cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0001517
title: CATseq a comparative Arabidopsis Transcriptome - RNA-Seq part

description: A comparative assessment between both technologies, RNASeq and microarrays to detect differential expression in Arabidopsis transcriptome. The sequencing approach use High-throughput sequencing on different Solexa technologies (GAII,HiSeq2000 multiplex or not) Wild type samples were analyzed from 2 tissus (flower buds and leaves) which have a very contrasted transcriptomic profile (i.e very high number of genes differentially expressed). Overall design: The RNA was extracted from 2 tissus Flower Buds and Leaves from Arabidopsis. The associated GEO series with array part is GSE45345
DOI: 10.26036/cnphis0001518
title: Equus przewalskii Genome sequencing

description: Whole Equus przewalskii genome sequencing
DOI: 10.26036/cnphis0001519
title: Equus caballus Genome sequencing

description: Horse Whole genome shotgun sequencing Project
DOI: 10.26036/cnphis0001520
title: Xiphophorus Map

description: Mammalian karyotypes vary wildly in haploid number (e.g., 3-40 in deer) compared to stability in teleost fish (24-25 in 58% of teleosts), but we don't understand the mechanisms that account for differences in karyotype stability. Among perciform teleosts, platyfish (Xiphophorus maculatus) and medaka (Oryzias latipes) both have 24 chromosome pairs but threespine stickleback (Gasterosteus aculeatus) and green pufferfish (Tetraodon nigroviridis) have just 21 pairs. What mechanisms reduced chromosome number? Under one hypothesis, six ancestral chromosomes fused in pairs to make three chromosomes. Alternatively, four ancestral chromosomes might have fused to make a single large derived chromosome. More complicated hypotheses are also possible. Furthermore, chromosome fusions could be shared or lineage specific. To distinguish among hypotheses, we made a meiotic map for platyfish with over 16,000 mapped markers. Along the map we tiled genomic contigs, and compared genomes using the Synteny Database. Analysis showed that chromosomes of platyfish and medaka (both Atherinomorpha within Percomorpha) remained remarkably unchanged by translocation, but experienced numerous transpositions and inversions since their lineages diverged about 120 million years ago. In contrast, reduced chromosome numbers in other Percomorpha groups (stickleback (Gasterosteidae) and green pufferfish (Tetraodontoformes)) arose by fusion of pairs of ancestral chromosomes after their lineage diverged from platyfish about 195 million years ago. These studies reveal stability of syntenies and gene orders in teleost chromosomes over hundreds of millions of years, identify what are likely genome assembly errors, characterize chromosome fusion events, and distinguish independent chromosome fusions.
DOI: 10.26036/cnphis0001521
title: Pimephales promelas Genome sequencing and assembly

description: Draft assembly of the Fathead Minnow (Pimephales promelas) genome. A collaboration between DuPont, US Environmental Protection Agency and University of Illinois HPCBio.
DOI: 10.26036/cnphis0001522
title: Canis lupus familiaris Genome sequencing

description: Whole genome sequencing of six dog breeds from continuous altitude
DOI: 10.26036/cnphis0001523
title: Pediculus schaeffi Genome sequencing

description: Raw Reads from Pediculus schaeffi
DOI: 10.26036/cnphis0001525
title: Equus Genome sequencing, comparing polymerase

description: for ancient methylation signatures
DOI: 10.26036/cnphis0002201
title: Heliconius clysonymus 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/cnphis0002202
title: Heliconius telesiphe 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/cnphis0002203
title: Rana temporaria low-coverage genome sequence

description: To facilitate genetic research on Ranid frogs, we assembled a low-coverage draft genome of the common frog Rana temporaria.
DOI: 10.26036/cnphis0002204
title: Solanum aethiopicum Transcriptome or Gene expression

description: Scarlet eggplant (S. aethiopicum) is the second most important cultivated eggplant, and its cultivation is widespread in Africa, mainly in the west and central part, as well as in some part of Caribbean, Brazil and south Italy. This species is considered as hypervariable from the morphological point of view as it presents great differences in plant and fruit traits. Generally, this species is divided in four cultivar groups, namely Aculeatum, Gilo, Kumba, and Shum. It is used as rootstock for common eggplant due to its resistance at some biotic stresses.
DOI: 10.26036/cnphis0002205
title: Genomic Signatures of Speciation in Sympatric and Allopatric Hawaiian picture-winged Drosophila

description: Understanding the genomic changes involved in speciation is a major goal of modern evolutionary biology. Such understanding will require the combined analysis of genome structural differences, gene-level divergence, and phenotypic measures of reproductive barriers between closely related species representing a range of speciation modes.The Hawaiian archipelago provides a natural arena for understanding adaptive radiation and speciation. The Hawaiian Drosophila are one of the most diverse endemic groups in Hawaii with up to 1000 species. We sequenced and analyzed entire genomes of recently diverged species of Hawaiian picture-winged Drosophila, D. silvestris and D. heteroneura from Hawai’i Island, in comparison with D. planitibia, their sister species from Maui.
DOI: 10.26036/cnphis0002206
title: Transcriptome-wide high-throughput deep m6A-seq reveals unique m6A methylation differential patterns among three organs in Arabidopsis

description: m6A is a ubiquitous RNA modification in eukaryotes. Transcriptome-wide m6A patterns in Arabidopsis have been assayed recently. However, m6A differential patterns among organs have not been well characterized. The goal of the study is to comprehensively analyze m6A patterns of numerous types of RNAs, the relationship between transcript level and m6A methylation extent, and m6A differential patterns among organs in Arabidopsis. Overall design: In total, 18 libraries were sequneced. For the 3 organs: leaf, flower and root, each organ has mRNA-Seq, m6A-Seq and Input sequenced. And each sequence has 2 replicats.
DOI: 10.26036/cnphis0002207
title: Sturnus vulgaris Genome sequencing and assembly

description: Native to Europe, Asia and North Africa, Sturnus vulgaris (the European starling) has been introduced globally, save in Neotropical regions. The European starling prefers lowland habitats and is an aggressive omnivore. S. vulgaris costs hundreds of millions of dollars in agricultural damage each year (estimated annual cost to agriculture in the USA is $800 million, based on $5/ha damage; Linz et al. 2007). S. vulgaris also contributes to the decline of local native bird species through competition for resources and nesting spaces. S. vulgaris can also act as a disease vector with implications for livestock and human health. The European starling has been nominated as among 100 of the "World''s Worst" invaders.
DOI: 10.26036/cnphis0002208
title: Syncytiotrophoblast generation from human pluripotent stem cells

description: Purpose: Syncytiotrophoblast (STB) is a multi-nucleated, terminally differentiated syncytium that covers the surface of the villous placenta and forms the major interface with maternal blood. It releases placental hormones and plays a primary role in exchange of gases, nutrients and waste products. Alterations in STB development and turnover have been implicated in placental diseases, including preeclampsia (PE). In vitro cell models are badly needed to study STB development and physiology due to inaccessibility to placental tissues during gestation. To establish in vitro STB model system, we generate STB and its mononucleated precursors from human embryonic stem cells (hESC) and profile for RNA content by RNAseq. Methods: H1 Human ESC (WA01) were treated with BMP4, the ALK4/5/7 inhibitor (A83-01), and the FGF2 signaling inhibitor (PD173074) (BAP) to direct them to the trophoblast lineage and provided both STB and extravillous trophoblast. Syncytial areas emerged at day 8 BAP treatment ranged in diameter from ~40 µm to &gt; 100 µm. The intact syncytial areas were isolated by sieving successively through 70 µm and 40 µm mesh cell strainers. The captured cells are recovered by inverting the strainer and rinsing with culture medium to separate large (&gt;70 µm) and middle size cell sheets (40-70 µm). The fraction that passes through both sieves represents cells of smallest diameter (&lt; 40 µm), presumably cytotrophoblast. Total 12 RNA samples from triplicate three size-fractioned BAP treated and three untreated hESC cultured in a FGF2 supplemented medium in parallel were analyzed. Results: The larger &gt; 70 µm areas stained positively for STB markers while ultrastructural analysis clearly revealed multi-nuclear cells with an extensive cytoplasm containing many prominent secretion granules. The larger STB areas also had a larger DNA content that &gt; 70 µm fraction contained 37 times more nuclear content and 40-70 µm fraction did 16 times more. Compared to the &lt; 40 µm cell fraction, these larger cells over-expressed a full repertoire of genes characteristic of STB, e.g. CGA, CGB, PGF, ERVW1, GCM1. The smallest cell fraction had a DNA content consistent with mononuclear diploid cells, contained few secretory granules, and were only weakly positive for STB markers. Conclusion: The data are consistent with the &gt; 70 µm cells being mature STB, while the intermediate fraction may represent a precursor population. Human ESC directed along the trophoblast lineage by BAP treatment offers a useful model for following STB formation in vitro and suggest that this protocol may have utility in studying the basis of certain placental diseases, especially preeclampsia, where placental tissue isolated at term or after pregnancy terminations can only offer limited information. Overall design: Three size fraction mRNA profiles of syncytial areas emerged at day 8 BAP treatment of hESC were generated by deep sequencing along with untreated hESC, in triplicate, using Illumina HiSeq 2500.
DOI: 10.26036/cnphis0002209
title: Complex Genome Evolution in A. coluzzii Associated with Increased Insecticide Usage in Mali

description: We compared A. coluzzii genomes before and after an adaptive introgression event involving the insecticide resistance gene kdr.
DOI: 10.14457/cu.the.2004.1320
title: โมเดลเชิงสาเหตุประสิทธิผลการประกันคุณภาพภายใน สำหรับกลุ่มสาขาวิทยาศาสตร์สุขภาพ
DOI: 10.26036/cnphis0001524
title: Dynamics and Characterization of Small RNAs of Virus and Host Origin from Wheat Streak Mosaic Virus- and/or Triticum Mosaic Virus-infected Susceptible and Temperature-Sensitive Resistant Wheat Cultivars

description: Wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV) are type members of Tritimovirus and Poacevirus genera, respectively, in the family Potyviridae, and are transmitted by wheat curl mites. Co-infection of these two viruses causes synergistic interaction with increased virus accumulation and disease severity in wheat. In this study, we examined the effects of synergistic interaction between WSMV and TriMV on endogenous small (s) RNAs and virus-specific small interfering RNAs (vsiRNAs) in susceptible (Arapahoe) and temperature-sensitive resistant (Mace) wheat cultivars at 27ºC and 18ºC. Single- and double-infections in wheat caused a shift in the profile of endogenous sRNAs from 24 nt being the most predominant in healthy plants to 21 nt in infected wheat. Additionally, we report high-resolution vsiRNA maps of WSMV and TriMV in singly- and doubly-infected wheat cultivars Arapahoe and Mace at 18ºC and 27ºC. Massive amounts of 21 and 22 nt vsiRNA reads were accumulated in Arapahoe at both temperatures and in Mace at 27ºC but not at 18ºC. The plus- and minus-sense vsiRNAs were distributed throughout the genomic RNAs in Arapahoe at both temperature regimens and in Mace at 27ºC, although some regions of genomic RNAs serve as hot-spots with an excessive number of vsiRNAs. The positions of vsiRNA peaks were conserved among wheat cultivars Arapahoe and Mace, suggesting that Dicer-like enzymes of susceptible and resistant wheat cultivars are similarly accessed the genomic RNAs of WSMV and TriMV. Additionally, several cold-spot regions were found in the genomes of TriMV and WSMV with no or a few vsiRNAs, indicating that certain regions of WSMV and TriMV genomes are not accessible to Dicer-like enzymes. The high-resolution map of endogenous and vsiRNAs from wheat cultivars synergistically infected with WSMV and TriMV at two temperature regimens form a foundation for understanding the virus-host interactions, effect of synergistic interactions on host defense mechanisms, and virus resistance mechanisms in wheat. Overall design: Small RNA was sequenced from two wheat cultivars (Mace and Araphahoe), at two temperatures 18ºC and 27ºC, for healthy (control/uninfected), infected with wheat streak mosaic virus (WSMV), infected with Triticum mosaic virus (TriMV), and a double-infecttion of WSMV and TriMV.
DOI: 10.26036/cnphis0001526
title: Papilio polytes Genome sequencing

description: With the aim of investigating of sex-limited mimicry in Papilio polytes, genomic DNA from 30 lab-reared Papilio polytes individuals (15 polytes and 15 cyrus) was extracted. Illumina paired-end libraries were constructed using Illumina Truseq protocol and sequenced with an Illumina Hiseq 2000. Low quality data were filtered from the raw reads and only high quality reads were kept for downstream analyses.
DOI: 10.26036/cnphis0001527
title: Anser cygnoides Transcriptome or Gene expression

description: goose
DOI: 10.26036/cnphis0001528
title: Ancylostoma ceylanicum genome sequence

description: Genome sequence component of "Genome and transcriptome of the zoonotic hookworm Ancylostoma ceylanicum"
DOI: 10.26036/cnphis0001529
title: Homo sapiens Exome

description: NPC Exome Sequencing
DOI: 10.26036/cnphis0001530
title: Cavia aperea Genome sequencing and assembly

description: Whole genome sequencing of the wild guinea pig
DOI: 10.26036/cnphis0001531
title: Schistosoma mansoni strain:BRE Transcriptome or Gene expression

description: Schistosoma mansoni Transcriptomics
DOI: 10.26036/cnphis0001532
title: Sequencing the genome of an early branching echinoderm; the crinoid Oxycomanthus japonicus

description: Echinoderms are an important model system for developmental biology, as they are closely related to chordates. A number of species of echinoderms also have remarkable abilities of regeneration, especially those of the crinoids. Crinoids also occupy an important evolutionary node; they are the earliest branching extant echinoderm. As such, we sequenced and assembled a crinoid genome, Oxycomanthus japonicus to compare to other available genomes.
DOI: 10.26036/cnphis0001533
title: RNA sequencing of 15 genomes of Anopheles

description: None
DOI: 10.26036/cnphis0001534
title: Salmonella enterica subsp. enterica serovar Typhi str. STH2370 Genome sequencing and assembly

description: Salmonella enterica serovar Typhi strain STH2370 was isolated from a typhoid fever in Santiago, Chile. This clinical isolate has been used as a reference wild-type strain in many studies conducted during the last 15 years
DOI: 10.26036/cnphis0002210
title: Link_ADI Metagenome

description: Metagenomic characterization of metabolic network from an ammonia rich biogas reactor with emphasis on cellulose degrading bacteria.
DOI: 10.26036/cnphis0002211
title: Drosophila yakuba ecological genomics

description: Investigation of ecological specialization in D. yakuba
DOI: 10.26036/cnphis0002212
title: CVM NARMS Salmonella

description: Whole genome sequencing of foodborne pathogens as part of the US Food and Drug Administration surveillance project for NARMS.
DOI: 10.26036/cnphis0002213
title: Bos primigenius isolate:CPC98 Raw sequence reads

description: Domestication of the now-extinct wild aurochs (Bos primigenius) gave rise to the two major domestic extant cattle taxa—B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between the European aurochs and modern cattle, important questions remain unanswered, including (1) clarification of the phylogenetic status of the aurochs, (2) whether gene flow from aurochs into early domestic populations occurred, and (3) identification of genomic regions subject to selection processes during and after domestication. With this project we address these questions using a whole genome sequence generated from a ~6,750 year-old British aurochs bone.
DOI: 10.26036/cnphis0002214
title: Primary human trophoblast from term placenta

description: We compare two groups of transcriptome profiles. They are 1) primary human trophoblasts (PHT) and 2) syncytiotrophoblast from human pluripotent stem cells. This data set represents the former data set and the latter has been deposited separately at GSE72712. Primary human trophoblasts (PHT) were purified cytotrophoblast populations from whole term placentas and then cultured in vitro. The cytotrophoblasts were cultured for short (9 h) or long (48 h) term that show undifferentiated (PHTu) or differentiated (PHTd) phenotype that led syncytialization, respectively. Transcriptome profiles of PHTu and PHTd were compared with three size fractioned syncytiotrophoblasts and trophoblasts from human pluripotent stem cells that are named ESCd_gt70 (greater than 70 µm), ESCd_40-70 (size between 40 and 70 µm), ESCd_lt40 (smaller than 40 µm) and undifferentiated progenitor (ESCu; see GSE72712). Overall design: Primary human trophoblasts (PHT) were derived and cultured from three term human placentas obtained by the Obstetrical Specimen Procurement Unit from women after a healthy pregnancy, labor, and delivery at Magee-Womens Hospital of the University of Pittsburgh Medical Center. Isolated PHT lines obtained from three individual (1 female and 2 male) placentas were cultured separately.
DOI: 10.26036/cnphis0002215
title: Salmonella enterica subsp. enterica serovar Typhimurium Genome sequencing

description: Longitudinal isolates of Salmonella enterica serovar Typhimurium associated with prolonged carriage
DOI: 10.26036/cnphis0002216
title: Ovaries transcriptome sequencing of Drosophila mojavensis, Drosophila arizonae and their hybrids

description: We performed reciprocal crosses of D. mojavensis and D. arizonae and sequenced the transcriptome of the ovaries from the two parental line and the two crosses (10-day-old flies).
DOI: 10.26036/cnphis0002217
title: GenomeTrakr Project: California Department of Public Health - FDLB Micro

description: Whole genome sequencing of cultured Salmonella enterica as part of the US Food and Drug Administration''s WGS surveillance effort for the rapid traceback of foodborne pathogens.
DOI: 10.5284/1049646
title: The Former Norville Factory Site, Tarrington Road, Tredworth. Archaeological Evaluation (OASIS ID: borderar1-272557)

description: Border Archaeology Limited performed an Archaeological Field Evaluation in 2016 and an Archaeological Standing Building Recording in 2017 at the Former Norville Factory Site, Tarrington Road, Tredworth, Gloucester. Border Archaeology Ltd was instructed by Markey Construction to undertake a programme of Archaeological Field Evaluation on the site of the former Norville Factory Tarrington Road Tredworth Gloucester. The site was originally established in 1885 to accommodate the Hatherley Step Works producing furniture and patented 'lattice' stepladders, which, by the late 19th century, had achieved worldwide distribution. The site was occupied by the Gloster Aircraft Company During the Second World War and latterly by the Norville Optical Company Limited. Structural remains presumed to have been associated with the original factory premises, including footings and pipework, were recorded. No other deposits or features of archaeological significance were encountered, although pottery and clay tobacco pipe recovered during the course of the work indicated that, until the construction of the Hatherley Step Works in the latter part of the 19th century, the site had been under cultivation. A single flint flake recovered from the subsoil in Trench 3 had suffered heavy post-depositional damage and could not be dated.
DOI: 10.5284/1049647
title: Water Pipeline Replacement Works, Rainbow Hill, Worcester. Archaeological Observation (OASIS ID: borderar1-289629)

description: Border Archaeology Ltd was commissioned to undertake a programme of Archaeological Observation in connection with approximately 800m of water pipeline replacement works in Worcester affecting Rainbow Hill, Lansdowne Crescent Lane, Lansdowne Walk, part of Lansdowne Crescent and Roger's Hill. These streets all lay in an area with the potential to encounter deposits of Roman, medieval and Civil War date. All features and deposits encountered during the course of the engineering groundworks related to modern road surfaces and existing pipes and services. The open-cut trenching largely followed the route of an existing cast-iron main and any archaeological features or deposits which may have been present would probably have been damaged prior to commencement of the present scheme. Although areas of natural clay were revealed, particularly on Rainbow Hill and Lansdowne Walk, no evidence of archaeological features or early road surfaces was present and it would appear likely that these must have been removed during construction of the existing road. However, the fact that no residual finds or material were seen suggests that archaeological activity in this area was limited and that, prior to residential development in the 19th century and subsequently, it may have lain under cultivation. The reported discovery of musket balls, clay pipe and a stamped silver coin on allotments at the northeast end of Lansdowne Walk may relate to the Civil War period but no evidence for features or deposits of that date was seen in the nearby access pits.
DOI: 10.26036/cnphis0001535
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001536
title: Influenza Virus Genome Sequencing Project

description: The Influenza Genome Sequencing Project is a collaborative effort designed to increase the genome knowledge base of influenza and help researchers understand how flu viruses evolve, spread, and cause disease. By putting critical genome knowledge in the public domain, the project leaders hope to provide researchers with the infrastructure needed to develop new vaccines, therapies, and diagnostics, and improve understanding of the overall molecular evolution of influenza and other genetic factors that determine their virulence. Such knowledge could not only help mitigate the impact of annual influenza epidemics but also improve the scientific knowledge of the emergence of pandemic flu viruses. The sequencing effort is helping to reveal the complete genetic blueprints of thousands of known human and avian influenza viruses.
DOI: 10.26036/cnphis0001537
title: We are sequencing multiple species to identify microsatellite repeats and design primers. The species range across classes and Kingdoms. Genome sequencing

description: We are isolating microsatellite loci (genetic markers) from species so they can be used to conduct various molecular ecology studies such as measuring genetic variation in populations, managing endangered populations, and doing behavioral studies.
DOI: 10.26036/cnphis0001538
title: Calanus finmarchicus Genome sequencing

description: Genome sequencing of C. finmarchicus for development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification