cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0001492
title: Hi-C map of the three-dimensional genome organization

description: The spatial arrangement of interphase chromosomes in the nucleus is important for gene expression and genome function in animals and in plants. The recently developed Hi-C technology is an efficacious method to investigate genome packing. Here we present a detailed Hi-C map of the three-dimensional genome organization of the plant Arabidopsis thaliana. We find that local chromatin packing differs from the patterns seen in animals, with kilobasepair-sized segments that have much higher intra-chromosome interaction rates than neighboring regions and which represent a dominant local structural feature of genome conformation in A. thaliana. These regions appear as positive strips on two-dimensional representations of chromatin interaction and they are enriched in epigenetic marks H3K27me3, H3.1 and H3.3. We also identify over 400 insulator-like regions. Furthermore, although topologically associating domains (TADs), which are prominent in animals, are not the dominant feature of A. thaliana genome packing, we found over 1,000 regions that have properties of TAD boundaries, and a similar number of regions similar to the interior of TADs. These insulator-like, TAD-boundary-like, and TAD-interior-like regions show strong enrichment for distinct epigenetic marks, and correlate with gene transcription levels. We conclude that epigenetic modifications, gene density, and transcriptional activity all contribute to shaping the local structure of the A. thaliana nuclear genome.
DOI: 10.26036/cnphis0001495
title: Pseudo-temporal ordering of individual cells reveals regulators of differentiation

description: Single-cell expression profiling by RNA-Seq promises to exploit cell-to-cell variation in gene expression to reveal regulatory circuitry governing cell differentiation and other biological processes. Here, we describe Monocle, a novel unsupervised algorithm for ordering cells by progress through differentiation that dramatically increases temporal resolution of expression measurements. This reordering unmasks switch-like changes in expression of key regulatory factors, reveals sequentially organized waves of gene regulation, and exposes regulators of cell differentiation. A functional screen confirms that a number of these regulators dramatically alter the efficiency of myoblast differentiation, demonstrating that single-cell expression analysis with Monocle can uncover new regulators even in well-studied systems. Overall design: We selected primary human myoblasts as a model system of cell differentiation to investigate whether ordering cells by progress revealed new regulators of the process. We sequenced RNA-Seq libraries from each of several hundred cells taken over a time-course of serum-induced differentiation. Please note that this dataset is a single-cell RNA-Seq data set, and each cell comes from a capture plate. Thus, each well of the plate was scored and flagged with several QC criteria prior to library construction, which are provided as sample characteristics; CONTROL indicates that this library is a off-chip tube control library constructed from RNA of approximately 250 cells and ''DEBRIS'' indicates that the well contained visible debris (and may or may not include a cell). Libraries marked DEBRIS thus cannot be confirmed to come from a single cell.
DOI: 10.26036/cnphis0001497
title: Rhinopithecus multi-species

description: The genomic project of snub nosed monkeys tries to investigate the evolutionary history, dietary adaptation and demographic history of primates.
DOI: 10.26036/cnphis0001498
title: Trichuris suis isolate:DCEP-RM93M Genome sequencing and assembly

description: Draft whole genome sequence of a male Trichuris suis individual
DOI: 10.26036/cnphis0002175
title: Genome Sequencing Highlights the Dynamic Early History of Dogs

description: The process of dog domestication is still poorly understood, largely because no studies thus far have leveraged deeply sequenced whole genomes from wolves and dogs to simultaneously evaluate support for the proposed source regions: East Asia, the Middle East, and Europe. To investigate dog origins, we sequence three wolf genomes from the putative centers of origin, two basal dog breeds (Basenji and Dingo), and a golden jackal as an outgroup.
DOI: 10.26036/cnphis0002176
title: Shiraia bambusicola raw sequence reads

description: Shiraia bambusicola is a popular Chinese medicinal fungus with pharmacological properties that are used to treat rheumatic arthritis,sciatica,pertussis,tracheitis and so forth.
DOI: 10.26036/cnphis0002177
title: Chaetodon austriacus Genome sequencing and assembly

description: We selected one of the most iconic Red Sea butterflyfish species, Chaetodon austriacus, for whole genome sequencing. This species is distributed almost exclusively in the northern and central Red Sea region. Chaetodon austriacus has three closely related sister taxa found together in the Coralochaetodon subgenus, Chaetodon trifasciatus, Chaetodon lunulatus, and Chaetodon melapterus, which live exclusively in the Indian Ocean, Pacific Ocean, and Arabian Sea, respectively. The genome of C. austriacus will provide a scaffold for analyzing apparent patterns in SNP datasets for this and related species, especially loci that appear to be under some form of selection. Annotation will provide a means to identify genes that may control unique adaptations to the Red Sea environment. This project has direct applications to the fields of biogeography, phylogeography, population genetics, meta-population dynamics, and regulating the international exchange of marine resources
DOI: 10.26036/cnphis0002178
title: Myodes glareolus isolate:BV_1_Jyvaskyla Genome sequencing and assembly

description: De novo assembly of the bank vole (Myodes glareolus) genome; produced as part of a study into the diversity and evolution of immune genes in wild rodents.
DOI: 10.26036/cnphis0002179
title: Marsupenaeus japonicus Raw sequence reads

description: High-resolution linkage mapping and quantitative trait locus (QTL) identification aided by genome survey sequencing in marsupenaeus japonicus
DOI: 10.26036/cnphis0002180
title: Homo sapiens Genome sequencing

description: To compare different types of tumor lesions in hepatocellular carcinoma from genomic level and provide valuable information for diagnosis, prognosis and treatment of this disease
DOI: 10.26036/cnphis0002181
title: Hyla arborea low-coverage genome sequence

description: To facilitate genetic research on tree frogs, we assembled a low-coverage draft genome of the European tree frog Hyla arborea.
DOI: 10.26036/cnphis0002182
title: Coturnix japonica Genome sequencing and assembly

description: The Japanese quail is an important animal model used in a range of scientific disciplines including embryonic development, behavior, physiology, genetics and biomedicine. Sequencing the Japanese quail is one of the first steps in developing it as a genetic model organism.
DOI: 10.26036/cnphis0001499
title: Mus musculus Transcriptome or Gene expression

description: Normal mouse liver transcriptome landscape
DOI: 10.26036/cnphis0001500
title: Opisthorchis viverrini Genome sequencing and assembly

description: Whole genome sequencing of the Asian liver fluke, Opisthorchis viverrini
DOI: 10.26036/cnphis0001501
title: Eurytemora affinis strain:Atlantic clade Genome sequencing and assembly

description: Whole genome assembly of Common copepod (Eurytemora affinis) as part of the BCM-HGSC i5k Pilot Project.
DOI: 10.26036/cnphis0001502
title: Salmonella enterica subsp. enterica serovar Gallinarum str. SG9Ra Genome sequencing

description: Genomic re-sequencing of Salmonella Gallinarum from outbreaks in laying hens.
DOI: 10.26036/cnphis0001503
title: Salmonella enterica subsp. enterica serovar Gallinarum str. SG9Rb Genome sequencing

description: Genomic re-sequencing of Salmonella Gallinarum from outbreaks in laying hens.
DOI: 10.26036/cnphis0001504
title: Salmonella enterica subsp. enterica serovar Gallinarum str. MB4523 Genome sequencing

description: Genomic re-sequencing of Salmonella Gallinarum from outbreaks in laying hens.
DOI: 10.26036/cnphis0001505
title: Salmonella enterica subsp. enterica serovar Gallinarum str. SG9 Genome sequencing

description: Genomic re-sequencing of Salmonella Gallinarum from outbreaks in laying hens.
DOI: 10.26036/cnphis0001506
title: Macaca mulatta Targeted Locus (Loci)

description: Single-cell and deep sequencing of macaque B cells reveal a diverse IGHV repertoire following immunization
DOI: 10.26036/cnphis0001507
title: Apis mellifera intermissa strain:Blida - Haddad Genome sequencing and assembly

description: Apis mellifera intermissa (Buttel-Reepen, 1906) is the native honeybee subspecies of Algeria. A.m.intermissa occurs in Tunisia, Algeria and Morocco, between the Atlas and the Mediterranean and Atlantic coasts (Ruttner, 1988), in an area of more than 2500 km long. Intermissa indicates the position through this bee races between tropical Africa and European breeds (Peyvel, 1994). The settlement area of the Tellian extends from Tunisia to Morocco. Ruttner et al (1978) describes the pure Tellian. It is a black hair of his coat poverty brings out the black color. It is a small size, there are some times light illumination on the tergites. This bee is very aggressive, nervous, sick to take part, as swarms huge fall and even produced many brood and can build up to one hundred queen cells (Le Conte, 2002). A.m.intermissa is prone to swarming, shows an defensive behaviour and an abundant use of propolis (Ruttner 1988). Extraction had been done of Leg samples by Qiagen Blood & Tissue Mini kit.Then sequencing done at Illumina GAIIX Sequencer. Assembly of the reads done and contigs are generated.Contigs were assembled to scaffolding and draft Genome of Algerian bee formed.AGP file were made for submission.
DOI: 10.26036/cnphis0002183
title: Mangifera indica cultivar:Tommy Atkins Transcriptome or Gene expression

description: Mangifera indica transcripts were sequenced and assembled for use as a reference to assess genetic diversity in mango germplasm collections, and to generate SNP-based markers for construction of a mango genetic map. This reference represents genes expressed in cultivar 'Tommy Atkins.'
DOI: 10.26036/cnphis0002184
title: Tethya wilhelma Genome sequencing and assembly

description: Genome sequencing project of the demosponge Tethya wilhelma, to enable more detailed study of a model sponge and for comparison to other sponges
DOI: 10.26036/cnphis0002185
title: Ginkgo biloba Raw sequence reads

description: transcriptome of Ginkgo biloba kernels for differentially expressed genes
DOI: 10.26036/cnphis0002186
title: Sequence capture of ultraconserved elements from bird museum specimens

description: Raw sequence reads from Aphelocoma jays of various species (Aphelocoma californica; Aphelocoma sumichrasti; Aphelocoma woodhouseii) as well as three chicken (Gallus gallus) positive controls.
DOI: 10.26036/cnphis0002187
title: Salmo salar genome re-sequencing SALMAT

description: Whole genome re-sequencing of Atlantic salmon from six rivers in western Norway.
DOI: 10.26036/cnphis0002188
title: Pseudopodoces humilis Genome sequencing

description: Pseudopodoces humilis
DOI: 10.26036/cnphis0002189
title: Illumina paired-end sequencing with varying library average insert sizes

description: Optimized sample preparation for Illumina paired-end sequencing libraries
DOI: 10.26036/cnphis0002190
title: Triticum aestivum Transcriptome or Gene expression

description: transcriptome response of two wheat cultivers to salt stress
DOI: 10.26036/cnphis0002191
title: Replicated divergence in cichlid radiations mirrors a major vertebrate innovation

description: Decoupling of the upper jaw bones - jaw kinesis - is a distinctive feature of the ray-finned fishes, but it is not clear how the innovation is related to the extraordinary diversity of feeding behaviors and feeding ecology in this group. We address this issue in a lineage of ray-finned fishes that is well-known for its ecological and functional diversity – African rift lake cichlids. We sequenced ultraconserved elements found across the genome to generate the first well-resolved phylogeny of both the Lake Tanganyika and Lake Malawi cichlid radiations. We filmed a diverse array of over fifty cichlid species capturing live prey and quantified the extent of jaw kinesis using geometric morphometrics. Our combination of phylogenomic and kinematic data reveals a strong association between biting modes of feeding and reduced cranial kinesis, suggesting that the contrasting demands of biting and suction feeding have strongly influenced cranial evolution in both cichlid radiations.
DOI: 10.26036/cnphis0001508
title: GenomeTrakr Project: Virginia - Division of Consolidated Laboratory Services

description: GenomeTrakr Project: Virginia - Division of Consolidated Laboratory Services (VA-DCLS)
DOI: 10.26036/cnphis0001509
title: Anas platyrhynchos strain:Pekin Duck Transcriptome or Gene expression

description: Anas platyrhynchos Transcriptome or Gene expression from muscle and fat strains
DOI: 10.26036/cnphis0001510
title: Genomic sequencing of murine small cell lung carcinoma

description: None
DOI: 10.26036/cnphis0001511
title: A Comprehensive Genome-wide Study on Tissue- and Abiotic Stress-specific miRNAs in Triticum aestivum

description: Purpose: To identify abiotic stress responsive and tissue specific miRNAs at genome wide level in wheat (Triticum aestivum) Results: Small RNA libraries were constructed from four tissues (root, shoot, mature leaf and spikelets) and three stress treatments of wheat seedlings (control, high temperature, salinity and water-deficit). A total of 59.5 million reads were obtained by high throughput sequencing of eight wheat libraries, of which 32.5 million reads were found to be unique. Using UEA sRNA workbench we identified 47 conserved miRNAs belonging to 20 families, 1030 candidate novel and 51 true novel miRNAs. Several of these miRNAs displayed tissue specific expression whereas few were found to be responsive to abiotic stress treatments. Target genes were predicted for miRNAs identified in this study and their grouping into functional categories revealed that the putative targets were involved in diverse biological processes. RLM-RACE of predicted targets of three conserved miRNAs (miR156, miR160 and miR164) confirmed their mRNA cleavage, thus indicating their regulation at post-transcriptional level by corresponding miRNAs. Expression profiling of confirmed target genes of these miRNAs was also performed. Conclusions: This is the first comprehensive study on profiling of miRNAs in a variety of tissues and in response to several abiotic stresses in wheat. Our findings provide valuable resource for better understanding on the role of miRNAs in stress tolerance as well as plant development. Additionally, this information could be utilized for designing wheat plants for enhanced abiotic stress tolerance and higher productivity. Overall design: Total eight (three stress, one control and four tissue specific small RNA libraries were pepared and sequenced independently [wheat control (WC), wheat high temperature stressed (WHTS), wheat salinity stressed (WSS) and wheat drought stressed (WDS), wheat shoot(WSH), wheat leaf (WLF), wheat flower(WFL), wheat root(WRT)] on Illumina GAIIx
DOI: 10.26036/cnphis0001512
title: Leptinotarsa decemlineata Genome sequencing

description: Whole genome assembly of Colorado potato beetle (Leptinotarsa decemlineata) as part of the BCM-HGSC i5k Pilot Project.
DOI: 10.26036/cnphis0001513
title: Characterization of the Merkel cell carcinoma miRNome

description: MicroRNAs have been implicated in various skin cancers, including melanoma, squamous cell carcinoma, and basal cell carcinoma; however, the expression of microRNAs and their role in Merkel cell carcinoma (MCC) have yet to be explored in depth. To identify microRNAs specific to MCC (MCC-miRs), next-generation sequencing (NGS) of small RNA libraries was performed on different tissue samples including MCCs, other cutaneous tumors, and normal skin. Comparison of the profiles identified several microRNAs upregulated and downregulated in MCC. For validation, their expression was measured via qRT-PCR in a larger group of MCC and in a comparison group of non-MCC cutaneous tumors and normal skin. Eight microRNAs were upregulated in MCC: miR-502-3p, miR-9, miR-7, miR-340, miR-182, miR-190b, miR-873, and miR-183. Three microRNAs were downregulated: miR-3170, miR-125b, and miR-374c. Many of these MCC-miRs, with the miR-183/182/96a cistron in particular, have connections to tumorigenic pathways implicated in MCC pathogenesis. In situ hybridization confirmed that the highly expressed MCC-miR, miR-182, is localized within tumor cells. Furthermore, NGS and qRT-PCR reveals that several of these MCC-miRs are highly expressed in the patient-derived MCC cell line, MS-1. These data indicate that we have identified a set of MCC-miRs with high implications for MCC research. Overall design: To identify microRNAs specific to Merkel cell carcinoma (MCC) next-generation sequencing (NGS) of small RNA libraries was performed on different tissue samples including MCCs, other cutaneous tumors, and normal skin
DOI: 10.26036/cnphis0001514
title: 32 Heliconius Butterflies: Genome sequencing

description: 10 genomes each from H. cydno galanthus, H. pachinus and H. melpomene rosina from populations in Costa Rica. We also sequenced an additional genome each from H. hecale and H. ismenius.
DOI: 10.26036/cnphis0001515
title: Anser sp. Transcriptome or Gene expression

description: unpublished
DOI: 10.26036/cnphis0001516
title: Petromyzon marinus Meiotic Mapping

description: None
DOI: 10.26036/cnphis0002192
title: Global DNA methylation changes in Nile tilapia gonad during high-temperature induced masculinization

description: In fish, the sex determining mechanisms can broadly be classified as genotypic (GSD), temperature-dependent (TSD), or genotypic plus temperature effects (GSD+TE). For the fish species with TSD or GSD+TE, extremely high or low temperature can affect its sex determination and differentiation. For long time, the underlying changes in DNA methylation that occur during high or low temperature induced sex reversal have not been fully clarified. In this study, we used Nile tilapia as a model to perform a genome-wide survey of differences in DNA methylation in female and male gonads between control and high temperature induced groups using methylated DNA immunoprecipitation (MeDIP). We identified the high temperature induction-related differentially methylated regions (DMRs), and performed functional enrichment analysis for genes exhibiting DMR. These identified differentially methylated genes were potentially involved in the connection between environmental temperature and sex reversal in Nile tilapia. Overall design: In this study, four samples (control females, CF; control males, CM; induced females, IF; induced males, IM) were analyzed.
DOI: 10.26036/cnphis0002193
title: Phylogenomics of the ant subfamily Formicinae, based on UCE sequences

description: Ultraconserved elements (UCEs) have been successfully used in phylogenomics for a variety of taxa, but their power in phylogenetic inference has not yet been extensively compared with traditional Sanger sequencing data sets. Moreover, UCE data on invertebrates, such as insects, is sparse. We compared the phylogenetic potency and informativeness of 959 UCE loci with a multi-locus data set of ten nuclear markers, by testing these two types of data and methods in their ability to resolve and date the evolutionary history of the ant subfamily Formicinae. Phylogenetic estimations show that UCEs are superior in resolving ancient and shallow relationships of formicine ants, demonstrated by increased node support and a more resolved phylogeny. Quantifications of phylogenetic informativeness further evidence a two-fold increase relative to the 10-gene data set. We were able to significantly improve formicine tribal classification based on our comprehensive UCE phylogeny for the group. Our divergence age estimations, using both UCE and Sanger data, indicate that crown-group formicine ants (104–117 Ma) are relatively older than previous studies have suggested. Biogeographic analyses infer the diversification of the subfamily as fairly spread out across all continents with no particular and apparent hub of cladogenesis. Much of the early history of the clade, however, remains uncertain due to ancient rapid divergence events unsolvable even with our genomic data. Our comparative study highlights the promise of UCEs for insect phylogenomics, as well as limitations, and will prove highly useful for the growing number of evolutionary biologists considering the transition from Sanger to next-generation sequencing approaches.
DOI: 10.26036/cnphis0002194
title: Orchesella cincta Genome sequencing and assembly

description: Here we present sequencing, de novo assembly and annotation of the genome of the model soil ecotoxicological organism Orchesella cincta (Hexapoda: Collembola).
DOI: 10.26036/cnphis0002195
title: FSIS NARMS Salmonella

description: Whole genome sequencing of foodborne pathogens as part of the US Department of Agriculture surveillance project for NARMS.
DOI: 10.26036/cnphis0002196
title: Sediment from river isolate:Yvette Metagenome

description: Sample from sediment river (near Paris) and enriched in LB.
DOI: 10.26036/cnphis0002197
title: Mix of 11 yeasts species metagenome

description: Mix of 11 yeasts species
DOI: 10.26036/cnphis0002198
title: mix of E.coli; B. subtilis; V. cholerae metagenomic assembly

description: Mix of 3 bacteria
DOI: 10.26036/cnphis0002199
title: Heliconius himera Genome sequencing

description: We use whole genome resequencing of individuals from hybrid zones across Central and South America to reconstruct a speciation continuum in the Heliconius erato clade and examine processes that drive genomic divergence during speciation.
DOI: 10.26036/cnphis0002200
title: Heliconius erato cyrbia Genome sequencing

description: We use whole genome resequencing of individuals from hybrid zones across Central and South America to reconstruct a speciation continuum in the Heliconius erato clade and examine processes that drive genomic divergence during speciation.
DOI: 10.14457/cu.res.2004.25
title: การสังเคราะห์และศึกษาสมบัติของเปปไทด์นิวคลีอีกชนิดใหม่ ที่มีสะพานเชื่อมเป็นกรดเบต้าอะมิโน
DOI: 10.14457/cu.the.2003.377
title: ความสัมพันธ์ระหว่างปัจจัยส่วนบุคคล การเห็นคุณค่าในตนเอง สภาพแวดล้อมในการทำงาน กับผลิตผลของความคิดสร้างสรรค์ของหัวหน้าฝ่ายการพยาบาล โรงพยาบาลชุมชน
DOI: 10.14457/cu.the.2004.1298
title: การศึกษาความชุกและปัจจัยที่เกี่ยวข้องกับการทำงาน กับการเกิดอาการทางระบบกล้ามเนื้อและกระดูกโครงร่าง ในบุคลากรทางการพยาบาลในโรงพยาบาลจุฬาลงกรณ์
DOI: 10.14457/cu.the.2004.1299
title: การพัฒนาซอฟต์แวร์สำหรับการหาตำแหน่งจุดเดี่ยวที่ให้ความละเอียดสูง โดยใช้ข้อมูลเฟสของคลื่นส่ง
DOI: 10.14457/cu.the.2004.1301
title: ความสัมพันธ์ระหว่างการมีคุณค่าในตน บรรยากาศจริยธรรมในการทำงาน กับความพึงพอใจในงานตามการรับรู้ของพยาบาลวิชาชีพ โรงพยาบาลเอกชนในกำกับมูลนิธิ กรุงเทพมหานคร
DOI: 10.14457/cu.the.2004.1305
title: การแตกตัวพอลิสไตรีนใช้แล้ว โดยใช้ตัวเร่งปฏิกิริยากรด
DOI: 10.14457/cu.the.2004.1308
title: ผลของพริกขี้หนูป่นต่อ rectal perception และ rectal compliance ในอาสาสมัครสุขภาพดี
DOI: 10.14457/cu.the.2004.1319
title: การพัฒนารูปแบบการสอนศิลปศึกษา โดยวิธีศิลปวิจารณ์ตามแนวทฤษฎีของ ยีน เอ มิทเลอร์ ที่ส่งเสริมการรับรู้ทางศิลปะของนักเรียนประถมศึกษา ช่วงอายุ 7-9 ปี