cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0002701
title: Comparison of transcriptionnal changes in Petunia hybrida WT and ram1-2 induced by mycorrhiza

description: Aim: compare the transcriptionnal responses induced by mycorrhiza in wild type and GRAS transcription factor RAM1 mutant ram1-2 in roots. Results: 650 genes were upregulated in mycorrhized WT (fold change &gt;5; FDR&lt;0,05, experiment difference&gt;10) and 201 in the ram1 mutant. 182 genes were induced in both WT and ram1. 468 and 19 genes were induced only in WT or ram1-2 respectively. 91 genes were downregulated in mycorrhized WT (fold change &lt;5; FDR&lt;0,05, experiment difference&gt;10) and 51 in ram1-2. There was no overlap in the downregulated genes. Conclusion: The transcriptionnal response to mycorrhiza is more important in WT than in ram1-2. Gene induction in ram1 mostly overlap with wild type. Our results confirm that ram1 plays a central role in the root response to mycorrhization. Overall design: mRNA profile comparition of control (NM) and mycorrhized (M) roots in wild type (WT) and ram1-2 Petunia, generated by deep sequencing, in triplicate, using Illumina.
DOI: 10.14457/cmu.res.2009.561
title: การพัฒนาเครื่องมือวัดเจตคติต่อวิทยาศาสตร์
DOI: 10.14457/cmu.res.2009.572
title: ภาวะผู้นำของผู้บริหารสถานศึกษา อำเภอเวียงแหง สังกัดสำนักงานเขตพื้นที่การศึกษาเชียงใหม่ เขต 3
DOI: 10.14457/cmu.the.2009.814
title: การวิเคราะห์รูปแบบและเนื้อหา ของข้อมูลข่าวสารด้านสุขภาพบนอินเทอร์เน็ต
DOI: 10.26036/cnphis0002683
title: human gut Metagenome

description: To reveal the relationship between the gut microbiome and ankylosing spondylitis, a quantitative metagenomics study that was based on deep shotgun sequencing of the gut microbial DNA from 211 Chinese individuals (97 patients and 104 healthy controls) was carried out. A total of 23,709 genes and 16 metagenomic species that were differentially abundant in the two groups were identified.
DOI: 10.26036/cnphis0002691
title: Chrysoperla externa isolate:Chrysoperla externa larvae Raw sequence reads

description: DNA gut content of Chrysoperla externa 3rd instar larvae.
DOI: 10.26036/cnphis0002702
title: Rapana venosa Genome sequencing and assembly

description: De novo Genome Survey of Rapana venosa
DOI: 10.26036/cnphis0002706
title: fruitENCODE: An encyclopedia of DNA elements for fruit ripening

description: Fleshy fruit ripening is an irreversible developmental process that the physiological and biochemical properties of the seed-bearing organ are altered to aid seed dispersal. Significant progress has been made in the model fruit tomato, in which the plant hormone ethylene, fruit specific transcription factors and epigenome reprograming fine tune the ripening processes. The complexity in ripening regulation could be of significant evolutionary advantage, as accidental activation of ripening would attract frugivores prematurely and cause unnecessary seed loss, and the relatively stable epigenome could serve as a checkpoint to prevent ripening before seed maturation. However, as fleshy fruit evolved independently in different plant lineages, it would be naive to consider the observations made in tomato could be universal. The goal of this fruit ENCODE project is to provide a comprehensive annotation of functional elements in not just the tomato genome, but a wide-range of fleshy fruit species in order to examine the diversity of fruit ripening processes.
DOI: 10.26036/cnphis0002707
title: RNA-seq data from somatic tissues and gonads from Anolis, human, mouse, opossum, platypus, chicken and xenopus Raw sequence reads

description: None
DOI: 10.26036/cnphis0002709
title: RAD-seq study of four species of Southeast Asian birds

description: A current model of rain forest population diversification in Sundaland specifies east-west vicariance into refugia during the early Pleistocene. In some taxa, this division was followed by dispersal and secondary contact on Borneo in the late Pleistocene. To investigate genetic, morphological, spatial, and temporal characteristics of the model, we compared genomic population and plumage variation among four bird species with known east-west mtDNA and plumage division.
DOI: 10.26036/cnphis0002715
title: Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements

description: Phylogenetics is undergoing a revolution as large-scale molecular datasets reveal unexpected but repeatable rearrangements of clades that were previously thought to be disparate lineages. One of the most unusual clades of fishes that has been recovered by large-scale molecular datasets is an expanded Syngnathiformes including traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), as well as a diverse set of largely benthic-associated fishes (Callionymoidei, Dactylopteridae, Mullidae, Pegasidae) that were previously dispersed across three orders. The monophyly of this surprising clade of fishes has been upheld by recent studies utilizing both nuclear and mitogenomic data, but the relationships among major lineages within Syngnathiformes remain ambiguous; previous analyses have recovered inconsistent topologies and are plagued by low support at deep divergences between the major lineages. In this study, we use a dataset of ultraconserved elements (UCEs) to conduct the first phylogenomic study of Syngnathiformes. UCEs have been shown to be effective markers for resolving deep phylogenetic relationships in fishes and, combined with increased taxon sampling, we expected UCEs to resolve problematic syngnathiform relationships. Overall, UCEs were effective at resolving relationships within Syngnathiformes at a range of evolutionary timescales. We find consistent support for the monophyly of traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), which better agrees with morphological hypotheses than previously published topologies from molecular data. This result was recovered in all Bayesian and maximum likelihood analyses, was robust to differences in matrix completeness and potential sources of bias, and was also recovered with high support from ASTRAL coalescent-based analyses when matrices were filtered to contain the most phylogenetically informative loci. While Bayesian and maximum likelihood analyses found support for a monophyletic benthic-associated clade (Callionymidae, Dactylopteridae, Mullidae, and Pegasidae) as sister to the long-snouted clade, this result was not replicated in the ASTRAL analyses. The base of our phylogeny is characterized by short internodes separating major syngnathiform lineages and is consistent with the hypothesis of an ancient rapid radiation at the base of Syngnathiformes. Syngnathiformes therefore present an exciting opportunity to study patterns of morphological variation and functional innovation arising from rapid but ancient radiation.
DOI: 10.14457/cmu.the.2009.810
title: การวิเคราะห์แนวทางการนำเสนอภาพยนต์แนวสยองขวัญ
DOI: 10.26036/cnphis0002684
title: Menidia menidia Raw sequence reads

description: Raw low-coverage genomic sequencing reads from population samples
DOI: 10.26036/cnphis0002704
title: Novel co-symbiosis in the unique lucinid bivalve Phacoides pectinatus

description: None
DOI: 10.26036/cnphis0002705
title: Panthera pardus japonensis Genome sequencing

description: Whole genome sequencing of Leopard to test the phylogenomic variation in genus Panthera
DOI: 10.26036/cnphis0002708
title: Ectopistes migratorius Raw sequence reads

description: The UCSC Paleogenomics Laboratory and academic collaborators in partnership with Revive & Restore have sequenced DNA from multiple passenger pigeon tissue and subfossil samples for population and comparative genomics research. Before the species'' extinction in 1914, passenger pigeons were the most numerous bird in North America, and possibly the world: numbering 3-5 billion individuals in the early 1800''s. Genomes of passenger pigeons offer a rare opportunity to research the effects of large population size on the evolution of eukaryotic genomes.
DOI: 10.26036/cnphis0002711
title: Pogonus Variation

description: Draft genome assembly and RAD tag sequencing of Pogonus chalceus
DOI: 10.26036/cnphis0002713
title: Deep whole-genome sequencing of 38 Tibetans and 39 Han Chinese

description: None
DOI: 10.26036/cnphis0002714
title: Dry habitats were crucibles of domestication in the evolution of agriculture in ants

description: The evolution of ant agriculture, as practiced by the fungus-farming “attine” ants, is thought to have arisen in the wet rainforests of South America about 55-65 Ma. Most subsequent attine agricultural evolution, including the domestication event that produced the ancestor of higher attine cultivars, is likewise hypothesized to have occurred in South American rainforests. The “out-of-the-rainforest” hypothesis, while generally accepted, has never been tested in a phylogenetic context. It also presents a problem for explaining how fungal domestication might have occurred, given that isolation from free-living populations is required. Here, we use phylogenomic data from ultra-conserved element (UCE) loci to reconstruct the evolutionary history of fungus-farming ants, reduce topological uncertainty, and identify the closest non-fungus-growing ant relative. Using the phylogeny we infer the history of attine agricultural systems, habitat preference, and biogeography. Our results show that the out-of-the-rainforest hypothesis is correct with regard to the origin of attine ant agriculture; however, contrary to expectation, we find that the transition from lower to higher agriculture very likely occurred in a seasonally dry habitat, inhospitable to the growth of free-living populations of attine fungal cultivars. We suggest that dry habitats favored the isolation of attine cultivars over the evolutionary time spans necessary for domestication to occur.
DOI: 10.26036/cnphis0002716
title: Pseudois_nayaur Genome sequencing and assembly

description: structure a Pan-genome of Caprinae
DOI: 10.26036/cnphis0002717
title: Danio choprae and Danio albolineatus Raw sequence reads

description: Danio fishes, a small type animal with short sexual cycles, are model vertebrate species. To investigate the genic evolution of this genus, the transcriptomes from Danio choprae and Danio albolineatus were sequenced by Illumina HiSeq 4000 platform.
DOI: 10.26036/cnphis0002718
title: Coturnix japonica Genome sequencing and assembly

description: We did this work to characterize the mechanisms of early maturity and resolve the phylogeny of quail, detect domestication footprints in quail genome, and identify one widely used plumage color marker in the quail breeding.
DOI: 10.26036/cnphis0002719
title: Eurosta solidaginis Genome sequencing and assembly

description: Eurosta solidaginis
DOI: 10.26036/cnphis0002720
title: Eschrichtius robustus Genome sequencing and assembly

description: Sequencing of two western gray whales (WGW) and one eastern gray whale (EGW). The male WGW was used for gene annotation and for comparative analysis.
DOI: 10.26036/cnphis0002728
title: Most common agricultural predators and prey in Brazil raw sequence reads

description: None
DOI: 10.26036/cnphis0002732
title: Paralichthys olivaceus Blood Transcriptome against Edwardsiella tarda

description: None
DOI: 10.7910/dvn/7zoapg/amokss
title: Script Do Concepts Matter.Rmd
DOI: 10.7910/dvn/7zoapg/jg5jgq
title: corpus.rar
DOI: 10.7910/dvn/7zoapg/qlnmzq
title: Script_Do_Concepts_Matter.html
DOI: 10.14457/cmu.the.2009.811
title: กลุ่มอาการพร่องฮอร์โมนเพศชาย และภาวะเสี่ยงต่อสุขภาพ ในผู้ชายวัยทอง ตำบลแม่ป้าก อำเภอวังชิ้น จังหวัดแพร่
DOI: 10.26036/cnphis0002703
title: The m6A pathway facilitates sex determination in Drosophila

description: N6-methyladenosine (m6A) has recently emerged as a widespread and conserved RNA modification that modulates messenger RNA (mRNA) processing and activity. As most m6A studies have been conducted in cultured cells, we established Drosophila as a model system that combines molecular and genomic analyses of m6A with investigations of organismal biology. We first apply miCLIP sequencing to map m6A modifications at single-nucleotide resolution during Drosophila embryogenesis. We next characterize Drosophila components of the m6A "writer" methyltransferase complex [MTC factors, METTL3/IME4, METTL14, FL(2)D and Nito], and characterize m6A-binding properties of the YTH domain-containing proteins, YT521-B and CG6422. We complement this by generating a collection of mutants in m6A writer and reader components. While Drosophila orthologs of mammalian MTC factors that have additional roles in splicing are lethal, our mutants in METTL and YTH factors are viable but present specific developmental and behavioral defects. We note that several mammalian m6A factors were originally identified as Drosophila regulators of Sxl splicing, which generates the master determinant of female identity. While our mutants in dedicated writer and reader machinery are not required to accumulate Sxl protein in the ovary, maternal loss of m6A writers and readers collaborates with reduction of Sxl to induce female lethality. Our data indicate Sxl is directly regulated by the m6A pathway, since miCLIP data show Sxl is a substantial target of intronic m6A in early embryos, in addition to bearing exonic m6A. Consistent with this, female-specific Sxl splicing is defective in m6A pathway mutants. YT521-B appears to be the major effector of m6A for Sxl regulation, as it shows much stronger genetic interactions with Sxl than CG6422 and YT521-B overexpression can induce female-specific Sxl splicing. Overall, our transcriptomic and genetic toolkit for studying the m6A pathway in Drosophila reveals a major biological utilization in establishing sex-specific splicing. Overall design: UV-crosslinking and immunoprecipitation with m6A-antibodies was used to map m6A sites with single nucleotide resolution
DOI: 10.26036/cnphis0002710
title: Helicoverpa armigera Genome sequencing and assembly

description: Helicoverpa armigera is a major pest of agriculture in the Old World. This project has generated the first complete genome available for this insect, using both 454 and Illumina sequencing technology, and working in collaboration with the Baylor Human Genome Sequencing Centre.
DOI: 10.26036/cnphis0002722
title: Species delimitation and taxonomy of the breve species group including analysis of genomic architecture of type specimen

description: The breve species group includes closely related Bembidion Latreille ground beetles commonly found at high elevation in the mountains of western North America. For several decades the group has been considered to consists of two species. Here we present evidence from morphological, molecular and geographic data that the group contains nine species: Bembidion. ampliatum, B. breve, B. geopearlis, B. laxatum, B. lividulum, B. oromaia, B. saturatum, B. testatum, and B. vulcanix. We describe three species (B. geopearlis, B. oromaia, and B. vulcanix) as new, and resurrect four previously synonymized names (B. ampliatum, B. lividulum, B. saturatum, and B. testatum). Species diversity is highest throughout the Sierra Nevada and Cascades in California, Oregon, and Washington, where up to seven species can occur in sympatry. We resolved challenging nomenclatural issues through analysis of sequences obtained from century-old type specimens by using a novel application of rDNA copy number analysis — an approach that may prove useful for other historical specimens.
DOI: 10.26036/cnphis0002723
title: Horse and donkey centromeres

description: Study of satellite-less centromeres in equine species
DOI: 10.26036/cnphis0002724
title: Zapatella davisae Raw sequence reads

description: Zapatella davisae is an outbreaking pest that is causing defoliation to black oaks in the Northeastern United States. To develop genomic resources for the study of Z. davisae, we conducted a whole genome sequencing project.
DOI: 10.26036/cnphis0002729
title: Viral and Bacterial Communities of Colorectal Cancer

description: Colorectal cancer is the second leading cause of cancer-related death in the United States and is a primary cause of morbidity and mortality throughout the world. Its risk has been linked to changes in colonic bacterial community composition. Viruses are another important component of the colonic microbial community, however they have yet to be studied in colorectal cancer despite their oncogenic potential. We evaluated the colorectal cancer virome (virus community) in stool using a cohort of 90 human subjects with either healthy, adenomatous (precancerous), or cancerous colons. We utilized 16S rRNA gene, whole shotgun metagenomic, and purified virus metagenomic sequencing methods to compare the colorectal cancer virome to the bacterial community. We identified no detectable difference in diversity (alpha or beta) between healthy, adenomatous, or cancerous colonic samples, but more sophisticated random forest models identified striking changes in the virus community. The majority of the cancer-associated virome consisted of temperate bacteriophages, suggesting that the community was indirectly linked to colorectal cancer by modulating bacterial community structure and function. Our data suggested that the influential phages did not exclusively infect influential bacteria, but rather acted through the community as a whole. These results provide foundational evidence that bacteriophage communities are associated with colorectal cancer and likely impact cancer progression by altering the bacterial host communities.
DOI: 10.26036/cnphis0002730
title: Heteroplasmy, structure and evolution of terrestrial isopods mitochondrial genome

description: The aim of the study was to use SMRT sequencing technology to study the Heteroplasmy, structure and evolution of an atypical mitochondrial genome in terrestrial isopods.
DOI: 10.26036/cnphis0002738
title: Myotis lucifugus lucifugus Raw sequence reads

description: To obtain nuclear mitochondrial DNA sequences
DOI: 10.7910/dvn/7zoapg/4gigd0
title: Script Replicability Do Concepts Matter.Rproj
DOI: 10.7910/dvn/7zoapg/vzrdy6
title: codebook.docx
DOI: 10.7910/dvn/ebt3uz/2zlast
title: Internet and Politics studies in Brazil.xls

description: Dictionary
DOI: 10.7910/dvn/ln9ekn
title: Replication Data for: Preparing the Terrain: Conditioning Factors for the Regionalization of the Vote for Federal Deputy in São Paulo

description: Replication Data for: "Preparing the Terrain: Conditioning Factors for the Regionalization of the Vote for Federal Deputy in São Paulo" as published in BPSR, vol. 12, nº 2, 2018.
DOI: 10.14457/cmu.res.2008.922
title: การผลิตและวิเคราะห์วัสดุห้ามเลือดเฉพาะที่ทางศัลยศาสตร์ชนิดใหม่ ในรูปแบบแผ่นฟองคาร์บอกซีเมทธิลเชลลูโลส
DOI: 10.26036/cnphis0002721
title: Acropora muricata Transcriptome

description: Transcriptomic response in Acropora muricata under acute temperature stress follows seasonal temperature adaptation
DOI: 10.26036/cnphis0002725
title: Transcriptomic analysis of purified human cortical microglia reveals age-associated changes

description: Purpose: Microglia are essential for central nervous system (CNS) homeostasis and innate neuroimmune function, and play important roles in neurodegeneration and brain aging. Here, we present gene expression profiles of purified microglia isolated at autopsy from the parietal cortex of 39 human subjects with intact cognition. We identified an age-associated gene signature in human microglia that was enriched for genes involved in cell adhesion, axonal guidance, cell surface receptor expression, and actin disassembly. Methods: mRNA profiles of 39 human microglia samples isolated from subjects with intact cognition, 16 corresponding superior parietal cortex tissue and 10 epilepsy surgical samples were generated in a Illumina HiSEQ 2500 sequencer. mRNA profiles of 6 parietal cortex from mice were prepared with a Quantseq 3'mRNA-Seq kit (Lexogen, USA). Reads were aligned to the hg38 assembly of the human genome using STAR and quantified at the gene level by featureCounts. Differential expression between whole brain tissue, surgical samples and isolated microglia was assessed with limma. Results: Overall, genes expressed by human microglia are similar to those in mouse, including established microglia genes CX3CR1, P2YR12, and ITGAM/CD11B. However, a number of immune genes, not identified as part of the mouse microglial signature, were abundantly expressed in human microglia, including TLR, Fc-gamma? and SIGLEC receptors, as well as TAL1 and IFI16, regulators of proliferation and cell cycle. Age-associated changes in human microglia were enriched for genes involved in cell adhesion, axonal guidance, cell surface receptor expression, and actin (dis)assembly. Limited overlap was observed in microglial genes regulated during aging between mice and humans, indicating that human and mouse microglia age differently. Conclusions: Here we present the an extensive human microglia gene expression profile. Critical differences with mouse microglia, especially in the context of aging, were observed which highlight the necessity to independently study human microglia. These data and analyses serve as a starting point to address human-specific microglia genes and functions under physiological and neuropathological conditions. Overall design: mRNA profiles of 39 human microglia samples isolated from subjects with intact cognition, 16 corresponding superior parietal cortex tissue and 10 epilepsy surgical samples were generated in a Illumina HiSEQ 2500 sequencer. mRNA profiles of 6 parietal cortex from mice were prepared with a Quantseq 3'mRNA-Seq kit (Lexogen, USA).
DOI: 10.26036/cnphis0002734
title: Trichomalopsis sarcophagae strain:Alberta Genome sequencing

description: Trichomalopsis sarcophagae creates a monophyletic clade with the Nasonia genus and is considered its sister taxa. Because Nasonia is an emerging model organism, the genome of T. sarsophagae provides important evolutionary information to map key molecular innovations in the Nasonia clade. Besides, T. sarsophagae is distributed throughout North America, is a generalist that can parasitize species from Diptera, Coleoptera, and Lepidoptera, and is used as a biocontrol agent. Samples obtained from several feedlots in Alberta (Canada), by Kevin Floate from Lethbridge Research Center, Lethbridge, Canada
DOI: 10.26036/cnphis0002735
title: Spodoptera frugiperda isolate:Sf9 Raw sequence reads

description: PacBio reads were obtained from sequencing of whole genome from Sf9 cells.
DOI: 10.26036/cnphis0002739
title: Distinct cellular mechanisms underlie anti-CTLA-4 and anti-PD-1 checkpoint blockade [WES]

description: Immune checkpoint blockade is able to achieve durable responses in a subset of patients, however we lack a satisfying comprehension of the underlying mechanisms of anti-CTLA-4 and anti-PD-1 induced tumor rejection. To address these issues we utilized mass cytometry to comprehensively profile the effects of checkpoint blockade on tumor immune infiltrates in human melanoma and murine tumor models. These analyses reveal a spectrum of tumor infiltrating T cell populations that are highly similar between tumor models and indicate that checkpoint blockade targets only specific subsets of tumor infiltrating T cell populations. Anti-PD-1 predominantly induces the expansion of specific tumor infiltrating exhausted-like CD8 T cell subsets. In contrast, anti-CTLA-4 induces the expansion of an ICOS+ Th1-like CD4 effector population in addition to engaging specific subsets of exhausted-like CD8 T cells. Thus, our findings indicate that anti-CTLA-4 and anti-PD-1 checkpoint blockade induced immune responses are driven by distinct cellular mechanisms. Overall design: Mouse cell lines B16BL6 and MC38 were analyzed using whole exome sequencing
DOI: 10.26036/cnphis0002741
title: Monodelphis domestica strain:Lab strain Raw sequence reads

description: This project aims to understand the gene expression changes in the uterus through the reproductive cycle of the grey short tailed opossum.