cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0002639
title: Syngnathus scovelli RAD-seq of a single population

description: Wild-caught Syngnathus scovelli from a single population in the Gulf of Mexico near Corpus Christi, TX. A total of 228 individuals (females, pregnant males, and non-pregnant males) were collected and sequenced, along with 130 offspring from pregnant males'' pouches. Other data are archived on Dryad (http://dx.doi.org/10.5061/dryad.5c1tj) and all the code is archived at https://zenodo.org/badge/latestdoi/51270799. These data accompany the paper "Genome-wide selection components analysis in a fish with male pregnancy" by Flanagan & Jones in Evolution.
DOI: 10.26036/cnphis0002644
title: Chrysina resplendens genome sequencing

description: None
DOI: 10.26036/cnphis0002649
title: Deinopsis erosa Genome sequencing and assembly

description: Deinopsis erosa
DOI: 10.26036/cnphis0002627
title: Transcriptome Sequencing and Analysis of Three Sheep Intestinal Regions

description: To identify intestinal metabolic related genes and reveal these molecular regulation mechanisms, we sequenced and compared the transcriptomes of mucosal epithelial tissues between cecum, proximal colon and duodenum. A total of 5420 genes constructed by 8055 transcripts were identified as differential expressed genes. Overall design: Transcriptome comparison of three sheep intestinal regions.
DOI: 10.26036/cnphis0002636
title: Equus caballus breed:Lipizzan Horse Genome sequencing

description: whole genome sequencing of Lipizzan horses
DOI: 10.26036/cnphis0002641
title: Pseudomimeciton antennatum genome sequencing

description: None
DOI: 10.26036/cnphis0002643
title: Lythrypnus dalli Genome sequencing and assembly

description: Lythrypnus dalli
DOI: 10.26036/cnphis0002646
title: Charaxes varanes Genome sequencing and assembly

description: Charaxes varanes
DOI: 10.26036/cnphis0002640
title: Stiretrus anchorago Genome sequencing and assembly

description: Stiretrus anchorago genome sequencing and assembly
DOI: 10.26036/cnphis0002642
title: Dorylogaster longipes genome sequencing

description: None
DOI: 10.26036/cnphis0002647
title: Bolitophila cinerea Genome sequencing and assembly

description: Bolitophila cinerea
DOI: 10.26036/cnphis0002648
title: Microtus oregoni Genome sequencing and assembly

description: Microtus oregoni
DOI: 10.26036/cnphis0002650
title: Diadocidia ferruginosa Genome sequencing and assembly

description: Diadocidia ferruginosa
DOI: 10.26036/cnphis0002651
title: Bolitophila hybrida Genome sequencing and assembly

description: Bolitophila hybrida
DOI: 10.26036/cnphis0002653
title: Earota dentata Genome sequencing and assembly

description: Earota dentata
DOI: 10.26036/cnphis0002654
title: Oxypoda opaca Genome sequencing and assembly

description: Oxypoda opaca
DOI: 10.26036/cnphis0002657
title: Gene expression atlas of pigeonpea

description: Pigeonpea (Cajanus cajan) is an important grain legume of the semi-arid tropics, mainly used for its protein rich seeds. To be able to link the genome sequence information to the phenotype, especially those related to developmental processes, a gene expression atlas of Cajanus cajan (CcGEA) have been developed. In this study, we have used 30 samples from Asha genotype (ICPL 87119), representing different developmental stages from germination to senescence. CcGEA provides a valuable resource for pigeonpea to identify candidate genes involved in specific developmental processes and to understand the well-orchestrated growth and developmental process in this resilient crop.
DOI: 10.26036/cnphis0002659
title: Myodes glareolus Raw sequence reads

description: We used whole genome sequencing techniques to sample the mitochondrial genomes of Bank voles (Myodes glareolus) residing within the radioactive zone surrounding Chernobyl and samples from reference sites in Ukraine not contaminated by radiation. The goal of this study was to determine if voles living in radioactive environments had increased levels of genetic variation within the mitochondria compared to reference samples.
DOI: 10.26036/cnphis0002662
title: Phytosciara flavipes Genome sequencing and assembly

description: Phytosciara flavipes
DOI: 10.26036/cnphis0002664
title: Symmerus nobilis Genome sequencing and assembly

description: Symmerus nobilis
DOI: 10.14457/kku.the.2008.510
title: การปนเปื้อนจุลินทรีย์และโลหะหนักในภาชนะสัมผัสอาหารหลังการจุ่มน้ำร้อนเพื่อฆ่าเชื้อโรค
DOI: 10.26036/cnphis0002652
title: Gnoriste bilineata Genome sequencing and assembly

description: Gnoriste bilineata
DOI: 10.26036/cnphis0002655
title: Delphinapterus leucas Genome sequencing and assembly

description: Genomic sequencing of the Beluga whale (Delphinapterus leucas)
DOI: 10.26036/cnphis0002656
title: Citrus Microbiome Raw sequence reads

description: We used 16S Illumina sequencing to define the leaf- and root-associated microbiomes of citrus trees across several variables, including Huanglongbing (Citrus greening) disease symptom severity, location, citrus cultivar, season, and time. This plant host/disease model was used to investigate: (a) the relationship between leaf- and root-associated microbial communities and host plant, (b) the interactions between native microbiota and a phytopathogen (i.e., Liberibacter, the causative agent of Huanglongbing), and (c) the core microbiota, their prevalence among broader microbial communities, and correlations between community structure and plant disease, among other factors.
DOI: 10.26036/cnphis0002658
title: Solenodon paradoxus Genome sequencing and assembly

description: Five specimens of Solenodon paradoxus woodi were sequenced, and a genome assembly was performed. One specimen of Solenodon paradoxus paradoxus was sequenced as well. Based on this data, gene discovery and annotation was performed, the genome was mined for venomous genes, phylogeny was inferred, sequence variation in both subspecies was annotated, and demographic histories of the subspecies were inferred.
DOI: 10.26036/cnphis0002663
title: Trichosia splendens Genome sequencing and assembly

description: Trichosia splendens
DOI: 10.26036/cnphis0002665
title: Phylogenomic Systematics of Ostariophysan fishes: Ultraconserved Elements Support the Surprising Non-monophyly of Characiformes

description: Ostariophysi is a superorder of bony fishes including more than 10,200 species in 1,100 genera and 70 families. This superorder is traditionally divided into five major groups (orders): Gonorynchiformes (milkfishes and sandfishes), Cypriniformes (carps and minnows), Characiformes (tetras and their allies), Siluriformes (catfishes), and Gymnotiformes (electric knifefishes). Unambiguous resolution of the relationships among these lineages remains elusive, with previous molecular and morphological analyses failing to produce a consensus phylogeny. In this study, we use over 350 ultraconserved element (UCEs) loci comprising five million base pairs collected across thirty-five representative ostariophysan species to compile one of the most data-rich phylogenies of fishes to date. We use these data to infer higher-level (interordinal) relationships among ostariophysan fishes, focusing on the monophyly of the Characiformes— one the most contentiously debated groups in fish systematics. As with most previous molecular studies, we recover a non-monophyletic Characiformes with the two monophyletic suborders, Citharinoidei and Characoidei, more closely related to other ostariophysan clades than to each other. We also explore incongruence between results from different UCE datasets, issues of orthology, and the use of morphological characters in combination with our molecular data.
DOI: 10.26036/cnphis0002669
title: Acanthurus_olivaceus_RADSeq_data

description: RADSeq data for the reef fish Acanthurus olivaceus
DOI: 10.26036/cnphis0002645
title: Aratinga solstitialis Genome sequencing and assembly

description: Aratinga solstitialis
DOI: 10.26036/cnphis0002666
title: B Chromosomes in the Cichlid Fish Astatotilapia latifasciata

description: Origin and Evolution of B Chromosomes in the Cichlid Fish Astatotilapia latifasciata Based on Integrated Genomic Analyses
DOI: 10.26036/cnphis0002668
title: Acanthurus_reversus_RADSeq_data

description: RADSeq data for the reef fish Acanthurus reversus
DOI: 10.26036/cnphis0002671
title: Transcriptome profiling of human dermal lymphatic endothelial cells

description: RNAseq on human dermal lymphatic endothelial cells treated with FGF2 or FGFR1 siRNA
DOI: 10.26036/cnphis0002673
title: Lestremia cinerea Genome sequencing and assembly

description: Lestremia cinerea
DOI: 10.26036/cnphis0002678
title: Ecitomorpha arachnoides Genome sequencing and assembly

description: Ecitomorpha nevermanni
DOI: 10.14457/kku.the.2008.514
title: การพัฒนาบริการอนามัยการเจริญพันธุ์แก่วัยรุ่น
DOI: 10.26036/cnphis0002661
title: Sylvicola fuscatus Genome sequencing and assembly

description: Sylvicola fuscatus
DOI: 10.26036/cnphis0002667
title: Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded DNA

description: Despite advances that allow DNA sequencing of old museum specimens, sequencing small-bodied, historical specimens can be challenging and unreliable as many contain only small amounts of fragmented DNA. Dependable methods to sequence such specimens are especially critical if the specimens are unique. We attempt to sequence small-bodied (3–6 mm) historical specimens (including nomenclatural types) of beetles that have been housed, dried, in museums for 58–159 years, and for which few or no suitable replacement specimens exist. To better understand ideal approaches of sample preparation and produce preparation guidelines, we compared different library preparation protocols using low amounts of input DNA (1–10 ng). We also explored low-cost optimizations designed to improve library preparation efficiency and sequencing success of historical specimens with minimal DNA, such as enzymatic repair of DNA. We report successful sample preparation and sequencing for all historical specimens despite our low-input DNA approach. We provide a list of guidelines related to DNA repair, bead handling, reducing adapter dimers, and library amplification. We present these guidelines to facilitate more economical use of valuable DNA, and enable more consistent results in projects that aim to sequence challenging, irreplaceable historical specimens.
DOI: 10.26036/cnphis0002672
title: Bellamya quadrata, Cipangopaludina cathayensis Genome sequencing and assembly

description: Mitochondrial (mt) genome sequencing of Bellamya quadrata, Cipangopaludina cathayensis
DOI: 10.26036/cnphis0002679
title: Ecitoglossa quadriceps Genome sequencing and assembly

description: Ecitoglossa quadriceps
DOI: 10.14457/cmu.the.2009.809
title: การพัฒนาศักยภาพของผู้ปกครอง ในการดูแลอนามัยส่วนบุคคล ของเด็กออทิสติก โรงเรียนกาวิละอนุกูล อำเภอเมืองเชียงใหม่
DOI: 10.14457/kku.the.2008.512
title: การพัฒนาดัชนีคุณภาพทางประสาทสัมผัสของผลิตภัณฑ์แหนม
DOI: 10.26036/cnphis0002660
title: Transcriptome analysis of B vitamin deficiency in plants

description: Transcriptomes of vitamin deficient maize and Arabidopsis mutants
DOI: 10.26036/cnphis0002674
title: Porricondyla nigripennis Genome sequencing and assembly

description: Porricondyla nigripennis
DOI: 10.26036/cnphis0002675
title: Exechia fusca Genome sequencing and assembly

description: Exechia fusca
DOI: 10.26036/cnphis0002680
title: Paracentrotus lividus Raw sequence reads

description: The application of a seascape genetics approach to explore connectivity patterns of the long-distance dispersal sea urchin Paracentrotus lividus (Lamarck, 1816) in the Central and Western Mediterranean Sea.The multidisciplinary approach integrates population genomics, based on Single Nucleotide Polymorphisms (SNPs) obtained from 2b-RAD, with Lagrangian simulations performed with a biophysical model of larval dispersal.
DOI: 10.26036/cnphis0002681
title: Novel gut-microbiota based metagenomic signature for advanced fibrosis in nonalcoholic fatty liver disease

description: The presence of advanced fibrosis in nonalcoholic fatty liver disease (NAFLD) is the most important predictor of liver mortality. The aim of this study was to examine the diagnosticaccuracy of a gut-microbiota derived metagenomic signature for detecting the presence of advanced fibrosis in NAFLD. In this prospective study, we characterized the microbiome signatures associated with advanced fibrosis (defined as stage 3 or 4 fibrosis) in uniquely well characterized biopsy- and imaging-phenotyped patients with NAFLD. Gut microbiomecompositions of the patients were determined using whole-genome shotgun sequencing of DNA extracted from stool samples.
DOI: 10.26036/cnphis0002685
title: Plebejus melissa samuelis Raw sequence reads

description: These data were generated to sequence to obtain molecular markers for population genetic study of the Karner blue butterfly, and to sequence the complete mitochondrial DNA molecule.
DOI: 10.26036/cnphis0002689
title: Genome Scale Analysis of miRNA and mRNA regulation during preterm labor [whole blood]

description: The goal of this study was to define relationships between peripheral blood miRNAs and mRNAs of women undergoing idiopathic preterm labor (PTL) and compare network level changes to control women that deliver at term.Using RNA Sequencing we have performed global miRNA and mRNA profiling in both monocytes and whole blood leukocytes of women who underwent PTL (N=15) matched to non-pathological controls (N=30) as a part of the Ontario Birth Study cohort. We have identified differentially expressed miRNAs, mRNAs and pathways associated with PTL. Intriguingly, we found perturbations in many cellular signaling pathways, particularly in interleukin signaling. We also predicted mRNA targets for specific miRNAs and used these predictions to build putative miRNA-mRNA networks. We identified 6 miRNAs significantly associated with PTL whose expression is negatively correlated with expression of 14 predicted mRNA targets that are also significantly associated with PTL. Overall design: miRNA and mRNA were quantified from whole blood and monocytes of women undergoing spontaneous preterm labor compared to nonlabor controls matched on gestational age
DOI: 10.26036/cnphis0002690
title: Hippodamia convergens isolate:Hippodamia convergens larvae Raw sequence reads

description: DNA gut content of Hippodamia convergens 3rd instar larvae.
DOI: 10.14457/cmu.the.2008.1045
title: ปรัชญาเศรษฐกิจพอเพียงกับการดูแลสุขภาพของชุมชนบ้านงามเมือง ตำบลยางฮอม อำเภอขุนตาล จังหวัดเชียงราย
DOI: 10.14457/cmu.the.2009.806
title: การใช้กิจกรรมทักษะชีวิต ในการส่งเสริมพฤติกรรมการบริโภคอาหาร ของนักเรียนชั้นประถมศึกษา เขตเทศบาล จังหวัดแพร่
DOI: 10.14457/cmu.the.2009.807
title: การใช้เทคนิคการส่งเสริมความคิด โดยใช้ภาพเป็นสื่อ เพื่อส่งเสริมความสามารถในการอ่าน และการเขียนภาษาอังกฤษเชิงสร้างสรรค์ ของผู้เรียนระดับปริญญาตรี
DOI: 10.14457/cmu.the.2009.808
title: การพัฒนาความคิดสร้างสรรค์ทางวิทยาศาสตร์ สำหรับนักเรียนช่วงชั้นที่ 4 ที่มีความสามารถพิเศษทางวิทยาศาสตร์ โดยใช้ชุดกิจกรรมวิทยาศาสตร์สร้างสรรค์
DOI: 10.14457/kku.the.2008.517
title: ตัวประมาณอัตราส่วนของยอดรวมประชากร
DOI: 10.26036/cnphis0002670
title: Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye

description: Flatfish cranial asymmetry represents one of the most remarkable morphological innovations among vertebrates, and has fueled vigorous debate on the manner and rate at which strikingly divergent phenotypes evolve. A surprising result of many recent molecular phylogenetic studies is the lack of support for flatfish monophyly, where increasingly larger DNA datasets of up to 23 loci have yielded a polyphyletic or only weakly supported flatfish clade. Lack of resolution for flatfish relationships has been attributed to analytical limitations for dealing with processes such as nucleotide non-stationarity and incomplete lineage sorting (ILS). We tackle this phylogenetic problem using a sequence dataset comprising more than one thousand ultraconserved DNA element (UCE) loci covering 45 carangimorphs, the broader clade containing flatfishes and several other specialized lineages such as remoras, billfishes, and archerfishes. We present a phylogeny based on UCE loci that unequivocally supports flatfish monophyly and a single origin of asymmetry. We document similar levels of discordance among UCE loci as in previous, smaller molecular datasets. However, relationships among flatfishes and carangimorphs recovered from multilocus concatenated and species tree analyses of our data are robust to the analytical framework applied and size of data matrix used. By integrating the UCE data with a rich fossil record, we find that the most distinctive carangimorph bodyplans arose rapidly during the Paleogene (66.0-23.03 Ma). Flatfish asymmetry, for example, likely evolved over an interval of no more than 2.9 million years. The longstanding uncertainty in phylogenetic hypotheses for flatfishes and their carangimorph relatives highlights the limitations of smaller molecular datasets when applied to successive, rapid divergences. Here, we recovered significant support for flatfish monophyly and relationships among crangimorphs through analysis of over 1,000 UCE loci. The resulting time-calibrated phylogeny points to phenotypic divergence early within carangimorph history that broadly matches with the predictions of adaptive models of lineage diversification.
DOI: 10.26036/cnphis0002677
title: Platyura marginata genome sequencing

description: Platyura marginata
DOI: 10.26036/cnphis0002686
title: Hemipteroid Insect Assembling the Tree of Life Project

description: The hemipteroid insect orders (Hemiptera, Psocodea, and Thysanoptera) are a diverse group among the insects, including over 120,000 described species. This group contains many species of ecological, economic, or medical importance, and many of the lineages within this group have piercing-sucking mouthparts. The backbone phylogenetic relationships of this group have not been well studied. One of the major goals of this project is to combine transcriptome and genome sequences (using Illumina sequencing technology) for representatives of all the major lineages of this group and most families to construct a well resolved phylogenetic tree.
DOI: 10.26036/cnphis0002692
title: Harmonia axyridis isolate:Harmonia axyridis larvae Raw sequence reads

description: DNA gut content of Harmonia axyridis 3rd instar larvae.
DOI: 10.26036/cnphis0002693
title: Xenocypris argentea Raw sequence reads

description: This in-depth transcriptome sequencing aims to provide reference genome sequences for study Xenocypris argentea.
DOI: 10.26036/cnphis0002700
title: Single-Cell Whole Genome Analyses by Linear Amplification via Transposon Insertion (LIANTI)

description: Single-cell genomics is important for biology and medicine. However, current whole genome amplification (WGA) methods are limited by low accuracy of copy number variation (CNV) detection and low amplification fidelity. Here we report an improved single-cell WGA method, Linear Amplification via Transposon Insertion (LIANTI), which outperforms existing methods, enabling micro-CNV detection with kilobase resolution. This allowed direct observation of stochastic firing of DNA replication origins, different from cell to cell. We also show that the predominant cytosine-to-thymine mutations observed in single-cell genomics often arise from the artifact of cytosine deamination upon cell lysis. However, calling single nucleotide variations (SNVs) can be accomplished by sequencing kindred cells. We determined the spectrum of SNVs in a single human cell after ultraviolet radiation, revealing their nonrandom genome-wide distribution.
DOI: 10.14457/cmu.the.2008.1044
title: ผลของความหนาของการพอกเมล็ดต่อคุณภาพเมล็ดพันธุ์ข้าวโพดหวาน
DOI: 10.14457/cmu.the.2009.813
title: การวิเคราะห์ความผันผวนของอัตราผลตอบแทนของดัชนีราคาหลักทรัพย์ล่วงหน้า ในตลาดอนุพันธ์ไทย สหรัฐอเมริกา ญี่ปุ่น และฮ่องกง
DOI: 10.14457/kku.the.2008.511
title: การศึกษากำลังอัดและความทนทานของจีโอโพลิเมอร์จากเถ้าลอยแม่เมาะ
DOI: 10.14457/kku.the.2008.516
title: ความหลากหลายของด้วงมูลสัตว์ในกลุ่มป่าภูเขียว-น้ำหนาว
DOI: 10.26036/cnphis0002682
title: human gut metagenome Metagenome

description: In this study, we performed a randomized, placebo-controlled, double-blind study in newly diagnosed T2D patients on a calorie-restricted diet and showed that metformin, but not calorie restriction, had rapid effects on the composition and function of the gut microbiota.
DOI: 10.26036/cnphis0002688
title: Genome Scale Analysis of miRNA and mRNA regulation during preterm labor [monocytes]

description: The goal of this study was to define relationships between peripheral blood miRNAs and mRNAs of women undergoing idiopathic preterm labor (PTL) and compare network level changes to control women that deliver at term.Using RNA Sequencing we have performed global miRNA and mRNA profiling in both monocytes and whole blood leukocytes of women who underwent PTL (N=15) matched to non-pathological controls (N=30) as a part of the Ontario Birth Study cohort. We have identified differentially expressed miRNAs, mRNAs and pathways associated with PTL. Intriguingly, we found perturbations in many cellular signaling pathways, particularly in interleukin signaling. We also predicted mRNA targets for specific miRNAs and used these predictions to build putative miRNA-mRNA networks. We identified 6 miRNAs significantly associated with PTL whose expression is negatively correlated with expression of 14 predicted mRNA targets that are also significantly associated with PTL. Overall design: miRNA and mRNA were quantified from whole blood and monocytes of women undergoing spontaneous preterm labor compared to nonlabor controls matched on gestational age
DOI: 10.26036/cnphis0002694
title: Metastatic Breast Cancer Sample Sequencing

description: Metastatic Breast Cancer patient tumor mass whole exome and transcriptome sequencing
DOI: 10.26036/cnphis0002695
title: Capra hircus Raw sequence reads

description: For the difference
DOI: 10.26036/cnphis0002696
title: MECFS metagenomics

description: Fecal metagenomic profiles in subgroups of patients with Myalgic Encephalomyelitis/ Chronic Fatigue Syndrome
DOI: 10.14457/cmu.res.2009.570
title: ผลของการฝึกด้วยน้ำหนักของกล้ามเนื้อขา ที่มีต่อความแม่นยำ ในการเสิร์ฟลูกตะกร้อ ของนักกีฬาเซปักตะกร้อหญิง
DOI: 10.14457/cmu.the.2009.805
title: การพัฒนาความรู้สึกเห็นคุณค่าในตนเอง เพื่อส่งเสริมพฤติกรรมสุขภาพของเด็ก ที่มีความบกพร่องทางการเห็นโดยใช้กิจกรรมกลุ่ม
DOI: 10.14457/cmu.the.2009.812
title: การจัดทำกระดาษทำการตามมาตรฐานการสอบบัญชีของสหกรณ์ภาคการเกษตร สำหรับผู้สอบบัญชีภาครัฐ ในพื้นที่สำนักงานตรวจบัญชีสหกรณ์ที่ 7
DOI: 10.14457/kku.the.2008.513
title: ปฏิสัมพันธ์ระหว่างเชื้อ Trichoderma spp. กับจุลินทรีย์ปฏิปักษ์อื่น และประสิทธิภาพในการควบคุมโรคเหี่ยวเหลืองและโคนเน่าของมะเขือเทศ
DOI: 10.14457/kku.the.2008.515
title: การศึกษาบทบาทของครูคณิตศาสตร์ที่ใช้โปรแกรม The Geometer's Sketchpad เป็นเครื่องมือประกอบการเรียนรู้ : กรณีศึกษา
DOI: 10.26036/cnphis0002676
title: Macrocera vittata Genome sequencing and assembly

description: Macrocera vittata
DOI: 10.26036/cnphis0002697
title: Carcinus maenas Raw sequence reads

description: Raw RAD-tag reads from the Illumina platform for 11 populations of green crab collected from eastern North America.
DOI: 10.26036/cnphis0002698
title: Dominette stranded RNA-seq

description: Transcriptomes of tissues from L1 Dominette 01449 (the bovine reference genome individual) and SuperBull 99375 were sequenced to annotate a newly assembled bovine reference genome.