cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0002357
title: Plant parasitic nematode genome sequencing

description: Genome skimming of six plant parasitic nematode (PPN) species (Anguina agrostis, Globodera ellingtonae, Pratylenchus neglectus, P. penetrans, P. thornei, and Xiphinema americanum) revealed evidence for potential genomic hybridization, effector genes, and endosymbionts.
DOI: 10.26036/cnphis0002358
title: Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila

description: Transgenerational epigenetic inheritance entails transmission of epigenetically determined phenotypic traits through multiple generations. However, very little is known on the principles and the mechanisms governing this type of inheritance. Here, we established stable and isogenic Drosophila epilines by transiently enhancing long-range chromatin interactions. Such epilines display two opposing chromatin states, which depend on differential levels of the H3K27me3 histone mark. Once established, both the active and the repressed epialleles can dominantly be transmitted to naïve flies and can induce paramutation. Importantly, both epilines can be reset to an intermediate naïve state by disrupting chromatin interactions. Finally, we show that the environment can modulate the expressivity of the epialleles and we extend our paradigm to naturally occurring genetic makeups. Our work sheds light on how nuclear organization contributes to epigenetically heritable phenotypic variability and therefore to evolution. Overall design: genomic DNA sequencing and RNA sequencing of Drosophila melanogaster epilines
DOI: 10.26036/cnphis0002359
title: Heliconius Genome sequencing

description: In order to characterize genome-wide patterns of introgression between distantly related Heliconius butterflies, genomic DNA from 29 Heliconius individuals was extracted. Illumina pair-end libraries were constructed using Illumina Truseq protocol and sequenced with an Illumina Hiseq 2000.
DOI: 10.26036/cnphis0002360
title: Eublepharis macularius transcriptome to identify immunoglobulins

description: The Squamata order represents a major evolutionary reptile lineage. From previous genomic studies of the IGHC locus from the Squamata species E. macularius, five immunoglobulin classes were shown to exist. In particular, this species has IgM, similar to that found in other vertebrates, one IgD consisting of eleven immunoglobulin domains characteristic of reptiles, an IgY, and additionally, an antibody similar to the IgA, an antibody formed by the recombination of an IgA-like, and a type of IgD, denominated IgD2. By obtaining the transcriptomes of E. macularius from different tissues (i.e., the spleen, lungs, and intestine), this study sought to characterize the differential expression of these immunoglobulin classes across different organs.
DOI: 10.26036/cnphis0002362
title: Brugia malayi Raw sequence reads

description: Brugia malayi genome sequencing from single males
DOI: 10.26036/cnphis0002363
title: Enterobacteriaceae Carbapenem Breakpoint genome sequencing and assembly

description: Collection of bacterial pathogens that demonstrate a range of carbapenem susceptibility
DOI: 10.26036/cnphis0002364
title: Enterobacteriaceae Carbapenemase Diversity genome sequencing and assembly

description: Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species
DOI: 10.26036/cnphis0001675
title: Bacteriome metagenome of Tettigades ulnaria specimen TETULN

description: Cicadas species are globally distributed and are important insects ecologically and economically. Their success depends upon amino acid providing bacteria that are harbored in specialized organs called bacteriomes. These bacteria have among the smallest genomes of any bacteria; how they function at a cellular level with such small genomes is unknown. To address this question, we sequenced the bacterial symbionts harbored by Cicada species from around the world.
DOI: 10.26036/cnphis0001677
title: Pimephales promelas Transcriptome or Gene expression

description: This submission is about the transcriptome analysis of Epithelioma Papulosum Cyprini cells following SVCV infection.
DOI: 10.26036/cnphis0001678
title: Rhinopithecus bieti Genome sequencing

description: provide a high-quality draft genome of Rhinopithecus bieti, resequencing data
DOI: 10.26036/cnphis0001679
title: Halyomorpha halys isolate:HHAL.00 Genome sequencing

description: Whole genome assembly of Brown marmorated stink bug (Halyomorpha halys) as part of the BCM-HGSC i5k Pilot Project
DOI: 10.26036/cnphis0001680
title: Marine Microbial Eukaryote Transcriptome Sequencing Project

description: The Marine Microbial Eukaryote Transcriptome Sequencing Project was a collaboration between the National Center for Genome Resources, the Gordon and Betty Moore Foundation's Marine Microbiology Initiative, and the international marine microbial eukaryote research community to sequence the transcriptomes of approximately 700 samples from hundreds of diverse organisms. Marine microbial eukaryotes are found in all major eukaryotic branches of the evolutionary tree. They perform a diverse range of functions in marine ecosystems, including photosynthesis, predation, and parasitism. Despite the great abundance of microeukaryotes in the ocean, their importance as absorbers of carbon dioxide and their critical contribution to marine food webs (among many ecological roles), the gene content of these microorganisms is only beginning to be explored because their genomes can be structurally complex and can be many gigabases in size. This program was intended to increase the research community's baseline of scientific knowledge by creating catalogs of genes that suggest how these organisms thrive in diverse marine habitats and how they influence marine ecosystems, biogeochemical cycles, and the composition of the atmosphere. Transcriptome datasets are complex and should be approached with awareness, especially in light of the very deep Illumina sequencing used to generate these data. While many researchers attempted to provide axenic and uni-algal total RNA extracts for sequencing, it did not always turn out to be that way. The deep Illumina sequencing may have occasionally picked up very low levels of non-target RNA, and low levels of bacteria may have been present but not known to the laboratory that provided the sample. For additional project information, details about the varied samples, and data, including transcriptome assemblies and annotations, please see: http://marinemicroeukaryotes.org/ and http://camera.calit2.net/mmetsp/.
DOI: 10.26036/cnphis0001682
title: Anas platyrhynchos Transcriptome or Gene expression

description: revealing the trancriptome basis underlying excessive adiposity in ducks
DOI: 10.26036/cnphis0001684
title: Peripheral blood Transcriptome or Gene expression

description: Gain-of-Function CCR4 Mutations in Adult T-cell Leukemia/Lymphoma
DOI: 10.26036/cnphis0001685
title: Analysis of the RDR6-dependent small RNA profile in ein5 ski2 in Arabidopsis with biological replications and increased sequencing depth

description: Post-transcriptional gene silence (PTGS) is employed in plants to shut down transgenes, invading viral genes and a certain group of endogenous genes. Meanwhile, it is not clear how the risk of expansive PTGS from endogenous genes featured by transitive siRNA production is minimized. Here we demonstrate two essential components of the SKI complex in cytoplasmic 3 -5 mRNA decay pathway, SKI2 and SKI3, function as negative regulators of transgene PTGS in Arabidopsis. The ski2 mutants manifested severe synthetic phenotypes with a 5 -3 exoribonuclease mutant, ein5, which were substantially suppressed by the PTGS mutants, rdr6 and ago1. RDR6 is essential for the altered gene expression in ein5 ski2 on a transcriptome-wide scale. mRNA-seq approach was used to investigate the physiological relevance veiled by the myriad developmental phenotypes in Col-0 (C), ein5-1 (e), ski2-3 (s), ein5-1 ski2-3 (es), rdr6-11 (r) and rdr6-11 ein5-1 ski2-3 (res). A number of endogenous genes, including many miRNA target genes, manifest transitive 21-22 nt siRNA production and compromised gene expression in ein5 ski2 in an RDR6-dependent manner. Taken together, our study brings to light a dual-safeguard system in preventing the expansive siRNA production by the 5 -3 and 3 -5 cytoplasmic mRNA decay pathways. In this experiment, we did three replicates in sequencing that help increase the power in identify the differentially represented genes.The sequencing depth was also increased. Therefore we identified more siRNA-generating loci than that in previous study (GSE52408) (441 vs. 200 loci). Overall design: Examination of small RNA profiles in 4 genotypes with 3 biological replicates each.
DOI: 10.26036/cnphis0001686
title: Polistes dominula isolate:PdomPennStateAug2009 Genome sequencing and assembly

description: De novo genome sequencing of a single haploid male Polistes dominula
DOI: 10.26036/cnphis0002365
title: Gymnopithys rufigula (Furnariidae) and Glyphorynchus spirurus (Thamnophilidae) raw sequence reads

description: WGS project of 2 suboscine species
DOI: 10.26036/cnphis0002367
title: The role of the piRNA pathway in mouse neocorticogenesis

description: PIWI-interacting RNAs (piRNAs) and their associated PIWI proteins play an important role in repressing transposable elements in animal germlines. However, there have been conflicting reports about piRNA expression and function in the soma, particularly in the brain. Here we investigated the role of piRNAs and an important PIWI family member, Piwi-like protein 1 (Piwil1; also known as Miwi in mouse) in the developing mouse neocortex. Using a Piwil1 knock-out mouse strain, we found that Piwil1 is essential for neocorticogenesis, including neocortical cell cycle, migration and dendritogenesis. Piwil1 deletion resulted in increased cell cycle re-entry at embryonic day 17 (E17) when predominantly intracortically projecting neurons are being produced. Prenatal Piwil1 deletion increased the number of Pax6+ radial glia at postnatal day 0 (P0) and disrupted migration of Satb2+ neurons within deep layers at E17, P0 and P7. Satb2+ neurons showed increased co-localization with Bcl11b, marker of subcortically projecting neurons. In addition, Piwil1 knock-outs have disrupted neocortical circuitry represented by thinning of the corpus callosum and altered dendritogenesis. These results are consistent with the rodent phenotypes reported by a recent study that mainly used RNAi knockdown experiments. We identified a disrupted set of genes associated with cell cycle, cell adhesion, transcription and migration in developing neocortices. We further investigated the potential role of piRNAs by sequencing piRNAs in developing neocortices in the wildtype and Piwil1 knock-out strain. Unexpectedly, we did not find a strong signal of absolute piRNA abundance or differential expression in the knock-out, suggesting that Piwil1 may act independently of piRNAs in mouse neocorticogenesis. Our results may help clarify some outstanding questions in the piRNA field about the role of the piRNA pathway in the brain.
DOI: 10.26036/cnphis0002368
title: Hipposideros armiger genome resequencing

description: Whole genome resequencing of Hipposideros armiger
DOI: 10.26036/cnphis0002369
title: Transcriptomic study of biological networks involving grapevine berry development

description: De-multiplexing the unique identifiers discovered data consisted of 28,808,716 clean reads from fruit samples at 40 DAF, 27,941,132 reads from 65 DAF, and 25,457,565 reads from fruit sample at 90 DAF. Overall design: To discover the whole transcriptomic change during grapevine fruit development (Sample number: 3, Sequencing platform: Illumina HiseqTM2500
DOI: 10.26036/cnphis0002370
title: Homo sapiens isolate:AK1 Genome sequencing and assembly

description: Homo sapiens AK1 genome sequencing and de novo assembly of an Asian individual
DOI: 10.26036/cnphis0002371
title: Metagenomic sequencing of preterm infant gut microbiota raw sequence reads

description: Dysbiotic colonization of the preterm infant gut microbiota may have lifelong effects on host health. The normal progression of colonization of preterm infants is a patterned, yet chaotic, process, and thought to be chiefly driven by host factors. While preterm infants almost universally receive early and often repeated and/or prolonged intravenous antibiotic therapy, it remains unclear if and how specific antibiotics alter the developmental progression of the gut microbiota in this population. By analyzing 401 fecal samples from 84 longitudinally-sampled preterm infants, we demonstrate that meropenem, cefotaxime, and ticarcillin-clavulanate significantly reduce species richness during their administration, and significantly enrich or deplete specific bacterial species and antibiotic resistance (AR) genes. In contrast, vancomycin and gentamicin, the antibiotics most commonly administered to preterm infants, have non-uniform effects on species richness. We show this response is predictable with 85% accuracy based on the relative abundance of only two bacterial species and two AR genes before treatment. To more fully investigate the role of the gut-associated resistome in response to specific antibiotics, we performed functional metagenomic selections for resistance to 16 clinically relevant antibiotics from a set of 21 preterm infants’ gut microbiota. Of the 794 AR genes identified, 79% had not previously been classified as providing any resistance phenotype. Combined with deep shotgun sequencing of all 401 fecal samples, we find that multidrug resistant Escherichia, Klebsiella, and Enterobacter species, which are commonly associated with nosocomial infections, dominate the preterm infant gut microbiota. We show that AR genes that are enriched following specific antibiotic treatments are generally unique to the specific treatment and highly correlated (p&lt;0.001) with the abundance of a single species. The most notable exception includes ticarcillin-clavulanate and ampicillin, both of which enrich a large number of overlapping AR genes, and are highly correlated with Klebsiella pneumoniae species in the preterm infant gut microbiota. In addition to AR genes relevant to specific antibiotics likely providing a protective function, we show that all antibiotic treatments also result in widespread collateral microbiome impact through enrichment of AR genes with no known direct activity against the specific antibiotic treatment.
DOI: 10.26036/cnphis0002372
title: Lates calcarifer isolate:ASB-BC8 Genome sequencing and assembly

description: Lates calcarifer genome sequencing and assembly
DOI: 10.26036/cnphis0002373
title: Capra hircus breed:San Clemente Raw sequence reads

description: This is a de novo assembly of the domestic goat (Capra hircus) exclusively using long reads. The assembly was scaffolded using a combination of optical map data, and Hi-C contact alignment graphs. Subsequent scaffolding was confirmed using a Radiation Hybrid map for the goat. This study was a proof of principle that a combination of cutting edge sequencing technologies can be used to efficiently create accurate chromosome-scale scaffolds.
DOI: 10.26036/cnphis0002374
title: Chelonibia testudinaria Raw sequence reads

description: First genomic resource of Chelonibia testudinaria. Used to develop microsatellite markers
DOI: 10.15468/dl.3eyts4
title: Occurrence Download

description: A dataset containing 451 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Biodiversidad de los mamíferos en el Estado de Michoacán",
 "Geometry POLYGON((-103.18153 18.68306,-99.88063 18.68306,-99.88063 21.09428,-103.18153 21.09428,-103.18153 18.68306))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Chiroptera"
 ]
}

 The dataset includes 451 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0298484-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zfm6r2
title: Occurrence Download

description: A dataset containing 153 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Machine Observation"
 ]
 },
 "CoordinateUncertaintyInMeters 0.0-1000.0",
 "OccurrenceStatus is Present",
 "TaxonKey is Metachirus Burmeister, 1854"
 ]
}

 The dataset includes 153 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0310995-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6s9q7k
title: Occurrence Download

description: A dataset containing 88 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Mentha ×carinthiaca Host)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 88 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051661-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dv2ph4
title: Occurrence Download

description: A dataset listing the 2 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is United States of America",
 "TaxonKey is Linaria vulgaris Mill."
 ]
}

 The dataset's 2 records were derived from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0221231-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.95qu56
title: Occurrence Download

description: A dataset containing 36182 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Observation",
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Material sample",
 "BasisOfRecord is Literature Occurrence",
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Living Specimen"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Carassius auratus (Linnaeus, 1758)"
 ]
}

 The dataset includes 36182 records from 234 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036501-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g1a1y9
title: Occurrence Download

description: A dataset containing 4682 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dyckia Schult. & Schult.f."
 ]
}

 The dataset includes 4682 records from 137 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008512-180412121330197/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.562vqj
title: Occurrence Download

description: A dataset containing 16681 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bactrocera dorsalis (Hendel, 1912)"
 ]
}

 The dataset includes 16681 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0302801-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r95aqm
title: Occurrence Download

description: A dataset containing 182985 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Danaus plexippus (Linnaeus, 1758)",
 "Year 2000-2021"
 ]
}

 The dataset includes 182985 records from 117 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0221218-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2bzgps
title: Occurrence Download

description: A dataset containing 1039110 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Apocynaceae"
 ]
}

 The dataset includes 1039110 records from 1296 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008512-180730143533302/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/jf7j8-rwf11
title: COS7 VPS4DN+pNLGFP

description: Cos7 cells transfected with VPS4DN (0.5 ug) and pNLGFP provirus construct (4 ug). Sample #C126
description: <strong>Tilt Series Date:</strong> 2012-05-04</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> Cercopithecus aethiops (monkey, African green)</p>
<strong>Strain:</strong> COS-7 ATCC CRL-1651</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.5°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -6.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> VPS4DN construct provided by Wes Sundquist. pNLGFP construct provided by Irvin Chen, UCLA. Cells transfected, frozen and imaged at Caltech by Cora Woodward</p>
<strong>Purification / Growth Conditions / Treatment:</strong> whole cells grown on grids and transfected with lipofectamine</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-05-04-19/3dimage_69235/</p>12may04_C126_3_pnlDN_Cos7_AT4BT1_0001_full.rec,  Reconstruction (Pixel Size 2.0 nm), 619.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        12may04_C126_3_pnlDN_Cos7_AT4BT1_0001.mrc,  Tilt Series (Pixel Size 0.5 nm), 677.3 MB  
        
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DOI: 10.6084/m9.figshare.30015322
title: Patterson et al., 2025 NatureGeo (IODP Exp. 374 U1524)

description: Data and code presented in Patterson et al., 2025 NatureGeo
DOI: 10.6084/m9.figshare.30015322.v1
title: Patterson et al., 2025 NatureGeo (IODP Exp. 374 U1524)

description: Data and code presented in Patterson et al., 2025 NatureGeo