cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh1141999.10fu
title: SH1141999.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.6084/m9.figshare.c.3642752_d5.v1
title: Additional file 2: Table S2. of A genome-wide approach to link genotype to clinical outcome by utilizing next generation sequencing and gene chip data of 6,697 breast cancer patients

description: The complete set of all genes included in the metagenes for each of the putative driver genes listed in Table 2. (XLSX 156 kb)
DOI: 10.6084/m9.figshare.c.3642758_d1.v1
title: MOESM2 of Identification of epitopes recognised by mucosal CD4+ T-cell populations from cattle experimentally colonised with Escherichia coli O157:H7

description: Additional file 2. Pooling strategy for EHEC O157 peptides. Details of peptide pools used to stimulate CD4+ T-cell lines from rectal lymph nodes of EHEC O157 challenged calves.
DOI: 10.5281/zenodo.14510558
title: Techno-economic dataset for long-term energy systems modelling in Sri Lanka

description: A technoeconomic dataset for modelling Sri Lanka's energy system.
description: This material has been produced under the Climate Compatible Growth (CCG) programme, which brings together leading research organizations and is led out of the STEER centre, Loughborough University. CCG is funded by UK aid from the UK government. However, the views expressed herein do not necessarily reflect the UK government's official policies. This work was developed with the Energy Transition Council (ETC), which assisted in identifying needed research areas and connected to relevant stakeholders for a discussion on essential aspects of research.
DOI: 10.5281/zenodo.14510559
title: Techno-economic dataset for long-term energy systems modelling in Sri Lanka

description: A technoeconomic dataset for modelling Sri Lanka's energy system.
description: This material has been produced under the Climate Compatible Growth (CCG) programme, which brings together leading research organizations and is led out of the STEER centre, Loughborough University. CCG is funded by UK aid from the UK government. However, the views expressed herein do not necessarily reflect the UK government's official policies. This work was developed with the Energy Transition Council (ETC), which assisted in identifying needed research areas and connected to relevant stakeholders for a discussion on essential aspects of research.
DOI: 10.6084/m9.figshare.c.3642821_d7.v1
title: Additional file 21: Table S9. of Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays

description: Genes whose expression in the founder lines matches founder effects (FDR &lt;0.05) in ± 1 Mb QTL intervals for GY. For each gene, chromosome (chr), test (high (H) or low (L)), P value (pval), q value (qval), and start and stop positions are given. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3642821_d5.v1
title: Additional file 20: Table S8. of Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays

description: Suggestive loci (P &lt;0.63) for days to pollen shed (PS), ear height (EH), plant height (PH), and grain yield (GY). Each row reports the phenotype (Trait), the covariates (Cov) eventually used in the QTL scan, the name of the marker (Marker) and chromosome (Chr) of the current association, the genomic position (in bp) of the interval determined by a 2 LOD drop from the highest association (Top), and the left (Left bound) and right (Right bound) bounds of this interval. The percent of variance explained (Variance) and the maximum LOD score are also shown. To avoid duplication, when a peak position was unchanged after scanning with a covariate, the latter scan is the only reported. QTL are listed individually if separated by at least 50 markers with LOD score below the suggestive threshold. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3642821_d4.v1
title: Additional file 22: Table S10. of Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays

description: Genes whose expression in the founder lines matches founder effects (FDR &lt;0.05) in ± 1 Mb QTL intervals for PS. For each gene, chromosome (chr), test (high (H) or low (L)), P value (pval), q value (qval), and start and stop positions are given. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3642821_d9.v1
title: Additional file 11: Table S5. of Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays

description: Summary of power simulation results with varying sample sizes (100, 200, 300, 400, 500). For each simulated QTL, the effect and the variance explained are given. The power to detect each QTL is averaged on 400 independent runs (100 for each of MAF 0.125, 0.25, 0.375, and 0.5). Results are given for h 2 = 0.4 and 0.7. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3642821_d10.v1
title: Additional file 8: Table S3. of Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays

description: The genetic map of the MM population. (XLSX 2159 kb)
DOI: 10.6084/m9.figshare.c.3642821_d14.v1
title: Additional file 15: Table S7. of Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays

description: Mean, range, genotypic variance (σ 2 g ), genotype × environment interaction variance (σ 2 ge ), residual (σ 2 ɛ), and heritability (h 2 ) of the MM lines for the investigated traits. (XLSX 9 kb)
DOI: 10.5519/qd.qi6r7ajx
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (3 records)
DOI: 10.6084/m9.figshare.c.3642821_d16.v1
title: Additional file 10: Table S4. of Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays

description: Quantitative data for MM founders’ sequencing and expression. For sequencing, raw reads count and mean and modal coverage (in folds) are given. For expression data, raw reads numbers are given for each biological replica (B1, B2, B3). (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3642821_d22.v1
title: Additional file 2: Table S2. of Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays

description: MM population breeding design, organized in 35 subfamilies. In blue and red, single and double introductions of the backup founder (CML91). (XLSX 23 kb)
DOI: 10.6084/m9.figshare.c.3642863_d1.v1
title: Additional file 2: of Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping

description: A) List of SNPs identified in 6 P. vulgaris and 2 P. acutifolius genotypes along with the corresponding homologues position in Pv1.0 assembly, B) SNPs exclusive to teparies, C) results of SNPs selected for KASP assay, D) Pv768 GoldenGate assay results, E) Pac768 GoldenGate assay results, and F) summary of assay results. (XLSX 20503Â kb)
DOI: 10.6084/m9.figshare.c.3642863_d2.v1
title: Additional file 3: of Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping

description: A) BR-06 map with binned marker loci and corresponding P. vulgaris pseudochromosome locations and B) SNP genotypes for 158 accessions using Pac768 GoldenGate assay. (XLSX 497Â kb)
DOI: 10.6084/m9.figshare.c.3642863_d4.v1
title: Additional file 1: of Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping

description: List of P. acutifolius accessions selected for phylogenetic analysis. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.c.3642887_d1.v1
title: Additional file 1: Table S1. of A plausible role for actin gamma smooth muscle 2 (ACTG2) in small intestinal neuroendocrine tumorigenesis

description: Patient characteristics, immunohistochemistry analysis of ACTG2 and miR-145 analysis in SI-NETs (XLSX 49 kb)
DOI: 10.6084/m9.figshare.c.3643013_d1.v1
title: MOESM1 of Lessons for livestock genomics from genome and transcriptome sequencing in cattle and other mammals

description: Additional file 1: Table S1. Description of tissue samples analyzed by RNA-seq by species or breed and the project associated with the analysis.
DOI: 10.6084/m9.figshare.c.3643037_d1.v1
title: Additional file 6: of RNA-seq analysis of the gonadal transcriptome during Alligator mississippiensis temperature-dependent sex determination and differentiation

description: Annotation of critical genes involved in sex determination. Annotation of candidate critical DEGs involved in sex determination during Day 0â  12. Ordered by decreasing fold change. DEGs with both significant development-dependent differential expression (Additional file 3) and sex-dependent differential expression (Additional file 4) were screened, as potential critical genes for alligator male and female cascade. (XLSX 64 kb)
DOI: 10.6084/m9.figshare.c.3643037_d3.v1
title: Additional file 4: of RNA-seq analysis of the gonadal transcriptome during Alligator mississippiensis temperature-dependent sex determination and differentiation

description: Annotation of sexually dimorphic genes in gonad during Day 0â  12. Annotation of significant sexually dimorphic DEGs at FDRâ
DOI: 10.6084/m9.figshare.c.3643037_d6.v1
title: Additional file 3: of RNA-seq analysis of the gonadal transcriptome during Alligator mississippiensis temperature-dependent sex determination and differentiation

description: Annotation of development-dependent dimorphic genes in gonad during Day 0â  12. Annotation of development-dependent significantly up- and down- regulated DEGs at FDRâ
DOI: 10.5281/zenodo.14506511
title: Supplementary Data for "Projecting global changes in land use and ecosystem services using SEALS (Spatial Economic Allocation Landscape Simulator)".

description: High-resolution (300m), global projections of land-use change under SSP-RCP scenarios derived from SEALS (Spatial Economic Allocation Landscape Simulator).
DOI: 10.5281/zenodo.14506512
title: Supplementary Data for "Projecting global changes in land use and ecosystem services using SEALS (Spatial Economic Allocation Landscape Simulator)".

description: High-resolution (300m), global projections of land-use change under SSP-RCP scenarios derived from SEALS (Spatial Economic Allocation Landscape Simulator).
DOI: 10.6084/m9.figshare.c.3643109_d2.v1
title: Additional file 2: of Prognostic relevance of caspase 8 -652 6N InsDel and Asp302His polymorphisms for breast cancer

description: Anonymized clinical dataset. All variables used for haplotype and diplotype construction, Kaplan-Meier curves, log-rank tests, univariate and multivariable analyses. Ages were replaced by age ranges to maintain participant confidentiality. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.c.3643154_d5.v1
title: Additional file 1: Table S1. of Errors in RNA-Seq quantification affect genes of relevance to human disease

description: Counts and FPKM for simulated data from all genes. FPKM and read counts calculated by 12 different methods for 19,654 human protein-coding genes. Can be downloaded from [43]. (XLSX 7248 kb)
DOI: 10.5281/zenodo.14501889
title: Maize ABS4 reference genome assembly and annotation

description: We created a reference genome assembly of the maize ABS4 line used for synthetic centromeres. The original ABS4 heterozygous line in a Hi-II background (Dawe et al. 2023 https://doi.org/10.1038/s41477-023-01370-8, Zhang et al. 2012 https://doi.org/10.1111/j.1365-313X.2011.04867.x) was selfed five times, and a sequencing library was prepared using a SMARTbell Express Template Prep Kit 3.0. Sequencing was conducted on a PacBio Revio system with a Revio Sequencing Plate in CCS mode. Raw PacBio reads in fastq format are available under NCBI Bioproject PRJNA874319, SRA accession SRR31749818. File AbsGenomePBHIFI_version_1.fa is the complete reference sequence in fasta format including 10 chromosomes and unplaced primary contigs. It was generated using primary contigs with hifiasm v0.19.4. Ragtag v2.1.0 was used to scaffold the contigs based on the maize A188 reference genome (Lin et al. 2021 https://doi.org/10.1186/s13059-021-02396-x). Heterozygous and misassembled contigs were processed through manual curation and RagTag v2.1.0 'correct' command. File AbsGenomePBHIFI_version_1.fa.mod.EDTA.intact.gff3 is a TE annotation file generated by EDTA v2.1.0. File AbsGenomePBHIFI_version_1_liftoffA188.gff3 is a gene annotation file generated using Liftoff v1.6.3 based on the A188 reference and gene annotation, version 1.0 (Zm-A188-REFERENCE-KSU-1.0).
DOI: 10.5281/zenodo.14501890
title: Maize ABS4 reference genome assembly and annotation

description: We created a reference genome assembly of the maize ABS4 line used for synthetic centromeres. The original ABS4 heterozygous line in a Hi-II background (Dawe et al. 2023 https://doi.org/10.1038/s41477-023-01370-8, Zhang et al. 2012 https://doi.org/10.1111/j.1365-313X.2011.04867.x) was selfed five times, and a sequencing library was prepared using a SMARTbell Express Template Prep Kit 3.0. Sequencing was conducted on a PacBio Revio system with a Revio Sequencing Plate in CCS mode. Raw PacBio reads in fastq format are available under NCBI Bioproject PRJNA874319, SRA accession SRR31749818. File AbsGenomePBHIFI_version_1.fa is the complete reference sequence in fasta format including 10 chromosomes and unplaced primary contigs. It was generated using primary contigs with hifiasm v0.19.4. Ragtag v2.1.0 was used to scaffold the contigs based on the maize A188 reference genome (Lin et al. 2021 https://doi.org/10.1186/s13059-021-02396-x). Heterozygous and misassembled contigs were processed through manual curation and RagTag v2.1.0 'correct' command. File AbsGenomePBHIFI_version_1.fa.mod.EDTA.intact.gff3 is a TE annotation file generated by EDTA v2.1.0. File AbsGenomePBHIFI_version_1_liftoffA188.gff3 is a gene annotation file generated using Liftoff v1.6.3 based on the A188 reference and gene annotation, version 1.0 (Zm-A188-REFERENCE-KSU-1.0).
DOI: 10.6084/m9.figshare.c.3643154_d9.v1
title: Additional file 6: Table S2. of Errors in RNA-Seq quantification affect genes of relevance to human disease

description: Counts and FPKM for simulated data from 958 problematic genes. FPKM and read counts calculated by 12 different methods for 958 problematic human protein-coding genes. Can be downloaded from [43]. (XLSX 311 kb)
DOI: 10.15468/dl.dph6r6
title: Occurrence Download

description: A dataset containing 20887 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Petrochelidon pyrrhonota (Vieillot, 1817)"
 ]
}

 The dataset includes 20887 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037988-241126133413365/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.3643154_d11.v1
title: Additional file 7: Table S3. of Errors in RNA-Seq quantification affect genes of relevance to human disease

description: Unique counts from Choi et al. [35]. Counts of reads from Choi et al. that map uniquely to genes using STAR and HTSeq. Can be downloaded from [43]. (XLSX 5833 kb)
DOI: 10.15468/dl.xef926
title: Occurrence Download

description: A dataset containing 4884 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Peucaea botterii (P.L.Sclater, 1858)"
 ]
}

 The dataset includes 4884 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037989-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jhu2y9
title: Occurrence Download

description: A dataset containing 397 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Thracides Hübner, 1819"
 ]
}

 The dataset includes 397 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037990-241126133413365/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.3643217_d1.v2
title: Additional file 5: of Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of 164 network objects from the MetaCore human protein interactome that are statistically significantly over-connected to the genes differentially expressed between MCF-7-Snail and MCF-7-Control cells. (XLS 71 kb)
DOI: 10.6084/m9.figshare.c.3643217_d2.v1
title: Additional file 3: of 
                     Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of 12,104 probe sets corresponding to differentially expressed transcripts between MCF-7-Snail and MCF-7-Control cells identified by Significance Analysis of Microarray (FDR = 2.12 % and |FC| ≥1.5). (XLSX 2199 kb)
DOI: 10.6084/m9.figshare.c.3643217_d3.v1
title: Additional file 1: of 
                     Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of 71 genes relevant to EMT and 53 genes relevant to anticancer drug resistance assembled by manual curation from appended references. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.c.3643217_d5.v1
title: Additional file 8: of 
                     Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of differentially expressed genes between MCF-7-Snail and MCF-7-Control cells known to MetaCore knowledgebase to be directly transcriptionally regulated by ESR-1. (XLS 339 kb)
DOI: 10.6084/m9.figshare.c.3643217_d3.v2
title: Additional file 1: of Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of 71 genes relevant to EMT and 53 genes relevant to anticancer drug resistance assembled by manual curation from appended references. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.c.3643217_d2.v2
title: Additional file 3: of Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of 12,104 probe sets corresponding to differentially expressed transcripts between MCF-7-Snail and MCF-7-Control cells identified by Significance Analysis of Microarray (FDR = 2.12 % and |FC| ≥1.5). (XLSX 2199 kb)
DOI: 10.6084/m9.figshare.c.3643217_d5.v2
title: Additional file 8: of Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of differentially expressed genes between MCF-7-Snail and MCF-7-Control cells known to MetaCore knowledgebase to be directly transcriptionally regulated by ESR-1. (XLS 339 kb)
DOI: 10.6084/m9.figshare.c.3643217_d7.v1
title: Additional file 6: of 
                     Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of 31 significant networks centered on transcription factors built from genes differentially expressed between MCF-7-Snail and MCF-7-Control cells. (XLS 39 kb)
DOI: 10.25345/c5474740c
title: MassIVE MSV000096677 - An X-linked long non-coding RNA, PTCHD1-AS regulates autistic behaviors in humans and in mice
title: Adult mouse dorsal striatum and frontal cortex samples (Wk 8 to 12) were processed by the Network Biology Collaborative Centre (NBCC) at the Lunenfeld Tanenbaum Research Institute (Toronto, Canada). Samples of 100 ug protein in RIPA lysis buffer (20 188, MilliporeSigma) were resuspended in 5 percent SDS, and 50 mM triethylammonium bicarbonate. 25 ug of protein was reduced (20mM DTT) and alkylated (40mM iodoacetamide in dark). Samples were processed with the standard S-trap micro spin column (C02 micro, Protifi) digestion protocol. 10 ug per sample was resuspended in 10 uL of 100 mM HEPES pH8 and labelled with 80 ug of a unique tandem mass tag (TMT) 16 plex channel (A44520, Thermo Fisher Scientific) in 4 uL of acetonitrile for 1 hour at RT. The reaction was quenched with 1 percent hydroxylamine. 5 percent of each sample was pooled and acquired with data dependent acquisition using nano high performance liquid chromatography tandem mass spectrometry. A Vanquish Neo UHPLC system was coupled to an Orbitrap Fusion Lumos Tribrid mass spectrometer (FETD2 10002, Thermo Fisher Scientific) and peptides were eluted off a nano-spray emitter generated from fused silica capillary tubing ( 75 um i.d., 365 um o.d. and 5 to 8 um tip opening, and packed to 15 cm with C18 reversed phase material (Reprosil Pur 120 C18 AQ, 3 um)) with a 120 min gradient. Flowrate was maintained at 400 nL per min with a consistent 0.1 percent formic acid background. There were 3 acetonitrile ramps: (1) 3.2 percent to 16.8percent over 72 minutes, (2) 16.8 percent to 24.8 percent over 28 minutes, and (3) 24.8 percent to 35.2 percent over 20 minutes. The first mass spectrometry scan ran for with accumulated time of 50 ms, a mass range of 400 to 16000 mz, orbitrap resolution of 120000, 30 percent radio frequency lens, 200 percent automatic gain control, and 1800 volts. The subsequent tandem mass spectrometry scan had cycle times of 2 s, 35 ms accumulation time, 33 percent higher-energy collisional dissociation collision energy and a first mass to charge ratio of 120 to 1800 mz. All candidate ions had a charge state from 2 to 7, and automatic gain control target of 400 percent isolated using an orbitrap resolution of 50000.
DOI: 10.6084/m9.figshare.c.3643217_d6.v1
title: Additional file 9: of 
                     Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of gene sets from C2: Curated Gene Sets and C6: Oncogenic Signatures gene sets ( http://www.broadinstitute.org/gsea/msigdb/collections.jsp ) significantly enriched in MCF-7-Snail or MCF-7-Control phenotypes. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.c.3643217_d7.v2
title: Additional file 6: of Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of 31 significant networks centered on transcription factors built from genes differentially expressed between MCF-7-Snail and MCF-7-Control cells. (XLS 39 kb)