cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0000763
title: shotgun 454 reads from Petromyzon marinus sperm gDNA

description: 454 Titanium chemistry was used to generate shotgun reads from sperm genomic DNA of the sea lamprey (Petromyzon marinus). Animal was collected from the Great Lakes population and obtained through the Great Lakes Fisheries Commission lamprey trapping program.
DOI: 10.26036/cnphis0000764
title: Epigenome and transcriptome of naive pluripotent mouse embryonic stem (ES) cells cultured in 2i serum-free medium

description: This study describes the epigenetic and transcriptome profiling of mouse ES cells cultures in 2i serum-free medium. The proteins for which ChIP-Seq profiles were generated in these cells, as well as for cells grown in serum conditions, include H3K4me3, H3K36me3, H3K27me3, H3K9me3, Suz12 and Ezh2. A sequence profile of genomic DNA is also included. Furthermore, we included RNA-Seq of ds_cDNA synthesized from double poly(A) selected mRNA and from rRNA depleted (strand specific) total RNA. Overall design: ChIP-Seq profiling and RNA-Seq profiling on mouse naive ES cells
DOI: 10.26036/cnphis0001453
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001456
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001457
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001458
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001459
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001460
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001461
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001462
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001463
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0002143
title: Salmonella enterica Genome sequencing and assembly

description: WGS of Salmonella enterica isolates from Colombia, we are interested in antimicrobial resistance mechanisms and possible genetic factors that use foodborne bacteria to increase pathogenic potential.
DOI: 10.26036/cnphis0002144
title: WIV-ISP - Salmonella

description: This BioProject contains the whole genome sequence data on Salmonella uploaded by the Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
DOI: 10.26036/cnphis0002145
title: Lerema accius isolate:1769 Genome sequencing and assembly

description: de novo genome sequencing of Lerema accius
DOI: 10.26036/cnphis0002146
title: Ophiophagus hannah Genome sequencing

description: The king cobra genome is being sequenced to study the evolution of venom genes and the snake body plan, and as a comparative genomics resource.
DOI: 10.26036/cnphis0002147
title: Cyprinodon nevadensis pectoralis Genome sequencing

description: The genus Cyprinodon includes species that inhabit a wide range of environmental conditions. In evolutionary biology, Cyprinodon has played an important role in understanding hybridization and introgression, sexual selection, adaptive radiation, adaptation, phenotypic plasticity, and vicariant speciation. Our studies focus on evolution in small, isolation populations and the inherent problems faced by populations subject to high rates of genetic drift owing to small effective size. The genus is also a model organism for studies of biochemistry, toxicology, physiology, and behavior. Here, we describe the first draft genome of Cyprinodon nevadensis in an effort to increase the tools available for studying a broad range of biological questions.
DOI: 10.26036/cnphis0002148
title: Single-end RAD libraries for Hylomyscus denniae and Sylvisorex granti groups for phylogeographic analysis Albertine Rift and Kenyan Highlands populations.

description: We analyzed restriction-site associated DNA-sequences (RAD-Seq) to study recent historical processes in co-distributed mouse (Hylomyscus) and shrew (Sylvisorex) species complexes, with an aim to better determine how historical paleoenvironmental processes might have contributed to the EABH’s high diversity.
DOI: 10.26036/cnphis0002149
title: Bumble Bee Gut Reduced Representation Genomic Libraries Raw sequence reads

description: For SNP discovery in Nosema bombi, an intracellular parasite of bumble bees.
DOI: 10.26036/cnphis0002150
title: Transcriptomes of 10 North American firefly species

description: Genes underlying signal reception should evolve to maximize signal detection in a particular environment. In animals, opsins, the protein component of visual pigments, are predicted to evolve according to this expectation. Fireflies are known for their bioluminescent mating signals. The eyes of nocturnal species are expected to maximize detection of conspecific signal colors emitted in the typical low-light environment. This is not expected for species that have transitioned to diurnal activity in bright daytime environments. Here we test the hypothesis that opsin gene sequence plays a role in modifying firefly eye spectral sensitivity. We use genome and transcriptome sequencing in four firefly species and transcriptome sequencing in six additional species to identify all opsin genes present in fireflies and to characterize their evolution. We also investigate expression of opsins in different tissues. Fireflies are a rich system in which to investigate the evolution of signals, receptors, and signaling environments. These resources usher these investigations into the genomic era.
DOI: 10.26036/cnphis0002151
title: Identification of Genetic Factors Responsible for Establishment of Equine Arteritis Virus Carrier State in Stallions

description: Horses have genetic differences in susceptibility to Equine Arteritis Virus, both for in vitro tests and for development of persistent carrier states. This project was designed to identify the underlying genetic causes and the physiological effects. The results are relevant to the biology of Arterivirus infection.
DOI: 10.14457/cu.res.2004.23
title: การพัฒนาระบบเฝ้าระวังด้านสิ่งแวดล้อมและสุขภาพ
DOI: 10.26036/cnphis0000765
title: genomic shot gun sequencing of R. balthica

description: genomic shot gun sequencing of the pond snail R. balthica to a) assemble the mitochondrial genome b) obtain repeat motives for marker generation
DOI: 10.26036/cnphis0000766
title: Next generation sequencing and analysis of a conserved transcriptome of New Zealand''s kiwi

description: Background To understand the patterns of molecular evolution of the nuclear protein-coding genes in brown kiwi (Apteryx australis mantelli) and to determine the timescale of avian history we sequenced a transcriptome obtained from a kiwi embryo using next generation sequencing methods. We then assembled the conserved protein-coding regions using the chicken proteome as a scaffold. Results Using 1,543 conserved protein coding genes we estimated the neutral evolutionary divergence between the kiwi and chicken to be ~45%, which is approximately equal to the divergence computed for the human-mouse pair using the same set of genes. A large fraction of genes was found to be under high selective constraint, as most of the expressed genes appeared to be involved in developmental gene regulation. Our study suggests a significant relationship between gene expression levels and protein evolution. Using sequences from over 700 nuclear genes we estimated the divergence between the two basal avian groups, Palaeognathae and Neognathae to be 132 million years, which is consistent with previous studies using mitochondrial genes. Conclusions The results of this investigation revealed patterns of mutation and purifying selection in conserved protein coding regions in birds. Furthermore this study suggests a relatively cost-effective way of obtaining a glimpse into the fundamental molecular evolutionary attributes of a genome, particularly when no closely related genomic sequence is available.
DOI: 10.26036/cnphis0000767
title: Caenorhabditis angaria genome sequencing project

description: This strain will be used for comparative genome analysis.
DOI: 10.26036/cnphis0000768
title: BAC library construction and BAC end sequencing for Phlebotomus papatasi

description: The Washington University Genome Sequencing Center will perform BAC library construction and BAC-end sequencing for the <i>Phlebotomus papatasi</i> genome. Sequences are available in the Trace Archive.
DOI: 10.26036/cnphis0000769
title: Linking chemical and microbial diversity in marine sponges: possible role for Poribacteria as producers of methyl-branched fatty acids.

description: For the symbiont-rich sponge Cacospongia mycofijiensis, a source of the tubulin-inhibiting fijianolides (=laulimalides), near-exhaustive large-scale sequencing of PKS gene-derived PCR amplicons was conducted.
DOI: 10.26036/cnphis0000770
title: Homo sapiens CEPH/UTAH Pedigree 1463 genome sequencing project

description: None
DOI: 10.26036/cnphis0000771
title: Nodeomics: pathogen detection in vertebrate lymph nodes using meta-transcriptomics

description: The ongoing emergence of human infections originating from wildlife highlights the need for better knowledge of the microbial community in wildlife species where traditional diagnostic approaches are limited. Here we evaluate the microbial biota in healthy mule deer (Odocoileus hemionus) by analyses of lymph node meta-transcriptomes. cDNA libraries from five individuals and two pools of samples were prepared from retropharyngeal lymph node RNA enriched for polyadenylated RNA and sequenced using Roche-454 Life Sciences technology. Protein-coding and 16S ribosomal RNA (rRNA) sequences were taxonomically profiled using protein and rRNA specific databases. Representatives of all bacterial phyla were detected in the seven libraries based on protein-coding transcripts indicating that viable microbiota were present in lymph nodes. Residents of skin and rumen, and those ubiquitous in mule deer habitat dominated classifiable bacterial species. Based on detection of both rRNA and protein-coding transcripts, we identified two new proteobacterial species; a Helicobacter closely related to Helicobacter cetorum in the Helicobacter pylori/Helicobacter acinonychis complex and an Acinetobacter related to Acinetobacter schindleri. Among viruses, a novel gamma retrovirus and other members of the Poxviridae and Retroviridae were identified. We additionally evaluated bacterial diversity by amplicon sequencing the hypervariable V6 region of 16S rRNA and demonstrate that overall taxonomic diversity is higher with the meta-transcriptomic approach. These data provide the most complete picture to date of the microbial diversity within a wildlife host. Our research advances the use of meta-transcriptomics to study microbiota in wildlife tissues, which will facilitate detection of novel organisms with pathogenic potential to human and animals.
DOI: 10.26036/cnphis0000772
title: Genome sequencing of the sea lamprey

description: The sea lamprey genome is expected to be sequenced at 4- to 6-fold coverage.
DOI: 10.26036/cnphis0000773
title: Macaca mulatta (Indian origin) genome re-sequencing of three animals

description: This project re-sequences the same rhesus monkey sample 17573 from the Southwest National Primate Research Center that has been used in other genome sequencing projects. This project uses SOLiD sequence data to generate approximately 10x coverage for this individual and 4-5x coverage each for two additional unrelated rhesus monkeys from the Wisconsin National Primate Research Center.
DOI: 10.26036/cnphis0000774
title: Salix purpurea L. genome sequencing project

description: There are two motivations to determine the genome sequence of <i>Salix purpurea</i>: 1) the organism is a bioenergy crop and knowing the genome sequence will facilitate further development 2) <i>Salix</i> and <i>Populus</i> are two genera in the tribe <i>Salicae</i> and knowing the genome sequence of both allows greater understanding of each.
DOI: 10.26036/cnphis0001464
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001465
title: Gene expression profiling study by RNA-seq in colorectal cancer

description: The objective of this study is to identify a prognostic signature in colorectal cancer (CRC) patients with diverse progression and heterogeneity of CRCs. We generated RNA-seq data of 54 samples (normal colon, primary CRC, and liver metastasis) from 18 CRC patients and, from the RNA-seq data, identified significant genes associated with aggressiveness of CRC. Through diverse statistical methods including generalized linear model likelihood ratio test, two significantly activated regulators were identified. In the validation cohorts, two activated regulators were independent risk factors and potential chemotherapy-sensitive agenets in colorectal cancers. Overall design: RNA-seq data of 54 samples (normal colon, primary CRC, and liver metastasis) were generated from 18 CRC patients. Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer''s protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR. Sequencing was performed in paired end reads (2x100 bp) using Hiseq-2000 (Illumina).
DOI: 10.26036/cnphis0001466
title: Tabanus nigrovittatus Random survey

description: Tabanus nigrovittatus partial genome sequencing for microsatellite screening. Legs and thoraces of two adult T. nigrovittatus females.
DOI: 10.26036/cnphis0001467
title: Diabrotica barberi strain:Field collection Genome sequencing

description: Collection of Northern corn rootworm from North American locations
DOI: 10.26036/cnphis0001468
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001469
title: Extensive Variation in Chromatin States Across Humans

description: The majority of disease-associated variants lie outside protein-coding regions, suggesting a link between variation in regulatory regions and disease predisposition. We studied differences in chromatin states using five histone modifications, cohesin, and CTCF in lymphoblastoid lines from 19 individuals of diverse ancestry. We found extensive signal variation in regulatory regions, which often switch between active and repressed states across individuals. Enhancer activity is particularly diverse among individuals, whereas gene expression remains relatively stable. Chromatin variability shows genetic inheritance in trios, correlates with genetic variation and population divergence, and is associated with disruptions of transcription factor binding motifs. Overall, our results provide insights into chromatin variation among humans. Overall design: To characterize human variation in diverse types of regulatory elements, we studied the chromatin state of lymphoblastoid cell lines (LCLs) derived from 19 individuals: 5 European (CEU), 7 Yoruban (YRI), and 2 Asian individuals from the 1000 Genomes Project (including two mother-father-daughter trios), an additional Caucasian individual), and four individuals from the San population). We used RNA-Seq to measure expression and Chromatin Immunoprecipitation followed by high-throughput sequencing (ChIP-Seq) to map five histone modifications (H3K27ac, H3K4me1, H3K4me3, H3K36me3, and H3K27me3) and two general factors (CTCF, and SA1, a subunit of cohesin). We generated 2 replicates per factor.
DOI: 10.26036/cnphis0001470
title: Citrullus lanatus subsp. vulgaris strain:Dumara Transcriptome or Gene expression

description: Many fruits, including watermelon, are proficient in carotenoid accumulation during ripening. While most genes encoding steps in the carotenoid biosynthetic pathway have been cloned, few transcriptional regulators of these genes have been defined to date. Here we describe the identification of a set of putative carotenoid-related transcription factors resulting from fresh watermelon carotenoid and transcriptome analysis during fruit development and ripening. Our goal is to both clarify the expression profiles of carotenoid pathway genes and to identify candidate regulators and molecular targets for crop improvement.
DOI: 10.26036/cnphis0001471
title: Caranx Genome sequencing

description: Partial genome sequence of Caranx ignobilis and Caranx melampygus
DOI: 10.26036/cnphis0001472
title: Peruvian Stick Insect RNA-Seq

description: The goals of this study are to identify the active proteins of the midgut of the Peruvian walking stick, Peruphasma schultei (Pseudophasmatidae: Phasmatodea). Male and female insects were sampled together. The anterior and posterior midguts were analyzed separately in efforts to identify the function of the "appendices of the midgut," a Phasmatodea-specific system of tubes on the posterior third of the midgut. By identifying genes expressed differentially in the posterior gut, we hoped to find the genes associated with the appendices and elucidate their roles. Other goals included identifying plant cell wall degrading enzymes expressed in the midgut, such as cellulases and pectinases, and determining if they are endogenously produced or microbial. The results demonstrate the extent to which the Phasmatodea digestive system is compartmentalized and provide a first look at the transcriptomics of phasmid digestion.
DOI: 10.26036/cnphis0002152
title: Calypte anna Genome sequencing and assembly

description: Anna''s Hummingbird genome sequencing and assembly
DOI: 10.26036/cnphis0002153
title: Cyprinus carpio Genome sequencing

description: Sequencing of the common carp (Cyprinus carpio carpio Linnaeus, 1758) genome, with the objective of establishing carp as a model organism to supplement the closely related zebrafish (Danio rerio). The sequenced individual is a homozygous female (by gynogenesis) of R3 x R8 carp, the heterozygous offspring of a cross between fish of Hungarian origin (R8 strain) and of Polish origin (R3 strain).
DOI: 10.26036/cnphis0002154
title: Salmonella enterica subsp. enterica serovar Gallinarum strain:ST572 Genome sequencing

description: Genome sequence of Salmonella Gallinarum (serogroup D; 1,9,12:-:-)
DOI: 10.26036/cnphis0002155
title: Felis catus Raw sequence reads

description: 99 Lives Cat Genome Sequencing InitiativeThis project proposes to sequence 99 cats to support health care for the normal household cat and our fancy cat breeds too. Many cats suffer from obesity, diabetes, asthma, urinary tract infections, cancers, heart disease and infectious diseases, just like humans. Deciphering the genetic causes for these conditions requires a database that describes all the NORMAL DNA variation in cats as well as the bad mutations!
DOI: 10.26036/cnphis0002156
title: Panthera tigris tigris Genome sequencing

description: To mapping the Golden tiger gene.
DOI: 10.26036/cnphis0002157
title: Drosophila simulans Genome sequencing

description: Whole genome sequencing of ''rescue'' interspecies hybrid males between D. simulans and D. melanogaster
DOI: 10.26036/cnphis0002158
title: Xiphophorus couchianus Genome sequencing and assembly

description: The sequence and assembly of Xiphophporus couchianus will allow investigations of interspecies hybrids, especially those of X. maculatus, to determine the genetics of underlying spontaneous and induced tumorigenesis.
DOI: 10.26036/cnphis0002159
title: Xiphophorus hellerii Genome sequencing

description: The sequence and assembly of Xiphophporus hellerii will allow investigations of interspecies hybrids, especially those of X. maculatus, to determine the genetics of underlying spontaneous and induced tumorigenesis.
DOI: 10.26036/cnphis0002160
title: Effects of biobanking on chromatin accessibility

description: The goal of this study was to test the effects of biobanking on chromatin assessibility, as defined by ATAC-seq. Human naïve B cells were FACS sorted from PBMCs that were either frozen or processed fresh. A range of cell numbers were used to identify technical limitations and reproducibility of the ATAC-seq assay on biobanked PBMCs comapred to freshly sorted material. To provide insight into a disease process, naive B cells were isolated from healthy donors or a biorepository of Systemic Lupus Erythematosus undergoing disease flares. These data identify a unique signature of accessible chromatin in SLE B cells. Overall design: ATAC-Seq on fresh and frozen B cells
DOI: 10.5284/1049643
title: Lutterworth Swinford Road, south of Lutterworth, Leicestershire. Archaeological Evaluation (OASIS ID: oxfordar1-295740)

description: Oxford Archaeology undertook an archaeological trial trench evaluation on land to the east of Swinford Road, south of Lutterworth, Leicestershire between 5th-16th December 2016. The evaluation was preceded by a magnetometer geophysical survey that provided clear evidence for archaeological activity across the southern and western part of the site. The trial trench evaluation was targeted to specifically investigate the geophysical survey results and to establish the presence/absence of remains across the northern part of the site. A total of 19 trenches were excavated, confirming the presence of a large, single-phase, rectangular enclosure measuring approximately 112m by 70m occupying the former high ground across the southern part of the site. Pottery assemblages recovered from the ditch securely date this to the late 2nd century AD. A series of ditches, gullies and pits were investigated within the enclosure area, although these lacked artefact assemblages. A clear association between the enclosure and other features was not established, although the propensity of these to be within the enclosure and the absence of similar features beyond suggests a link. Some ferrous metalworking activity (smithing) was undertaken at the site as evidenced by hammerscale and burnt clay fragments recorded in Trench 3. The topographical levels across the northern part of the site bordered by the M1 Junction 20 slip road and the A4303 had been substantially raised during the 20th century. Here made ground soil depths of up to 2m were recorded, probably related to the M1 construction, although the deposition of these had not been preceded by truncation. Archaeological features across the northern part of the site were limited to more sparsely arranged linear features that are likely to represent field boundaries peripheral to settlement activities.
DOI: 10.26036/cnphis0000775
title: Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing

description: RNA was extracted from eight tissues of wild great tit fledglings, and a normalised cDNA library generated and sequenced. Approximately 4.6 million sequences and 1.4 billion bases of DNA were generated and assembled into 95,979 contigs. Over 90% of contigs aligned with the zebra finch (Taeniopygia guttata) genome, and one third aligned with known Taeniopygia guttata (zebra finch) and Gallus gallus (chicken) transcripts. More than 35,000 single nucleotide polymorphisms and 10,000 microsatellite repeats were identified.
DOI: 10.26036/cnphis0000776
title: DOE Joint Genome Institute Crassostrea gigas EST project

description: None
DOI: 10.26036/cnphis0000777
title: ENCODE Cold Spring Harbor Labs Long RNA-seq (hg18)

description: .