cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0000446
title: Genome sequencing of PGD-trios

description: These data contains sequencing reads of 4 samples, including the g-DNA of the parents (blood), proband sister (blood), and IVF embryo (AF). Also, the single cell sequencing of the IVF embryo is included.
DOI: 10.26036/cnphis0001150
title: GenomeTrakr Project: US Food and Drug Administration

description: Currently encompasses whole genome sequencing of cultured pathogens as part of a surveillance project for the rapid detection of outbreaks of foodborne illnesses
DOI: 10.26036/cnphis0001151
title: Thamnophis sirtalis Genome sequencing and assembly

description: Research on the comparative genomics of mammals is now in high gear with the completion of complete genome sequences for several species and many additional species receiving high priority for lower coverage genomic sequencing. By contrast, the comparative genomics of Reptilia-the sister group of mammals, which includes birds and non-avian reptiles lags far behind. Although the recently completed chicken genome has made a significant contribution, there is nonetheless an urgent need to build genomic resources for the reptiles, the only major vertebrate lineage for which there is still no complete genome sequence. Only through studying the sister group of mammals will the idiosyncrasies of mammalian genome evolution become apparent. Furthermore, a number of reptile lineages serve as important models for developmental biology, neurobiology, physiology, endocrinology and other fields.
DOI: 10.26036/cnphis0001152
title: Mesocyclops edax Random survey

description: Here, we used high-throughput genomic sequencing to characterize the germline and somatic genomes of Mesocyclops edax, a freshwater cyclopoid copepod with a germline genome of ~15 Gb and a somatic genome of ~3 Gb.
DOI: 10.26036/cnphis0001153
title: Chinese pangolin, sometimes referred to as the spiny anteater

description: The <i>Manis pentadactyla</i> genome is being sequenced to ~2X coverage by the Washington University School of Medicine Genome Sequencing Center using a whole genome shotgun sequencing strategy.
DOI: 10.26036/cnphis0001154
title: Pseudopodoces humilis Transcriptome data used for gene annotation

description: To optimize the genome annotation, two tissue RNA libraries (i.e. liver and muscle) were constructed using the Illumina mRNA-Seq Prep Kit This study is a part of the Pseudopodoces humilis WGS project (BioProject ID: PRJNA179234) and was used for gene annotation improvement. Overall design: We sequenced two tissues using illumina Hiseq 2000 platform.
DOI: 10.26036/cnphis0001155
title: Haemorhous mexicanus Transcriptome or Gene expression

description: Identifying genes influenced by natural selection can provide information about lineage specific adaptations, and transcriptomes generated by next-generation sequencing are a useful resource for identifying such genes. Here we utilize a spleen transcriptome for the house finch (Haemorhous mexicanus), an emerging model for sexual selection and disease ecology, together with previously sequenced avian genomes (chicken, turkey, zebra finch), to investigate lineage-specific adaptations within birds. An analysis of 4398 orthologous genes revealed a significantly higher ratio of non-synonymous to synonymous substitutions and significantly higher GC content in passerines than in galliforms, an observation deviating from strictly neutral expectations but consistent with an effect of biased gene conversion on the evolutionary rate in passerines. The data also showed that genes exhibiting signs of positive selection and fast evolution in passerines have functional roles related to fat metabolism, neurodevelopment and ion binding.
DOI: 10.26036/cnphis0001156
title: Linking Lifestyle to the Oral and Gut Microbiota in a Large Prospective Cohort

description: Associating the biomolecular and metabolic activities of human-associated microbial communities with environment, diet, and conditions such as inflammatory bowel disease remains a significant challenge despite an ever-improving understanding of the human microbiome. This project aims to pilot detection of taxonomic and functional shifts with respect to diet and gastrointestinal disease status in a large prospective cohort: 1. We will establish a reliable and scalable collection method for the oral and gut microbiota. This will determine whether shippable collection kits are comparable to fresh frozen stool and/or saliva samples. 2. We will test the hypothesis that a Western dietary pattern correlates with microbiome community structures or functions enriched in inflammatory bowel disease in either the oral (saliva) or gut (stool) microbiota. By providing methodology to understand the human microbiome from the molecular to the population level, we hope to enable its future use as a diagnostic indicator and as a point of intervention to improve outcomes in IBD and other chronic diseases.
DOI: 10.26036/cnphis0001157
title: Canis lupus familiaris Genome sequencing

description: These are the DNA sequences generated in a requencing study looking at dog domestication. The details of the analysis can be found in the publication associated with this data.
DOI: 10.26036/cnphis0001158
title: Elysia chlorotica Genome sequencing

description: Elysia chlorotica germ line (egg) genome sequencing.
DOI: 10.26036/cnphis0001159
title: Dromaius novaehollandiae Embryonic Transcriptome

description: RNA-sequencing of emu (Dromaius novaehollandiae) male and female embryonic head/brain at 15 and 42 days of development.
DOI: 10.26036/cnphis0001831
title: Megachile rotundata genome sequencing project

description: Megachile rotundata, alfalfa leafcutting bee, is a solitary bee species. It is the #3 agricultural pollinator in the United States and is commercially managed for alfalfa seed production. A paper describing this project and its associated data has not been published at this time.
DOI: 10.26036/cnphis0001832
title: Cardiocondyla obscurior strain:BR alpha Variation

description: Trait variation between populations is a result of selection, genetic drift, or a combination of both. Adaptive evolution is based on selection of alternative phenotypes, implying heritable variation at the genotypic or epigenetic level. Genetic drift on the other hand results in a random distribution of genotypes drawn from a source population. We studied phenotypic differences and analyzed the genome of two introduced populations of the invasive ant Cardiocondyla obscurior to understand how variation is generated. In comparison to other sequenced ants, several subclasses of transposable elements (TEs) have selectively proliferated in C. obscurior. The genome is structured into low-density regions (LDRs) and distinct TE islands that comprise 7.18% of the genome and range between 0.19 and 1.46 Mb. TE islands evolve faster than LDRs with regard to SNVs, gene/exon duplications/deletions, and degree of orthology. A non-random distribution of gene families, larvae/adult specific expression of genes and signs of stronger past methylation in TE islands compared to LDRs indicate different degrees of evolutionary rates and differences in effective population size within the genome. We argue that TE islands have formed through genetic drift and have subsequently become adaptive by generating a substantial proportion of the genetic diversity and thus provide additional leverage for selection. Our approach allows studying genome evolution dynamics in response to drift and inbreeding in a species that successfully colonizes novel habitats.
DOI: 10.26036/cnphis0001833
title: Lamprotornis superbus transcriptome sequencing

description: Transcriptome sequencing from 4 Lamprotornis superbus females
DOI: 10.26036/cnphis0001834
title: Wheatstem sawfly Cephus cinctus Genome Sequencing

description: The wheatstem sawfly, Cephus cinctus, is a major pest of wheat in the USA, especially in the west. It also represents a basal herbivorous lineage of the insect order Hymenoptera.
DOI: 10.26036/cnphis0001835
title: Blattella germanica strain:American Cyanamid = Orlando Normal Genome sequencing

description: Whole genome assembly of German cockroach (Blattella germanica) as part of the BCM-HGSC i5k Pilot Project.
DOI: 10.26036/cnphis0001836
title: Epigenetic reprogramming and small RNA silencing of transposable elements in pollen.

description: The mutagenic activity of transposable elements (TEs) is suppressed by epigenetic silencing and small interfering RNAs (siRNAs), especially in gametes that would transmit transposed elements to the next generation. In pollen from the model plant Arabidopsis, we show that TEs are unexpectedly reactivated and transpose, but only in the pollen vegetative nucleus, which accompanies the sperm cells but does not provide DNA to the fertilized zygote. TE expression coincides with down-regulation of the heterochromatin remodeler DECREASE IN DNA METHYLATION 1 and of most TE siRNAs. However, 21 nucleotide siRNA from Athila retrotransposons is generated in pollen and accumulates in sperm, indicating that siRNA from TEs activated in the vegetative nucleus can target silencing in gametes. We propose a conserved role for reprogramming in germline companion cells, such as nurse cells in insects and vegetative nuclei in plants, to reveal intact TEs in the genome and regulate their activity in gametes. Overall design: Mature pollen was collected from Columbia reference strain plants by vacuum filtration (Johnson-Brousseau and McCormick, 2004). DNA and RNA were isolated from a ddm1-2 plant in the Columbia reference background. Small RNAs of 19–28 nt were size selected by denaturing 15% PAGE, and cloned as in Brennecke et al. (2007). Additional details regarding the cloning of small RNAs are found in the Supplemental Data. The small RNA libraries were sequenced on Illumina 1G sequencer. The total number of sequences perfectly matching the Arabidopsis genome were as follows: WT inflorescence, 4,158,848 (2,286,133 unique); WT pollen, 1,034,665 (437,984 unique); ddm1 inflorescence, 4,098,772 (1,637,771 unique); and WT sperm, 760,651 (429,972 unique).
DOI: 10.26036/cnphis0001838
title: Meleagris gallopavo Transcriptome expression in multiple tissues at 0, 7, 14, 21 and 28 days for both sexes

description: None
DOI: 10.26036/cnphis0001839
title: GenomeTrakr Project: Belgium

description: Whole genome sequencing of cultured Salmonella enterica as part of FDA/CFSAN''s surveillance project for rapid source tracking of foodborne illness outbreaks.
DOI: 10.26036/cnphis0001840
title: Mizuhopecten yessoensis strain:PY_sf001 Genome sequencing and assembly

description: Genome sequencing of Patinopecten yessoensis for understanding the biology and evolution of Pectinidae.
DOI: 10.26036/cnphis0000447
title: Capsicum annuum cultivar:Zunla1 Genome sequencing and assembly

description: Comparative study of domesticated pepper and its progenitor genome reveal signature of artificial selection. C. annuum var. annuum L. and C. annuum var. glabriusculum
DOI: 10.26036/cnphis0000448
title: Pyrus x bretschneideri Transcriptome or Gene expression

description: To research the characterization of expression in the cell of pear fruit, we sequenced 6 samples of pear fruit and obtained the raw data.
DOI: 10.26036/cnphis0000449
title: Mycobacterium tuberculosis Genome sequencing

description: Here we describe genomic sequencing and analysis of the clinical isolates with a range of DR profiles which led to the discovery of some genes or IGRs systematically closely associated with drug resistant.
DOI: 10.26036/cnphis0000450
title: Insect communities Metagenome

description: Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification. Insect communities collected from a terrestrial, sub-tropical, broad leaf, rich vegetation region.
DOI: 10.26036/cnphis0000451
title: Triticum urartu Genome sequencing

description: Re-seq project of Triticum urartu.
DOI: 10.26036/cnphis0000452
title: Fanconi anaemia Exome

description: We sequenced 16 human by exome.
DOI: 10.26036/cnphis0000453
title: AGS cell line and AGS-EBV cell line Transcriptome or Gene expression

description: The gastric cancer cell line AGS was purchased from the American Type Culture Collection (ATCC). And the AGS-EBV is the AGS cell line was infected by EBV
DOI: 10.26036/cnphis0000454
title: AGS cell line and AGS-EBV cell line Genome sequencing

description: The gastric cancer cell line AGS was purchased from the American Type Culture Collection (ATCC). And the AGS-EBV is the AGS cell line was infected by EBV
DOI: 10.26036/cnphis0001160
title: Dromaius novaehollandiae Genome sequencing

description: Emu (Dromaius novaehollandiae) Whole Genome sequencing.
DOI: 10.26036/cnphis0001161
title: RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655

description: Expression profiles of wild-type and SgrR mutant E. coli strains under aMG and 2-DG-induced stress. Expression profiles of E. coli overexpressing SgrS sRNA. Overall design: Illumina RNA-Seq of total RNA extracted from wild-type, SgrR/SgrS mutant and SgrS overexpressing E. coli strains grown in different conditions.
DOI: 10.26036/cnphis0001162
title: Anas platyrhynchos Transcriptome or Gene expression

description: duck with virus
DOI: 10.26036/cnphis0001163
title: CGCI: Non-Hodgkin Lymphoma (NHL)

description: The Office of Cancer Genomics (OCG) at the National Cancer Institute is sponsoring a series of studies as part of the Cancer Genome Characterization Initiative (CGCI) to assess novel emerging sequencing technologies in cancer. The CGCI program includes comprehensive characterization of the genetic aberrations found in different pediatric and/or adult tumors. CGCI is currently characterizing a number of B-cell non-Hodgkin lymphomas (including diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL), and adult and pediatric Burkitt lymphomas). In combination, the lymphoid cancers (non-Hodgkin lymphoma, Hodgkin lymphoma, myeloma and chronic lymphocytic leukemia), constitute the fourth most common malignancy in both men and women in North America. Lymphomas typically have characteristic abnormal chromosomes, including translocations, indicating the relevance of mutations to how NHLs develop and behave. This project uses detailed analysis on a specific... (for more see dbGaP study page.)
DOI: 10.26036/cnphis0001164
title: Adineta vaga Genome sequencing

description: This data is part of a project to sequence the complete genome of Adineta vaga. The data was used to error-check homopolymers in a 454 assembly and to verify scaffold assembly.
DOI: 10.26036/cnphis0001165
title: Salmonella enterica subsp. enterica serovar Typhimurium str. L945 Genome sequencing and assembly

description: Salmonella enterica L945 Genome sequencing.
DOI: 10.26036/cnphis0001166
title: Salmonella enterica subsp. enterica serovar Typhimurium str. L927 Genome sequencing and assembly

description: Salmonella enterica L927 Genome sequencing.
DOI: 10.26036/cnphis0001167
title: Salmonella enterica subsp. enterica serovar Typhimurium str. L904 Genome sequencing and assembly

description: Salmonella enterica L904 Genome sequencing.
DOI: 10.26036/cnphis0001837
title: Convergent genetic architecture underlies social organization in ants: Formica selysi Genome sequencing

description: Complex adaptive polymorphisms are common in nature, but what mechanisms maintain the underlying favourable allelic combinations? The convergent evolution of polymorphic social organization in two independent ant species provides a great opportunity to investigate how genomes evolved under parallel selection. Here, we demonstrate that a large, non-recombining ‘social chromosome’ is associated with social organization in the alpine ant Formica selysi. This social chromosome shares architectural characteristics with that of the fire ant Solenopsis invicta, but the two show no detectable similarity in gene content. The discovery of convergence at two levels – the phenotype and the genetic architecture associated with alternative social forms – points at general genetic mechanisms underlying transitions in social organization. More broadly, our findings are consistent with recent theoretical studies suggesting that suppression of recombination plays a key role in facilitating coordinated shifts in co-adapted traits.
DOI: 10.26036/cnphis0001841
title: A public-private-academic consortium hosted by NIST to develop reference materials and standards for clinical sequencing

description: The Genome in a Bottle Consortium (www.genomeinabottle.org) is a collaboration between NIST, FDA, NCBI, other government agencies, academic sequencing groups, sequencing technology developers, and clinical laboratories. A principal motivation for this consortium is to develop widely accepted reference materials and accompanying performance metrics to provide a strong scientific foundation for the development of regulations and professional standards for clinical sequencing. NIST is developing large batches of human genome DNA from several cell lines for NIST Reference Materials (RMs), which will be characterized by the Consortium for homogeneity, stability, and sequence with as much sequencing technologies and library preparation methods as possible. Information from these datasets will be integrated to form a high-confidence set of genotype calls, which can be used by clinical and research laboratories to understand performance of their sequencing and bioinformatics methods. NCBI is serving as the DCC and repository for the raw sequencing reads, mapped reads, genotypes, and other details for each sample on a dedicated FTP site ( ftp://ftp-trace.ncbi.nih.gov/giab/ftp/ ). The pilot sample is NA12878 (HG001), and NIST received over 8,000 aliquots in April 2013, which will initially be distributed to partners in the Consortium to assist in characterization, and later will be distributed by NIST as Reference Material 8398, likely in March or April 2015. Samples from an Ashkenazim trio (son HG002-NA24385-huAA53E0, father HG003-NA24149-hu6E4515, and mother HG004-NA24143-hu8E87A9), and a Han Chinese trio (son HG005-NA24631-hu91BD69, father NA24694-huCA017E, and mother NA24695-hu38168C) from Personal Genome Project (PGP) are also candidate NIST reference materials and are currently being characterized. The Ashkenazim trio will be available both as NIST RMs 8391 (son only) and 8392 (entire trio). Only the son of the Asian trio will be a NIST RM (8393). DNA and cell lines for all samples are also available from Coriell, but the NIST RMs are from a single homogenized batch of DNA, so there may be small differences between the samples at Coriell and the NIST RMs. Details about the NIST Reference Materials, data, and future plans are at https://sites.stanford.edu/abms/content/giab-reference-materials-and-data. When the NIST RMs are available, they can be purchased from NIST at http://www.nist.gov/srm/, where a Report of Investigation describing the DNA will also be available.
DOI: 10.26036/cnphis0001842
title: Trigoniulus corallinus strain:Rusty/Coral Millipede Genome sequencing

description: Sequencing of the Rusty/Coral Millipede (Trigoniulus corallinus) genome for use in a range of biological investigations
DOI: 10.26036/cnphis0001843
title: Paragonimus miyazakii Genome sequencing

description: Paragonimus spp., lung flukes, represent one of the most injurious of the food-borne helminths. These flukes cause paragonimiasis in people and other crab-eating mammals in Asia, parts of West Africa, and South and Central America. About 20 milion people are infected with lung flukes and an estimated 293 million people are at risk.
DOI: 10.26036/cnphis0001844
title: Trioxys pallidus Genome sequencing

description: Raw sequence reads were used to identify polymorphic microsatellite markers using a novel pipeline we developed iMSAT available through source forge.
DOI: 10.26036/cnphis0001845
title: Pol-IV dependent transcripts in Arabidopsis

description: small RNA, PATH and mRNA libraries were made to characterize Col and various small RNA biogenesis mutants. Overall design: Genome-wide RNA profiling was done by Illumina TruSeq sample preparation kits followed by high-throughput sequencing with Illumina HiSeq 2500 platform.
DOI: 10.26036/cnphis0001846
title: Propithecus coquereli Genome sequencing

description: Propithecus coquereli Genome sequencing and Diversity Panel
DOI: 10.26036/cnphis0001847
title: Salmonella enterica Genome sequencing

description: Surveillance of Salmonella Enteritidis using SNP based phylogenetic analysis.
DOI: 10.26036/cnphis0001848
title: Kudoa iwatai isolate:KIW-1.11.2010 Genome sequencing and assembly

description: Kudoa iwatai genomic sequencing for phylogenetic and genomic analysis. Sequencing technology: Illumina HiSeq
DOI: 10.26036/cnphis0001850
title: Molecular signatures of heterogeneous stem cell populations are resolved by linking single cell functional assays to single cell gene expression

description: The discovery of significant heterogeneity in the self-renewal durability of adult haematopoietic stem cells (HSCs) has challenged our understanding of the molecules involved in population maintenance throughout life. Gene expression studies in bulk populations are difficult to interpret since multiple HSC subtypes are present and HSC purity is typically less than 50% of the input cell population. Numerous groups have therefore turned to studying gene expression profiles of single HSCs, but again these studies are limited by the purity of the input fraction and an inability to directly ascribe a molecular program to a durable self-renewing HSC. Here we combine single cell functional assays with flow cytometric index sorting and single cell gene expression assays to gain the first insight into the gene expression program of HSCs that possess durable self-renewal. This approach can be used in other stem cell systems and sets the stage for linking key molecules with defined cellular functions. Overall design: single-cell RNA-Seq of haematopoietic stem cells
DOI: 10.26036/cnphis0000455
title: honeybee metagenome Metagenome

description: Survey virus in the enviromental samples by NGS sequencing. Foraging female worker honeybee (Apis mellifera) and bumblebee (Bombus pascuorum) individuals were net caught in Sept 2010 from the Bernwood Forest, Oxfordshire, UK.
DOI: 10.26036/cnphis0000456
title: Macrotermes natalensis Transcriptome or Gene expression

description: The sequencing of total RNA from a mixture sample of termite queen, king, worker and soldier.
DOI: 10.26036/cnphis0000457
title: Termitomyces sp. J132 Genome sequencing and assembly

description: Whole genome shoutgun sequence and the assembly of an unknown species in Termitomyces grown by Macrotermes natalensis.
DOI: 10.26036/cnphis0000459
title: De novo assembly and characterization of Litchi fruit transcriptome.SRP020089

description: Litchi (Litchi chinensis Sonn.) is one of the most important tropical and subtropical fruit trees. There is a lack of transcriptomic and genomic information in public databases for understanding the molecular mechanisms underlying fruit set and development in litchi. High throughput transcriptome sequencing is a convenient technique to explore a large quantity of transcript sequences.
DOI: 10.26036/cnphis0000460
title: Noninvasive Zygosity Diagnosis

description: Effective Noninvasive Zygosity Determination by Maternal Plasma Target Region Sequencing.
DOI: 10.26036/cnphis0000461
title: CompleteGenomics sequencing of (CEU) Utah residents with ancestry from Northern and Western Europe - CEPH - HapMap population

description: -
DOI: 10.26036/cnphis0001168
title: Salmonella enterica subsp. enterica serovar Typhimurium str. L852 Genome sequencing and assembly

description: Salmonella enterica L852 Genome sequencing.
DOI: 10.26036/cnphis0001169
title: Salmonella enterica subsp. enterica serovar Typhimurium str. L847 Genome sequencing and assembly

description: Salmonella enterica L847 Genome sequencing.
DOI: 10.26036/cnphis0001170
title: Salmonella enterica subsp. enterica serovar Typhimurium str. L796 Genome sequencing and assembly

description: Salmonella enterica L796 Genome sequencing.