcx
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is USA.34_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Scrofa Gray, 1868, Sus scrofa Linnaeus, 1758)"
 ]
}

 The dataset includes 46 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037528-241126133413365/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.3605426_d2.v1
title: Additional file 1 of Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis

description: Supplementary tables. Supplementary Table S1. Bacterial abundances in Simulation 1 (high-diversity communities). Supplementary Table S2. Bacterial abundances in Simulation 2 (low-diversity communities). Supplementary Table S3. List of genomes in taxonomic catalog for human gut. Supplementary Table S4. Taxonomic composition for real dataset (organism level). Supplementary Table S5. Taxonomic composition for real dataset (genus level). Supplementary Table S6. Functional composition for real dataset (COG). Supplementary Table S7. Taxonomic composition for real dataset by MetaPhlAn (organism level). Supplementary Table S8. Mapped read counts and percentage of mapping on taxonomic and functional catalog and phage genome. (XLS 2693 kb)
DOI: 10.6084/m9.figshare.c.3605492_d2.v1
title: Additional file 2: of Transcriptome profiling reveals distinctive traits of retinol metabolism and neonatal parallels in the MRL/MpJ mouse

description: The list of transcripts corresponding to the genes mentioned in the article. The list of transcripts corresponding to the genes mentioned in the article and their expression levels is attached as an excel file. (XLSX 979 kb)
DOI: 10.6084/m9.figshare.c.3605480_d4.v1
title: Additional file 4:Â Folder S1. of Non contiguous-finished genome sequence and description of Microbacterium gorillae sp. nov.

description: Annotation results. (RAR 1566Â kb)