cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh0188467.10fu
title: SH0188467.10FU

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: 10.15156/bio/sh0188468.10fu
title: SH0188468.10FU

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: 10.15156/bio/sh0188469.10fu
title: SH0188469.10FU

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: 10.15156/bio/sh0188470.10fu
title: SH0188470.10FU

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: 10.15156/bio/sh0188471.10fu
title: SH0188471.10FU

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: 10.15156/bio/sh0188472.10fu
title: SH0188472.10FU

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: 10.15156/bio/sh0188473.10fu
title: SH0188473.10FU

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: 10.25345/c5x05xq5s
title: MassIVE MSV000095605 - GNPS_toxoplasma_mouse_11(organs,contents)_positive
title: Metabolites (aqueous & organic) were extracted from mouse tissues and tissues' contents (SI duodenum, SI jejunum, SI ileum, cecum, large intestine, small intestine, contents, cecum contents, large intestine contents, heart, liver, and quad) and were run by LC-MS, C8 in positive mode.
DOI: 10.6084/m9.figshare.26571172
title: Additional file 7 of DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology

description: Additional file 7: Table S4. Cell Sorting and Sequencing Summary Statistics. Summary statistics for the number of cells collected per subpopulation for Kir2.1, total number of reads for each sample used in this study, number of reads that aligned to variants within the gene, and variants that we filtered for use in figures and fitness calculations because they were expected.
DOI: 10.6084/m9.figshare.26571169.v1
title: Additional file 6 of DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology

description: Additional file 6: Table S3. Primers used in this study. Primer names and their sequences are listed that were used for amplifying DNA for sequencing and those that were used for generating DIMPLE libraries.
DOI: 10.6084/m9.figshare.26571163
title: Additional file 4 of DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology

description: Additional file 4: Table S1. Inputs and outputs from test running DIMPLE. As discussed within the text, we tested the computational DIMPLE pipeline by including 25 genes. Within this table is their length, GC content, number variants DIMPLE generated, and the number of sub libraries for the gene.
DOI: 10.6084/m9.figshare.26571163.v1
title: Additional file 4 of DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology

description: Additional file 4: Table S1. Inputs and outputs from test running DIMPLE. As discussed within the text, we tested the computational DIMPLE pipeline by including 25 genes. Within this table is their length, GC content, number variants DIMPLE generated, and the number of sub libraries for the gene.
DOI: 10.6084/m9.figshare.26571157
title: Additional file 2 of DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology

description: Additional file 2. Enrich2 outputs for the Kir2.1 surface expression screen. HGVS identifier, surface fitness scores, epsilon, and standard errors for each variant used in this study.
DOI: 10.15468/dl.9jk5ju
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "MULTIPOLYGON (((148.904002 -32.656695, 148.906248 -32.656695, 148.906248 -32.652204, 148.904002 -32.652204, 148.904002 -32.656695)), ((148.904002 -32.656695, 148.89951 -32.656695, 148.89951 -32.658941, 148.904002 -32.658941, 148.904002 -32.656695)))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067314-240626123714530/datasets/export for details.
DOI: 10.6084/m9.figshare.26679305
title: Additional file 1 of Calcium signaling positively regulates cellulase translation and secretion in a Clr-2-overexpressing, catabolically derepressed strain of Penicillium funiculosum

description: Additional file 1. FPKM values of shortlisted transcription factors in P. funiculosum NCIM1228 and ΔMig1 when cultured in glucose and cellulose.
DOI: 10.6084/m9.figshare.26679305.v1
title: Additional file 1 of Calcium signaling positively regulates cellulase translation and secretion in a Clr-2-overexpressing, catabolically derepressed strain of Penicillium funiculosum

description: Additional file 1. FPKM values of shortlisted transcription factors in P. funiculosum NCIM1228 and ΔMig1 when cultured in glucose and cellulose.
DOI: 10.6084/m9.figshare.26607988
title: Additional file 3 of VariantscanR: an R-package as a clinical tool for variant filtering of known phenotype-associated variants in domestic animals

description: Additional file 3: Complete output of the variantscanR report for the 4 canine samples. Description of the data: Excel file containing the complete variantscanR output report, including 3 tables per sample analysed. Each sample is displayed on a different excel tab. First table: Priority list of variants that were found in the sample of interest and that are known to segregate in the breed (Labrador retriever) with an established genotype–phenotype association. Second table: Variants in the sample of interest, but not known to segregate in the breed (Labrador retriever). This warrants additional careful interpretation as the genotype–phenotype association can be breed-specific. Third table: Variants called in other samples of the multi-VCF file that are present in a wildtype homozygous state in the sample of interest.
DOI: 10.6084/m9.figshare.26571124
title: Additional file 1 of Comparison of antimicrobial resistant Escherichia coli isolated from Irish commercial pig farms with and without zinc oxide and antimicrobial usage

description: Additional file 1. Summary of analysed AmpC / ESBL E. coli isolates obtained in this study. Sample abbreviations: FW0 = faecal sample at day of weaning; FW1 = faecal sample 1 week after weaning; FW2 = faecal sample 2 week after weaning; SWD = environmental swab sample of cleaned drinkers and feeders before interaction with piglets; SWW = environmental swab sample of cleaned walls and floors before interaction with piglets.
DOI: 10.6084/m9.figshare.26607988.v1
title: Additional file 3 of VariantscanR: an R-package as a clinical tool for variant filtering of known phenotype-associated variants in domestic animals

description: Additional file 3: Complete output of the variantscanR report for the 4 canine samples. Description of the data: Excel file containing the complete variantscanR output report, including 3 tables per sample analysed. Each sample is displayed on a different excel tab. First table: Priority list of variants that were found in the sample of interest and that are known to segregate in the breed (Labrador retriever) with an established genotype–phenotype association. Second table: Variants in the sample of interest, but not known to segregate in the breed (Labrador retriever). This warrants additional careful interpretation as the genotype–phenotype association can be breed-specific. Third table: Variants called in other samples of the multi-VCF file that are present in a wildtype homozygous state in the sample of interest.
DOI: 10.6084/m9.figshare.26679377
title: Additional file 3 of A low-input high resolution sequential chromatin immunoprecipitation method captures genome-wide dynamics of bivalent chromatin

description: Additional file 3: Table S1. library statistics, list of all bivalent peaks and list of peaks called in each replicate for total H3K4me3, total H3K27me3, bivalent K4-K27 and K27-K4 reChIP datasets generated in this study (E14 rep1 and rep2), independently generated (GSE135841) and Dppa2/4 WT (clones 57 and 58) and double knockout (clones 43 and 53) samples. In the list of all bivalent peaks (tab 2), peaks are classified as high-confidence (hc), K4-biased (k4b), K27-biased (K27b), or low confidence (lc) using either in-line total ChIPs (column E) or independent total ChIPs (column F). Table S2. motif analysis of bivalent peaks using monaLisa along with associated statistics. Table S3. list of bivalent genes classified as high confidence, K4-biased, K27-biased and low confidence along with log2 CPM/bp enrichment scores for independent total H3K4me3 and H3K27me3, IgG-IgG, in-line total H3K4me3 and H3K27me3 ChIP and K4-K27 and K27-K4 bivalent reChIP datasets. Table S4. Gene ontology enrichment of different bivalent gene classifications (first column) together with associated statistics and list of associated genes. Table S5. list of EDGER differentially enriched peaks for bivalent K4-K27 (tab1) and K27-K4 (tab2) reChIP between Dppa2/4 WT and DKO clones. Consensus differentially enriched peak list is shown in tab 3 along with HOMER classification of peak, enrichment statistics and (for promoters) whether they were previously classified as differentially enriched.
DOI: 10.6084/m9.figshare.26679377.v1
title: Additional file 3 of A low-input high resolution sequential chromatin immunoprecipitation method captures genome-wide dynamics of bivalent chromatin

description: Additional file 3: Table S1. library statistics, list of all bivalent peaks and list of peaks called in each replicate for total H3K4me3, total H3K27me3, bivalent K4-K27 and K27-K4 reChIP datasets generated in this study (E14 rep1 and rep2), independently generated (GSE135841) and Dppa2/4 WT (clones 57 and 58) and double knockout (clones 43 and 53) samples. In the list of all bivalent peaks (tab 2), peaks are classified as high-confidence (hc), K4-biased (k4b), K27-biased (K27b), or low confidence (lc) using either in-line total ChIPs (column E) or independent total ChIPs (column F). Table S2. motif analysis of bivalent peaks using monaLisa along with associated statistics. Table S3. list of bivalent genes classified as high confidence, K4-biased, K27-biased and low confidence along with log2 CPM/bp enrichment scores for independent total H3K4me3 and H3K27me3, IgG-IgG, in-line total H3K4me3 and H3K27me3 ChIP and K4-K27 and K27-K4 bivalent reChIP datasets. Table S4. Gene ontology enrichment of different bivalent gene classifications (first column) together with associated statistics and list of associated genes. Table S5. list of EDGER differentially enriched peaks for bivalent K4-K27 (tab1) and K27-K4 (tab2) reChIP between Dppa2/4 WT and DKO clones. Consensus differentially enriched peak list is shown in tab 3 along with HOMER classification of peak, enrichment statistics and (for promoters) whether they were previously classified as differentially enriched.
DOI: 10.6084/m9.figshare.26607811
title: Additional file 8 of A symbiotic footprint in the plant root microbiome

description: Additional file 8: XLSX file of mean abundance (DESeq2 transformed counts) by plant species and symbiotype group, taxonomy assignment, symbiotype enrichment group, and primary symbiont status of the bacterial and fungal symbiotype specific OTUs.
DOI: 10.15468/dl.svrkmj
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((148.528954 -32.658941, 148.528954 -32.661187, 148.531199 -32.661187, 148.531199 -32.658941, 148.528954 -32.658941))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067315-240626123714530/datasets/export for details.
DOI: 10.6084/m9.figshare.26607793.v1
title: Additional file 2 of A symbiotic footprint in the plant root microbiome

description: Additional file 2: XLSX table with sample ID, barcode assignments, and primer sequences for each sample sequenced in both 16S rRNA and ITS MiSeq libraries.
DOI: 10.6084/m9.figshare.26607802.v1
title: Additional file 5 of A symbiotic footprint in the plant root microbiome

description: Additional file 5: Table of filtered bacteria OTU counts with taxonomy assignments in each sequenced sample.
DOI: 10.6084/m9.figshare.26607808
title: Additional file 7 of A symbiotic footprint in the plant root microbiome

description: Additional file 7: XLSX file of bacterial and fungal OTUs considered primary symbionts that were removed for some portions of the analysis and OTU counts of nodule samples used to define the bacteria primary symbionts.
DOI: 10.6084/m9.figshare.26607802
title: Additional file 5 of A symbiotic footprint in the plant root microbiome

description: Additional file 5: Table of filtered bacteria OTU counts with taxonomy assignments in each sequenced sample.
DOI: 10.6084/m9.figshare.26607805.v1
title: Additional file 6 of A symbiotic footprint in the plant root microbiome

description: Additional file 6: Table of filtered fungal OTU counts with taxonomy assignments in each sequenced sample.
DOI: 10.6084/m9.figshare.26607811.v1
title: Additional file 8 of A symbiotic footprint in the plant root microbiome

description: Additional file 8: XLSX file of mean abundance (DESeq2 transformed counts) by plant species and symbiotype group, taxonomy assignment, symbiotype enrichment group, and primary symbiont status of the bacterial and fungal symbiotype specific OTUs.
DOI: 10.6084/m9.figshare.26607793
title: Additional file 2 of A symbiotic footprint in the plant root microbiome

description: Additional file 2: XLSX table with sample ID, barcode assignments, and primer sequences for each sample sequenced in both 16S rRNA and ITS MiSeq libraries.
DOI: 10.15468/dl.bdmrkv
title: Occurrence Download

description: A dataset containing 122526 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((76.60939 30.57426, 76.90814 30.57426, 76.90814 30.78839, 76.60939 30.78839, 76.60939 30.57426))",
 "Year is greater than or equal to 2000",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 122526 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067306-240626123714530/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.26607796.v1
title: Additional file 3 of A symbiotic footprint in the plant root microbiome

description: Additional file 3: TXT file of all bacteria OTU representative sequences.
DOI: 10.6084/m9.figshare.26607799.v1
title: Additional file 4 of A symbiotic footprint in the plant root microbiome

description: Additional file 4: TXT file of all fungal OTU representative sequences.
DOI: 10.6084/m9.figshare.26608015
title: Additional file 5 of Analysis of differences in tobacco leaf microbial communities after redrying in Chinese provinces and from abroad

description: Additional file 5: Table S4. ASV of ITS1 sequences analyzed.
DOI: 10.6084/m9.figshare.26607796
title: Additional file 3 of A symbiotic footprint in the plant root microbiome

description: Additional file 3: TXT file of all bacteria OTU representative sequences.
DOI: 10.15468/dl.ane5ix
title: Occurrence Download

description: A dataset containing 643 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dipodomys phillipsii Gray, 1841"
 ]
}

 The dataset includes 643 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010011-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3jmrqa
title: Occurrence Download

description: A dataset containing 662 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Echium glomeratum Poir."
 ]
}

 The dataset includes 662 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033825-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dctpzr
title: Occurrence Download

description: A dataset containing 3349 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Ploceus castanops Shelley, 1888"
 ]
}

 The dataset includes 3349 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000169-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.