cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0000817
title: Necator americanus Genome Sequencing

description: The Genome Institute and collaborators are sequencing the human hookworm, Necator americanus. Hookworm diseases are extremely common in the tropics and sub-tropics, with a disease burden comparable to measles and exceeding that of diabetes and lung cancer. N. americanus is the most prevalent species of human parasite and therefore most important from a public health standpoint. It lives in the intestines and is particularly harmful to children, causing chronic anemia, stunting growth and imparing intellectual development. Providing as complete a genome sequence as possible for this hookworm species will aid in vaccine development.
DOI: 10.26036/cnphis0000508
title: Struthio camelus australis Genome sequencing and assembly

description: The whole genome sequencing of Struthio camelus australis.
DOI: 10.26036/cnphis0000853
title: Salmonella enterica subsp. enterica serovar Montevideo str. OH_2009072675 genome sequencing project

description: <b><i>Salmonella enterica</i> subsp. <i>enterica</i> serovar Montevideo str. OH_2009072675</b>. This strain will be used for comparative genome analysis.
DOI: 10.26036/cnphis0000914
title: Strongylocentrotus purpuratus isolate:Spur 01 Genome sequencing and assembly

description: The Strongylocentrotus purpuratus genome has been sequenced using a combination of Sanger (~8X coverage), SOLiD (~18X), Illumina (~40x), and PacBio (~11X) by the Human Genome Sequencing Center at Baylor College of Medicine, using a combination of whole genome shotgun (WGS) and BAC-based sequencing.
DOI: 10.26036/cnphis0000976
title: Metagenomic analysis of infant stool sample

description: Stool sample from a premature human infant (UC1). This study used metagenomic methods (community genomic analysis and sequencing of amplified 16S rRNA genes) to document microbial colonization of the gut of a premature infant born at 28 weeks gestation. Analysis of 16S rRNA gene sequences collected approximately daily revealed three compositional phases during colonization. We reconstructed genomes of the dominant organisms and intensively curated population genomic datasets from the third phase. In the third phase, the communities were dominated by a nearly clonal Serratia population, two Citrobacter strains sharing &gt;99% nucleotide identity, and contained a lower abundance Enterococcus population, multiple plasmids and bacteriophage. The relative abundance of the Citrobacter strains changed significantly over time. Modeling of Citrobacter strain abundances suggests differences in growth rates and/or host colonization patterns. We identified genotypic variation potentially responsible for divergent strain ecologies, including hotspots of sequence variation in regulatory genes and intergenic regions, and in genes involved in transport, flagellar biosynthesis, substrate metabolism, and host colonization, as well as differences in the complements of these genes. Our results demonstrate that a community genomic approach can elucidate gut microbial colonization at the resolution required to discern medically relevant strain and species population dynamics, and hence improve our ability to diagnose and treat microbial community-mediated disorders.
DOI: 10.26036/cnphis0001220
title: Gasterosteus aculeatus Genome sequencing

description: Threespine stickleback Gasterosteus aculeatus is an excellent model to study adaptation genomics. Marine and freshwater morphs of threespine sticklebacks differ from each other in a number of morphological, physiological and bihavioral traits, but retain the ability to mate and produce fertile offspring. We sequenced individuals from two marine and two freshwater populations in order to find substitutions responsible for adaptation to fresh water. We also sequenced additional populations: from two lakes and two quarries, to measure densities of freshwater alleles in marker SNPs in these populations.
DOI: 10.26036/cnphis0000586
title: 2012_sequencing_platform_comparison

description: This is a study to compare Illumina Miseq, HiSeq and GAIIx with Ion Torrent and PacBio. 4 test genomes with widely different GC content are sequenced with each platform. Specifically these are Bordetella pertussis (67.7 % GC, with some regions in excess of 90% GC content), Salmonella Pullorum (52% GC), Staphylococcus aureus (33%GC) and Plasmodium falciparum (19.3% GC, with some regions close to 0% GC content).
DOI: 10.26036/cnphis0000907
title: Profiling of differential allelic expression in horse, donkey, mule, and hinny placental tissues.

description: In eutherian mammals, dosage compensation of X-linked genes is achieved by X chromosome inactivation. X inactivation is random in embryonic and adult tissues, but imprinted X inactivation (paternal X silencing) has been identified in the extraembryonic membranes of the mouse, rat, and cow. Few other species have been studied for this trait, and the data from studies of the human placenta have been discordant or inconclusive. Here, we quantify X inactivation using RNA sequencing of placental tissue from reciprocal hybrids of horse and donkey (mule and hinny). In placental tissue from the equid hybrids and the horse parent the allelic expression pattern was consistent with random X inactivation, and imprinted X inactivation can clearly be excluded. We characterized horse and donkey XIST gene, and demonstrated that XIST allelic expression in female hybrid placental and fetal tissues is negatively correlated with the other X-linked genes chromosome-wide, which is consistent with the XIST-mediated mechanism of X inactivation discovered previously in mice. As the most structurally and morphologically diverse organ in mammals, the placenta also appears to show diverse mechanisms for dosage compensation that may result in differences in conceptus development across species. Overall design: Examine allelic expression from individual samples of invasive trophoblast tissue of the chorionic girdle from gestation day 33-34 conceptuses of 5 horses, 3 donkeys, 6 mules, and 1 hinny.
DOI: 10.26036/cnphis0001223
title: Elopichthys bambusa Transcriptome or Gene expression

description: Elopichthys bambusa transtriptome sequencing using Illumina HiSeq 2000, together with the published Hypophthalmichthys molitrix and Megalobrama amblycephala transcriptome to study the speciation of endemic cyprinidae of East Asia.
DOI: 10.26036/cnphis0001494
title: GenomeTrakr real-time SE: NY State Dept. of Health, Wadsworth Center

description: Surveillance of Salmonella Enteritidis using SNP based phylogenetic analysis
DOI: 10.26036/cnphis0001496
title: Euproctis chrysorrhoea de novo transcriptome

description: de novo transcriptome analysis of Euproctis chrysorrhoea to identify candidate genes involved in host switch and early diapause termination
DOI: 10.26036/cnphis0001615
title: Locusta migratoria Variation

description: Study of repeated sequences in the grasshopper Eyprepocnemis plorans
DOI: 10.26036/cnphis0001681
title: Single cell RNA-seq of primary human glioblastomas

description: We report transcriptomes from 430 single glioblastoma cells isolated from 5 individual tumors and 102 single cells from gliomasphere cells lines generated using SMART-seq. In addition, we report population RNA-seq from the five tumors as well as RNA-seq from cell lines derived from 3 tumors (MGH26, MGH28, MGH31) cultured under serum free (GSC) and differentiated (DGC) conditions. This dataset highlights intratumoral heterogeneity with regards to the expression of de novo derived transcriptional modules and established subtype classifiers. Overall design: Operative specimens from five glioblastoma patients (MGH26, MGH28, MGH29, MGH30, MGH31) were acutely dissociated, depleted for CD45+ inflammatory cells and then sorted as single cells (576 samples). Population controls for each tumor were isolated by sorting 2000-10000 cells and processed in parallel (5 population control samples). Single cells from two established cell lines, GBM6 and GBM8, were also sorted as single cells (192 samples). SMART-seq protocol was implemented to generate single cell full length transcriptomes (modified from Shalek, et al Nature 2013) and sequenced using 25 bp paired end reads. Single cell cDNA libraries for MGH30 were resequenced using 100 bp paired end reads to allow for isoform and splice junction reconstruction (96 samples, annotated MGH30L). Cells were also cultured in serum free conditions to generate gliomasphere cell lines for MGH26, MGH28, and MGH31 (GSC) which were then differentiated using 10% serum (DGC). Population RNA-seq was performed on these samples (3 GSC, 3 DGC, 6 total). The initial dataset included 875 RNA-seq libraries (576 single glioblastoma cells, 96 resequenced MGH30L, 192 single gliomasphere cells, 5 tumor population controls, 6 population libraries from GSC and DGC samples). Data was processed as described below using RSEM for quantification of gene expression. 5,948 genes with the highest composite expression either across all single cells combined (average log2(TPM)&gt;4.5) or within a single tumor (average log2(TPM)&gt;6 in at least one tumor) were included. Cells expressing less than 2,000 of these 5,948 genes were excluded. The final processed dataset then included 430 primary single cell glioblastoma transcriptomes, 102 single cell transcriptomes from cell lines(GBM6,GBM8), 5 population controls (1 for each tumor), and 6 population libraries from cell lines derived from the tumors (GSC and DGC for MGH26, MGH28 and MGH31). The final matrix (GBM_data_matrix.txt) therefore contains 5948 rows (genes) quantified in 543 samples (columns). Please note that the samples which are not included in the data processing are indicated in the sample description field.
DOI: 10.26036/cnphis0001683
title: Paragonimus westermani Genome sequencing

description: Identification of the most prevalent food/waterborne trematode parasites {liver flukes (Fasciola gigantica, Opisthorchis spp.), Intestinal flukes (Fasciolopsis buski, Artyfechinostoma surfratyfex), lungflukes (Paragonimus westermani) and Gastrodiscoides hominis) that are recognized as having zoonotic potential in the NE Region and extraction of their DNA and polyA+ RNA of high quality. ?Sequencing of the DNA and polyA+ RNA preparations using Illumina platform. ?Molecular characterization and partial/complete genome information for these choosen parasites. ?Genetic makeup of the species ?Functional genome and transcriptome analysis ?Identification of characteristic markers for the parasites ?Creation of a webserver for the sequence data
DOI: 10.26036/cnphis0001747
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001862
title: GenomeTrakr Project: United Kingdom, Food and Environment Research Agency

description: Whole genome sequencing of cultured Salmonella as part of a joint Fera, Food Standards Agency, US Food and Drug Administration project.
DOI: 10.26036/cnphis0001895
title: Black and white colobus reference genome project

description: A high quality draft sequence of the reference genome will be assembled from a single sample of Colobus angolensis, using read data produced by the Illumina platform. In addition to the deep genome sequence coverage for the reference colobus, BCM-HGSC will generate whole genome sequences from additional colobus monkeys in order to identify DNA sequence variation for this species.
DOI: 10.26036/cnphis0001232
title: Balaenoptera acutorostrata scammoni Genome sequencing

description: To provide a full genome sequence of the most abundant whale species in the world. It will provide a genetic diversity of the species and will help us understand how whales adapt to environmental stresses. Also, as whales are long-living, the genome comparisons may provide clues to their longevity. Finally, this study will help us figure out the evolution and phylogeny of whale.
DOI: 10.26036/cnphis0001493
title: Glossina austeni Genome sequencing and assembly

description: Glossina austeni is a major vector of the animal trypanosomes that cause nagana (sleeping sickness). The phylogenetic relationship of G. austeni to Palpalis and Morsitans complexes is unclear. Genomic data from this project will contribute to the understanding of Glossina biology and the broader field of vector biology.
DOI: 10.26036/cnphis0002302
title: Gelsemium sempervirens Transcriptome or Gene expression

description: Transcriptome sequencing of medicinal plant Gelsemium sempervirens
DOI: 10.26036/cnphis0002339
title: Centropyge flavissima strain:Cocos-Keeling Island Genome sequencing

description: Samples of Centropyge flavissima (voucher no. 364) were purchased from local aquarium and originally imported from Cocos-Keeling Island . Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002687
title: Helicoverpa zea Genome sequencing and assembly

description: Helicoverpa zea is a major pest of agriculture in the New World. This project has generated the first complete genome for this species, using both 454 and Illumina sequencing technology, and working in collaboration with the Baylor Human Genome Sequencing Centre.
DOI: 10.26036/cnphis0002712
title: Seriola lalandi intestinal directed Metagenome

description: Metagenomic directed of fish intestinal content
DOI: 10.26036/cnphis0001061
title: Brassica rapa subsp. chinensis strain:Wu Genome sequencing

description: Non-heading Chinese cabbage.
DOI: 10.26036/cnphis0001796
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0002054
title: Phlebotomus duboscqi genome sequencing.

description: Proposal for Sequencing the Genome of the Sand Flies, Lutzomyia longipalpis and Phlebotomus papatasi
DOI: 10.26036/cnphis0002318
title: Apolemichthys kingi Genome sequencing

description: Samples of Apolemichthys kingi (voucher no. 229) were purchased from local aquarium and originally imported from Durban, South Africa. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002503
title: Antheraea assamensis Mitochondrial Genome

description: Complete Mitochondrial Genome of Antheraea assamensis (Indian Muga silkmoth)
DOI: 10.26036/cnphis0002726
title: Capra hircus Raw sequence reads

description: Capra hicrus genome sequencing
DOI: 10.5441/001/1.1j802v05/1
title: Asian Openbill tagging with satellite telemetry in Thailand, 2007-2013

description: Ratanakorn P, Suwanpakdee S, Wiriyarat W, Eiamampai K, Chaichoune K, Wiratsudakul A, Sariya L, Puthavathana P (2018) Satellite telemetry tracks flyways of Asian Openbill storks in relation to H5N1 avian influenza spread and ecological change. BMC Veterinary Research 14(1):349. doi:10.1186/s12917-018-1683-x
description: Background: Asian Openbills, Anastomus oscitans, have long been known to migrate from South to Southeast Asia for breeding and nesting. In Thailand, the first outbreak of H5N1 highly pathogenic avian influenza (HPAI) infection in the Openbills coincided with the outbreak in the poultry. Therefore, the flyways of Asian Openbills was determined to study their role in the spread of H5N1 HPAI virus to poultry and wild birds, and also within their flocks. Results: Flyways of 5 Openbills from 3 colonies were monitored using Argos satellite transmitters with positioning by Google Earth Programme between 2007 and 2013. None of the Openbills tagged with satellite telemeters moved outside of Thailand. Their home ranges or movement areas varied from 1.6 to 23,608 km2 per month (95% utility distribution). There was no positive result of the viral infection from oral and cloacal swabs of the Openbills and wild birds living in the vicinity by viral isolation and genome detection during 2007 to 2010 whereas the specific antibody was not detected on both Openbills and wild birds by using microneutralization assay after 2008. The movement of these Openbills did not correlate with H5N1 HPAI outbreaks in domestic poultry but correlated with rice crop rotation and populations of the apple snails which are their preferred food. Viral spread within the flocks of Openbills was not detected. Conclusions: This study showed that Openbills played no role in the spread of H5N1 HPAI virus, which was probably due to the very low prevalence of the virus during the monitoring period. This study revealed the ecological factors that control the life cycle of Asian Openbills.
DOI: 10.5441/001/1.1j802v05/2
title: Asian Openbill tagging with satellite telemetry in Thailand, 2007-2013-reference-data

description: Ratanakorn P, Suwanpakdee S, Wiriyarat W, Eiamampai K, Chaichoune K, Wiratsudakul A, Sariya L, Puthavathana P (2018) Satellite telemetry tracks flyways of Asian Openbill storks in relation to H5N1 avian influenza spread and ecological change. BMC Veterinary Research 14(1):349. doi:10.1186/s12917-018-1683-x
description: Background: Asian Openbills, Anastomus oscitans, have long been known to migrate from South to Southeast Asia for breeding and nesting. In Thailand, the first outbreak of H5N1 highly pathogenic avian influenza (HPAI) infection in the Openbills coincided with the outbreak in the poultry. Therefore, the flyways of Asian Openbills was determined to study their role in the spread of H5N1 HPAI virus to poultry and wild birds, and also within their flocks. Results: Flyways of 5 Openbills from 3 colonies were monitored using Argos satellite transmitters with positioning by Google Earth Programme between 2007 and 2013. None of the Openbills tagged with satellite telemeters moved outside of Thailand. Their home ranges or movement areas varied from 1.6 to 23,608 km2 per month (95% utility distribution). There was no positive result of the viral infection from oral and cloacal swabs of the Openbills and wild birds living in the vicinity by viral isolation and genome detection during 2007 to 2010 whereas the specific antibody was not detected on both Openbills and wild birds by using microneutralization assay after 2008. The movement of these Openbills did not correlate with H5N1 HPAI outbreaks in domestic poultry but correlated with rice crop rotation and populations of the apple snails which are their preferred food. Viral spread within the flocks of Openbills was not detected. Conclusions: This study showed that Openbills played no role in the spread of H5N1 HPAI virus, which was probably due to the very low prevalence of the virus during the monitoring period. This study revealed the ecological factors that control the life cycle of Asian Openbills.
DOI: 10.5441/001/1.4f03k6s5/1
title: Gyps vultures with Pitot airspeed at Rocamadour (data from Williams et al. 2018)

description: Williams HJ, Duriez O, Holton MD, Dell-Omo G, Wilson RP, Shepard ELC (2018) Vultures respond to challenges of near-ground thermal soaring by varying bank angle. Journal of Experimental Biology: jeb.174995. doi:10.1242/jeb.174995
description: Many large birds rely on thermal soaring flight to travel cross-country. As such, they are under selective pressure to minimise the time spent gaining altitude in thermal updrafts. Birds should be able to maximise their climb rates by maintaining a position close to the thermal core through careful selection of bank angle and airspeed, however, there have been few direct measurements of either parameter. Here we apply a novel methodology to quantify the bank angles selected by soaring birds using on-board magnetometers. We couple these data with airspeed measurements to parameterise the soaring envelope of two species of Gyps vulture, from which it is possible to predict “optimal” bank angles. Our results show that these large birds respond to the challenges of gaining altitude in the initial phase of the climb, where thermal updrafts are weak and narrow, by adopting relatively high, and conserved, bank angles (25-35°). The angle of bank decreased with increasing altitude, in a manner that was broadly consistent with a strategy of maximising the rate of climb. However, the lift coefficients estimated in our study were lower than those predicted by theoretical models and wind-tunnel studies. Overall, our results highlight how the relevant currency for soaring performance changes within individual climbs; when thermal radius is limiting, birds vary bank angle and maintain a constant airspeed, but speed increases later in the climb in order to respond to decreasing air density.
DOI: 10.5441/001/1.4f03k6s5/2
title: Gyps vultures with Pitot airspeed at Rocamadour (data from Williams et al. 2018)-reference-data

description: Williams HJ, Duriez O, Holton MD, Dell-Omo G, Wilson RP, Shepard ELC (2018) Vultures respond to challenges of near-ground thermal soaring by varying bank angle. Journal of Experimental Biology: jeb.174995. doi:10.1242/jeb.174995
description: Many large birds rely on thermal soaring flight to travel cross-country. As such, they are under selective pressure to minimise the time spent gaining altitude in thermal updrafts. Birds should be able to maximise their climb rates by maintaining a position close to the thermal core through careful selection of bank angle and airspeed, however, there have been few direct measurements of either parameter. Here we apply a novel methodology to quantify the bank angles selected by soaring birds using on-board magnetometers. We couple these data with airspeed measurements to parameterise the soaring envelope of two species of Gyps vulture, from which it is possible to predict “optimal” bank angles. Our results show that these large birds respond to the challenges of gaining altitude in the initial phase of the climb, where thermal updrafts are weak and narrow, by adopting relatively high, and conserved, bank angles (25-35°). The angle of bank decreased with increasing altitude, in a manner that was broadly consistent with a strategy of maximising the rate of climb. However, the lift coefficients estimated in our study were lower than those predicted by theoretical models and wind-tunnel studies. Overall, our results highlight how the relevant currency for soaring performance changes within individual climbs; when thermal radius is limiting, birds vary bank angle and maintain a constant airspeed, but speed increases later in the climb in order to respond to decreasing air density.
DOI: 10.6084/m9.figshare.12981818
title: Male fertility assay

description: Numerical data on male fertility following RNAi in Tribolium beetles<br>
DOI: 10.14284/326
title: ScheldeMonitor: dataportaal met informatie, data en producten over het Schelde-estuarium
title: ScheldeMonitor: a data portal with information, data and products on the Scheldt Estuary

description: ScheldeMonitor (set up in 2004) is an online accessible database, which contains information on ongoing and past research and monitoring conducted in the Scheldt estuary. At the moment several information modules can be consulted: Persons, Institutes, Publications, Datasets and Maps. Also a dataplatform, dataproducts and geoviewer are available. This information system was set up in the framework of "long-term planning of the Scheldt estuary", which is a cooperation between Flanders and The Netherlands.