cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh3577648.08fu
title: SH3577648.08FU

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/sh3577649.08fu
title: SH3577649.08FU

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/sh2826877.08fu
title: SH2826877.08FU

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/sh2826878.08fu
title: SH2826878.08FU

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/sh3577650.08fu
title: SH3577650.08FU

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/sh3577651.08fu
title: SH3577651.08FU

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/sh2826879.08fu
title: SH2826879.08FU

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/sh2826880.08fu
title: SH2826880.08FU

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: 10.26036/cnphis0000137
title: Stegodyphus mimosarum Genome sequencing and assembly

description: Genomic analysis of Stegodyphus mimosarum
DOI: 10.26036/cnphis0000873
title: Erinaceus europaeus Genome sequencing

description: Erinaceus europaeus (European Hedgehog) genome sequencing using Illumina sequencing with multiple library types.
DOI: 10.26036/cnphis0000874
title: Population genomics in Atlantic cod, Gadus morhua

description: Investigation of population genomic structure and diversity of natural populations of Atlantic cod in the North Atlantic has relevance to management and conservation. The study uses a genome wide Next Generation Sequencing approach to scan nucleotide diversity and differentiation among migratory North East Arctic cod and stationary Norwegian coastal cod.
DOI: 10.26036/cnphis0000875
title: Canis lupus familiaris Transcriptome or Gene expression

description: Canis familiaris (Dog) RNA sequencing from multiple tissues.
DOI: 10.26036/cnphis0000876
title: Berlin - C167.4 F1 hybrid genomic DNA.

description: Using RNA-seq technology, a comprehensive assessment of cis regulatory divergence in interspecific hybrid female heads was conducted and patterns of sequence evolution (Begun et al. 2007) within causal loci were examined. Genotype specific references were shown to virtually eliminate the map bias plaguing this technology. A novel Bayesian model, which uses allele representation in F1 hybrid DNA sequence reads as a prior, was used to estimate allele frequencies in RNA sequences. The associated data is for the DNA control sequences from D. melanogaster - D. simulans interspecific hybrids. RNA sequencing data can be found at #GEO and at http://bioinformatics.ufl.edu/McIntyre_Lab/Interspecific_AI.
DOI: 10.26036/cnphis0000877
title: Rare alleles increase genome-wide in a hybrid zone

description: In mutation-order speciation, different series of alleles are fixed in populations adapting to identical environments1,2. These may include gene pairs which are beneficial within each population, but cause reproductive isolation when combined in hybrids. It has been predicted (Ref. 3: p. 372) that the continuous generation of genotypes recombined for such loci in the centre of a hybrid zone will create a novel selection regime, favouring variants at speciation genes that reduce hybrid disadvantage, and any markers associated with them. This process may explain the frequent observation4-10 of unexpected gene variants in hybrid zones, the so-called “rare-allele phenomenon”. Here, we use Illumina sequencing in a snail hybrid zone to reveal that this pattern is indeed widespread throughout the genome, involving thousands of loci. This “rare-allele phenomenon” allows more direct assessment of the genomic architecture of speciation, and in particular could be employed as a quick method for finding speciation genes in non-model organisms.
DOI: 10.26036/cnphis0000878
title: Three-dimensional folding and functional organization principles of the Drosophila genome

description: Chromosomes are the physical realization of genetic information and thus form the basis for its reading, hindering and propagation. Here we present a high-resolution chromosomal contact map derived from a new genome-wide chromosome conformation capture approach (a simplified version of the Hi-C method) applied to Drosophila embryonic nuclei. The data show that the entire genome is linearly partitioned into well-demarcated physical domains that overlap extensively with active and repressive epigenetic marks. Chromosomal contacts are hierarchically organized between domains. Global modeling of compaction and clustering of domains show that inactive domains are condensed and confined to their chromosomal territories, while active domains reach out of the territory to form remote intra- and inter-chromosomal contacts. Overall design: One pilot sample, comprising seven paired-end Illumina GA-II lanes; one deep-sequenced sample, comprising seven paired-end Illumina HiSeq lanes
DOI: 10.26036/cnphis0000879
title: Ochotona princeps Genome sequencing

description: American Pika genome sequencing using Illumina sequencing with multiple library types. The DNA is from a female, Ochotona princeps_07Jul2011
DOI: 10.26036/cnphis0000880
title: Mesocricetus auratus Genome sequencing

description: Mesocricetus auratus (Golden Hamster) genome sequencing using Illumina sequencing with multiple library types.
DOI: 10.26036/cnphis0000138
title: Stegodyphus mimosarum Transcriptome or Gene expression

description: Stegodyphus mimosarum Transcriptome sequencing
DOI: 10.26036/cnphis0000139
title: Whole Exome Sequencing of 10 Insulinoma patients Exome

description: Whole Exome Sequencing of 10 Insulinoma patients
DOI: 10.26036/cnphis0000140
title: Oryza sativa Genome sequencing

description: -
DOI: 10.26036/cnphis0000141
title: Acanthoscurria geniculata Genome sequencing and assembly

description: Genomic analysis of Acanthoscurria geniculata
DOI: 10.26036/cnphis0000142
title: Acanthoscurria geniculata Transcriptome or Gene expression

description: Acanthoscurria geniculata Transcriptome sequencing
DOI: 10.26036/cnphis0000143
title: Study of Parkinson Induced Pluripotent Stem Cellline

description: Study the disease of Parkinson in Human
DOI: 10.26036/cnphis0000144
title: Red clover cryptic virus 2 RefSeq Genome

description: Red clover cryptic virus 2 genome reference project
DOI: 10.26036/cnphis0000145
title: BGI Colorectal cancer exome sequencing

description: share Colorectal cancer exome sequencing
DOI: 10.26036/cnphis0000146
title: Auxenochlorella protothecoides sp 0710 Genome sequencing

description: Chlorella protothecoides (Trebouxiophyceae, Chlorophyta) is a genus of single-cell green algae, which was first described by Krüger in 1894. Now, it is highly regarded as one of the potential microalgae for biofuel production due to its ability to accumulate large quantity of lipids within the cell. C. protothecoides is a 2-10 mm in diameter, coccoid and free-living green alga. It contains multiple mitochondria, a single cup-shaped chloroplast, rigid cell wall and no flagella. Unlike most autotrophic green algae, C. protothecoides can not only live autotrophically by fixing sun’s energy through photosynthesis, but also can utilize organic components directly from environment for a heterotrophic growth. Compared with autotrophic cells, the intracellular structure and composition have undergone great changes in the heterotrophic cells. The most attractive phenomenon is the degradation of chloroplast and the accumulation of the oil bodies. The heterotrophic cells are more suitable for biodiesel production due to the increase in both biomass yield (51.2 g/L) and oil content (55.2%). Thus, C. protothecoides can serve as a model to study the mechanism of high oil accumulation and find ways to further reduce the cost of biodiesel
DOI: 10.26036/cnphis0000881
title: Octodon degus Genome sequencing

description: Octodon degus (Degu) genome sequencing using Illumina sequencing with multiple library types.
DOI: 10.26036/cnphis0000882
title: Genome-wide Profiling of Progesterone Receptor and GATA2 Binding in the Mouse Uterus [ChIP-Seq]

description: Progesterone (P4) signaling through its nuclear transcription factor, the progesterone receptor (PR), is essential for normal uterine function. Although deregulation of PR mediated signaling is known to underscore uterine dysfunction and a number of endometrial pathologies, the early molecular mechanisms of this deregulation are unclear. To address this issue, we have defined the genome-wide PR and GATA2 cistrome in the murine uterus using chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq). In uteri of ovariectomized mice, we identified 6367 PR binding sites in the absence of P4 ligand; however, this number increased at nearly three fold (18,432) following acute P4 exposure. Sequence analysis revealed that approximately 73% of these binding sites contain a progesterone response element (PRE) or a half-site motif recognized by the PR. Many previously identified P4 target genes known to regulate uterine function were found to contain PR binding sites, confirming the validity of our methodology. In addition we identified 46,183 GATA2 binding sites in P4 treatment conditions with 7,954 binding sites overlapping that of the PR. Overall design: Examination of PR and Gata2 binding in whole or epithelial isolated mouse uterine tissue upon acute vehicle/P4 treatement
DOI: 10.26036/cnphis0000883
title: Homo sapiens Exome

description: BRAFI treated V600E melanoma.
DOI: 10.26036/cnphis0000884
title: Lottia scabra Project

description: none provided
DOI: 10.26036/cnphis0000885
title: Conserved Topological Domains in Mammalian Genomes Identified by High-resolution Analysis of Chromatin Interactions

description: The spatial organization of the genome is intimately linked to its biological function, yet our understanding of higher order genomic structure is limited. Here we present high-resolution analyses of chromosomal organization in pluripotent and differentiated human and murine cell types determined using the Hi-C technique. We find that the mammalian genome is composed of over 1000 topological domains, which are stable among different cell types and highly conserved across species. These megabase-long genomic structures, defined by prominent local chromatin interactions and separated by narrow boundary regions, likely function to restrict regulatory interactions between cis-acting elements and limit the spreading of heterochromatin during cellular differentiation. Interestingly, the boundaries are enriched not only for binding sites of the insulator protein CTCF, but also for promoters of house keeping genes, supporting a role for both CTCF and housekeeping genes in the establishment or maintenance of the topological domains. Overall design: Hi-C experiment were conducted in mESC, hESC and IMR90 cells
DOI: 10.26036/cnphis0000886
title: Drosophila albomicans strain:KM-55-5 Genome sequencing

description: The project aims to decode the whole genome and transcriptome of D. albomicans, a unique fruitfly species evolved sex chromosomes in a very short time scale, in order to study patterns of incipient sex chromosome evolution.
DOI: 10.26036/cnphis0000887
title: Salmonella enterica subsp. enterica serovar Heidelberg str. N19992

description: None
DOI: 10.26036/cnphis0000888
title: Salmonella enterica subsp. enterica serovar Heidelberg str. 670102-5

description: None
DOI: 10.26036/cnphis0000889
title: Aplysia californica Genome Sequencing

description: Aplysia californica Genome Sequencing
DOI: 10.26036/cnphis0000148
title: Auxenochlorella protothecoides sp 0710 Transcriptome or Gene expression

description: Chlorella protothecoides (Trebouxiophyceae, Chlorophyta) is a genus of single-cell green algae, which was first described by Krüger in 1894. Now, it is highly regarded as one of the potential microalgae for biofuel production due to its ability to accumulate large quantity of lipids within the cell. C. protothecoides is a 2-10 mm in diameter, coccoid and free-living green alga. It contains multiple mitochondria, a single cup-shaped chloroplast, rigid cell wall and no flagella. Unlike most autotrophic green algae, C. protothecoides can not only live autotrophically by fixing sun's energy through photosynthesis, but also can utilize organic components directly from environment for a heterotrophic growth. Compared with autotrophic cells, the intracellular structure and composition have undergone great changes in the heterotrophic cells. The most attractive phenomenon is the degradation of chloroplast and the accumulation of the oil bodies. The heterotrophic cells are more suitable for biodiesel production due to the increase in both biomass yield (51.2 g/L) and oil content (55.2%). Thus, C. protothecoides can serve as a model to study the mechanism of high oil accumulation and find ways to further reduce the cost of biodiesel
DOI: 10.26036/cnphis0000149
title: CompleteGenomics sequencing of (PJL) Puerto Rican in Puerto Rico HapMap population DNA for sequencing was extracted from whole blood

description: -
DOI: 10.26036/cnphis0000150
title: Whole genome sequencing of the Sesamum indicum nuclear genome

description: We sequenced the whole nuclear genome of Sesamum indicum (Zhongzhi No.13) using the whole genome shotgun (WGS) strategy. Multiple pair-end libraries with insert size ranging from 170 bp to 20,000 bp were sequenced by Illumina Hiseq 2000 platform. All the data was filtered and the resulted clean data was assembled to scaffolds (supercontigs) using SOAPdenovo.
DOI: 10.26036/cnphis0000151
title: Sequencing the transcriptomes of Sesamum indicum across multiple tissues and conditions

description: We sequenced and analyzed the transcriptomes of Sesamum indicum across multiple tissues and conditions (e.g., seed in different development stages)
DOI: 10.26036/cnphis0000152
title: TARGET: Kidney - Clear Cell Sarcoma of the Kidney (CCSK)

description: To further explore some more aggressive subtypes in pediatric cancer already under study in OCG, CGCI is partnering with TARGET initiative to support extensive sequencing analysis of three hard to treat childhood cancers: refractory to treatment cases of acute myeloid leukemia and two rare kidney tumors; clear cell sarcoma of the kidney (CCSK) and rhabdoid tumor. CCSK is a rare, aggressive kidney tumor that usually occurs in children younger than 3 years of age and little is known about the biology of this disease. There are 13 patient cases in the CCSK dataset, each with gene expression, methylation and comprehensive next-generation sequencing to include whole genome sequencing of tumor/normal pairs and mRNA-seq. All cases can be sorted according to data type via the Case Matrix on the TARGET Data Matrix. Please visit the TARGET website listed above for additional information on this and other TARGET genomics projects. Please see the TARGET Publication... (for more see dbGaP study page.)
DOI: 10.26036/cnphis0000153
title: Whole genome and whole exome of esophageal cancer

description: We analysised 88 patients
DOI: 10.26036/cnphis0000154
title: CRC_BC Targeted

description: Colorectal and Breast Cancer Target Region Sequencing
DOI: 10.26036/cnphis0000890
title: Manduca sexta Genome sequencing

description: Whole genome sequence, assembly and annotation of the Manduca sexta genome.
DOI: 10.26036/cnphis0000891
title: Salmonella enterica subsp. enterica serovar Montevideo str. 19N genome sequencing

description: This strain will be used for comparative analysis.
DOI: 10.26036/cnphis0000892
title: Salmonella enterica subsp. enterica serovar Montevideo str. MB102109-0047 genome sequencing

description: Salmonella is an important foodborne pathogen.
DOI: 10.26036/cnphis0000893
title: Salmonella enterica subsp. enterica serovar Montevideo str. MB111609-0052 genome sequencing

description: Salmonella is an important foodborne pathogen.