cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0001990
title: Mouse gene expression with age in liver

description: We characterized gene expression in the livers of three 4-month old mice and three 28-month old mice with RNA-seq.
DOI: 10.26036/cnphis0001991
title: Drosophila busckii Genome sequencing

description: Here we collect genome, transcriptome, and epigenome data of D. busckii, to investigate the evolutionary trajectory of sex chromosomes from a heterochromatic ancestor.
DOI: 10.26036/cnphis0001992
title: Junonia iphita Genome sequencing and assembly

description: The Complete mitochondrial genome of Chocolate Pansy, Junonia iphita (Lepidoptera: Nymphalidae: Nymphalinae) collected from Mizoram, India
DOI: 10.26036/cnphis0001993
title: Female-limited color dimorphism in Drosophila kikkawai complex

description: We combine intra- and inter-specific introgression mapping and comparative genomics to identify the genetic loci underlying female-limited color dimorphism in the two closely-related species D. kikkawai and D. leontia.
DOI: 10.26036/cnphis0001994
title: Aedes albopictus Male DNAseq

description: None
DOI: 10.26036/cnphis0001995
title: Daphnia pulex Variation

description: Here, we provide the data for two, Daphnia pulex mutation accumulation lines, each initiated from a distinct genotype and propagated asexually. In total, we provide 7, Illumina paired-end sequenced genomes
DOI: 10.26036/cnphis0001996
title: Mollusc Genome Sequencing (Patella vulgata)

description: Genome sequencing was done using Illumina technology for a mollusc (Patellogastropod limpet), primarily for gene mining.
DOI: 10.26036/cnphis0001997
title: Annelid Genome Sequencing (Pomatoceros lamarcki)

description: Genome sequencing was done using Illumina technology for a serpulid annelid, primarily for gene mining.
DOI: 10.26036/cnphis0001998
title: Whole genome sequencing of Swainson''s thrushes

description: Whole genome sequencing to assemble a draft genome for the Swainson''s thrush. Whole genome re-sequencing of pools from two subspecies groups of the Swainson''s thrush.
DOI: 10.26036/cnphis0000611
title: IWGSC Chromosome sequence survey of hexaploid wheat CS42

description: An international project coordinated by the International Wheat Genome Sequencing Consortium (IWGSC, http://www.wheatgenome.org) to generate sequence reads from each of the 21 individual chromosomes of hexaploid wheat (Chinese Spring line 42). Illumina sequence reads for individual chromosome arms were generated from amplified DNA prepared by flow-sorting chromosomes from aneuploid wheat lines. Sequencing libraries were prepared from sheared 500bp fragments and sequenced on Hi-Seq or GAIIX instruments to produce 100 or 150bp paired reads. Reads were assembled with ABySS to produce a set of contigs for each of the chromosomes that have been used to assess a large part of the gene content of each chromosome and to derive a virtual gene order based on comparative genomics and colinearity with other grass genomes. IWGSC data repository can be accessed here: http://wheat-urgi.versailles.inra.fr/Seq-Repository.
DOI: 10.26036/cnphis0000614
title: Dietary intervention impact on gut microbial gene richness based on SOLiD next generation sequencing technology

description: Complex gene-environment interactions are considered important in the development of obesity. The composition of the gut microbiota can determine the efficacy of energy harvest from food and changes in dietary composition have been associated with changes in the composition of gut microbial populations. The capacity to explore microbiota composition was dramatically improved by the development of metagenomic approaches, which have already allowed production of the first human gut microbial gene catalogue and stratifying individuals by their gut genomic profile into different enterotypes, but the analyses were carried out mainly in non-intervention settings. To investigate the temporal relationships between food intake, gut microbiota and metabolic and inflammatory phenotypes, we conducted diet-induced weight loss and weight stabilisation interventions in a study sample of 38 obese and 11 overweight individuals. Here we report that individuals with reduced microbial gene richness (40%) present more pronounced dys-metabolism and low-grade inflammation, as observed concomitantly in the accompanying paper. Dietary intervention improves low gene richness and clinical phenotypes, but appears to be less efficient for inflammation variables in individuals with lower gene richness, which thus may have predictive potential for the efficacy of intervention.
DOI: 10.26036/cnphis0000615
title: Shotgun Sequencing of Tara Oceans DNA samples corresponding to size fractions for small DNA viruses.

description: Seawater from different depths was precipitaded then filtered to retain small particle sizes (Virus particles). The DNA was extracted and submitted to high throughput sequencing.
DOI: 10.26036/cnphis0000616
title: The aim of this study was to develop a method to allow whole-genome sequencing of major bacterial pathogens directly from single colonies.

description: Objective: As a result of the introduction of rapid benchtop sequencers, the time required to subculture a bacterial pathogen to extract sufficient DNA for library preparation can now exceed the time to sequence said DNA. We have eliminated this rate-limiting step by developing a protocol to generate DNA libraries for whole-genome sequencing directly from single bacterial colonies grown on primary culture plates. Methods: We developed our protocol using single colonies of 17 bacterial pathogens responsible for severe human infection that were grown using standard diagnostic media and incubation conditions. We then applied this method to four clinical scenarios that currently require time-consuming reference laboratory tests: full identification and genotyping of salmonellae; identification of the New Delhi metallo-β-lactamase, a highly transmissible carbapenem-resistance gene, in Klebsiella pneumoniae; detection of staphylococcal toxins associated with specific disease syndromes; and monitoring of vaccine targets to detect vaccine escape in Neisseria meningitidis. Results: We validated our single-colony whole-genome sequencing protocol for all 40 combinations of pathogen and selective, non-selective or indicator media tested in this study. Moreover, we demonstrated the clinical value of this method compared to current reference laboratory tests. Conclusion: This advance will facilitate the implementation of whole-genome sequencing into diagnostic and public health microbiology.
DOI: 10.26036/cnphis0000617
title: Bacterial Natural Transformation by Highly Fragmented and Damaged DNA

description: DNA molecules are continuously released through decomposition of organic matter and are ubiquitous in most environments. Such DNA becomes fragmented and damaged (often &lt;100bp) and may persist in the environment for more than half a million years. Fragmented DNA is recognized as nutrient source for microbes, but not as a potential substrate for bacterial evolution. Here we show that fragmented DNA molecules (longer than 20bp) that additionally may contain abasic sites, crosslinks or miscoding lesions are acquired by the environmental bacterium Acinetobacter baylyi through natural transformation. With uptake of DNA from a 43,000-yaer-old woolly mammoth bone, we further demonstrate that such natural transformation events include ancient DNA molecules. We find that the DNA recombination is RecA recombinase-independent and is directly linked to DNA replication. We show that the adjacent nucleotide variations generated by uptake short DNA fragments escape mismatch repair. Moreover double nucleotide polymorphisms appear more common among genomes of transformable than non-transformable bacteria. Our findings reveal that short and damaged, including truly ancient, DNA molecules, which are present in large quantities in the environment can be acquired by bacteria through natural transformation. Our findings open for the possibility that natural genetic exchange can occur with DNA up to several hundreds of thousands years old.
DOI: 10.26036/cnphis0000618
title: Whole genome sequences of two canine transmissible venereal tumours (CTVTs) and their hosts derived from Australia and Brazil

description: Canine transmissible venereal tumor (CTVT) is the oldest known somatic cell lineage. It is a transmissible cancer that propagates naturally in dogs. We sequenced the genomes of two CTVT tumors and found that CTVT has acquired 1.9 million somatic substitution mutations and bears evidence of exposure to ultraviolet light. CTVT is remarkably stable and lacks subclonal heterogeneity despite thousands of rearrangements, copy number changes and retrotransposon insertions. More than 10,000 genes carry non-synonymous variants and 646 genes have been lost. CTVT first arose in a dog with low genomic heterozygosity that may have lived approximately 11,000 years ago. The cancer spawned by this individual dispersed across continents approximately 500 years ago. Our results provide a genetic identikit of an ancient dog and demonstrate the robustness of mammalian somatic cells to survive for millennia despite a massive mutation burden.
DOI: 10.26036/cnphis0000619
title: European Outbreak of Salmonella Mikawasima in Autumn 2013

description: Whilst in Europe there is a frequent seasonal increase in Salmonella Mikawasima in the last quarter of the year, the increase this year exceeds that usually seen. The UK has borne the majority of the burden (75 of 117 total) of the increase in this rare serotype. Pulsed Field Gel Electrophoresis (PFGE) analysis of the England and Wales strains received during the outbreak time period showed several PFGE patterns with two predominant profiles. Whole genome sequencing was undertaken in order to determine whether strains with these two PFGE patterns varied on a genomic level. The high portability of this data will also allow comparison with European data, as this becomes available.
DOI: 10.26036/cnphis0000620
title: GRC_Tuebingen_DH2_Zebrafish_Whole_Genome_Sequencing

description: Whole genome sequencing of a zebrafish Tuebingen individual (DH2) on Illumina HiSeq2500 to generate a new WGS assembly. This new assembly will be used to supplement the zebrafish clone assembly to produce a new reference genome assembly, GRCz10.
DOI: 10.26036/cnphis0001315
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001316
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001317
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001318
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001319
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001320
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001321
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001322
title: Equus burchellii quagga Genome sequencing

description: Whole genome sequencing of E. q. quagga DNA for the examination of the effects of library preparation
DOI: 10.26036/cnphis0001999
title: Microplitis bicoloratus Transcriptome or Gene expression

description: Development and immunity of Micrioplitis bicoloratus in host Spodoptera litura
DOI: 10.26036/cnphis0002000
title: Bagrus docmak 454 next generation sequencing

description: Microsatellite discovery in a freshwater siluroid, Bagrus docmak
DOI: 10.26036/cnphis0002001
title: Opsaridium microlepis Raw sequence reads

description: Opsaridium microlepis (mpasa) is migratory cyprinid fish endemic to the Lake Malawi catchment that is threatened by overfishing and the alteration of breeding habitats. The sequences were generated for primary purpose of microsatellite DNA locus characterisation/primer development.
DOI: 10.26036/cnphis0002002
title: Pratylenchus coffeae Raw sequence reads

description: Pratylenchus coffeae is a plant-pathogenic nematode infecting several hosts including potato, banana, sweet potato, strawberry, Persian violet, peanut and citrus.
DOI: 10.26036/cnphis0002003
title: Atta cephalotes genome sequencing project

description: This is a de novo whole genome assembly of the Leaf-cutter ant, <i>Atta cephalotes</i>, using genomic DNA from an alate male ant. The approximate average depth of coverage is 18-20x, and the approximate estimated size of the genome is 300 Mbp. The sequencing technology used was 454 Titanium, including shotgun 8-kbp and 20-kbp paired-end sequencing datasets. The assembler software used was 454 GS De novo assembler software (R&D version, 03/06/2010).
DOI: 10.26036/cnphis0002004
title: Danio rerio Genome sequencing

description: To identify genetic variants causing post-developmental liver disease
DOI: 10.26036/cnphis0002005
title: Ovis canadensis Genome sequencing

description: Whole genome sequencing of big horn sheep (Ovis canadensis) to identify variants and genomic regions bearing signatures of historical directional selection (selective sweeps).
DOI: 10.26036/cnphis0002006
title: Gonioctena quinquepunctata Raw sequence reads

description: Two Gonioctena quinquepunctata individuals sampled from different host plants.
DOI: 10.26036/cnphis0000621
title: Phylogeography_of_Shigella_spp__in_Southeast_Asia

description: http://www.sanger.ac.uk/resources/downloads/bacteria/
DOI: 10.26036/cnphis0000622
title: B16-F10 RNA-Seq

description: RNA-Seq of B16-F10 mouse melanoma cell line and gene expression profiling
DOI: 10.26036/cnphis0000623
title: Exploiting the mutanome for tumor vaccination

description: Multiple genetic events and subsequent clonal evolution drive carcinogenesis, making disease elimination with single-targeted drugs difficult. The multiplicity of gene mutations derived from clonal heterogeneity therefore represents an ideal setting for multiepitope tumor vaccination. Here, we used next generation sequencing exome resequencing to identify 962 nonsynonymous somatic point mutations in B16F10 murine melanoma cells, with 563 of those mutations in expressed genes. Potential driver mutations occurred in classical tumor suppressor genes and genes involved in proto-oncogenic signaling pathways that control cell proliferation, adhesion, migration, and apoptosis. Aim1 and Trrap mutations known to be altered in human melanoma were included among those found. The immunogenicity and specificity of 50 validated mutations was determined by immunizing mice with long peptides encoding the mutated epitopes. One-third of these peptides were found to be immunogenic, with 60% in this group eliciting immune responses directed preferentially against the mutated sequence as compared with the wild-type sequence. In tumor transplant models, peptide immunization conferred in vivo tumor control in protective and therapeutic settings, thereby qualifying mutated epitopes that include single amino acid substitutions as effective vaccines. Together, our findings provide a comprehensive picture of the mutanome of B16F10 melanoma which is used widely in immunotherapy studies. In addition, they offer insight into the extent of the immunogenicity of nonsynonymous base substitution mutations. Lastly, they argue that the use of deep sequencing to systematically analyze immunogenicity mutations may pave the way for individualized immunotherapy of cancer patients.
DOI: 10.26036/cnphis0000624
title: Extensive characterization of the CT26 colorectal carcinoma genome, transcriptome and immunome

description: BACKGROUND: Tumor models are critical for our understanding of cancer and the development of cancer therapeutics. Here, we present an integrated map of the genome, transcriptome and immunome of an epithelial mouse tumor, the CT26 colon carcinoma cell line. RESULTS: We found that Kras is homozygously mutated at p.G12D, Apc and Tp53 are not mutated, and Cdkn2a is homozygously deleted. Proliferation and stem-cell markers, including Top2a, Birc5 (Survivin), Cldn6 and Mki67, are highly expressed while differentiation and top-crypt markers Muc2, Ms4a8a (MS4A8B) and Epcam are not. Myc, Trp53 (tp53), Mdm2, Hif1a, and Nras are highly expressed while Egfr and Flt1 are not. MHC class I but not MHC class II is expressed. Several known cancer-testis antigens are expressed, including Atad2, Cep55, and Pbk. The highest expressed gene is a mutated form of the mouse tumor antigen gp70. Of the 1,688 non-synonymous point variations, 154 are both in expressed genes and in peptides predicted to bind MHC and thus potential targets for immunotherapy development. Based on its molecular signature, we predicted that CT26 is refractory to anti-EGFR mAbs and sensitive to MEK and MET inhibitors, as have been previously reported. CONCLUSIONS: CT26 cells share molecular features with aggressive, undifferentiated, refractory human colorectal carcinoma cells. As CT26 is one of the most extensively used syngeneic mouse tumor models, our data provide a map for the rationale design of mode-of-action studies for pre-clinical evaluation of targeted- and immunotherapies.
DOI: 10.26036/cnphis0000625
title: Outbreaks of salmonellosis in Danish pig herds caused by Salmonella Choleraesuis var. Kunzendorf – the use of pulsed-field gel electrophoresis and whole genome sequencing for outbreak investigation

description: So far, most epidemiological investigations on S. Choleraesuis have been done using biotyping and pulsed-field gel electrophoresis (PFGE) (ref). More recently, also the use of multilocus sequence typing (MLST) has been suggested as a replacement for serotyping, but in general MLST typing is more applicable for population genetic studies than for outbreak investigations (Achtman et al,. 2012). The genome of strains of S. Choleraesuis has been sequenced (Chiu et al., 2005; Richardson et al., 2011). Results by Chiu et al. (2005) showed that S. Choleraesuis has a genome size of 4.6 Mb and contains several pseudogenes, which suggests host adaptation. In the present study we describe outbreaks of salmonellosis in pig farms in Denmark, and the use of both PFGE and whole genome sequencing as tools for the outbreak investigation. In has neither in relation to the Danish outbreak in 1999 (Baggesen et al., 2000) nor to the outbreaks in 2012/2013 been possible to identify the primarily introduction of infection to the Danish pig herds. This may have been coursed by limitation in the epidemiological information available but also by an insufficient resolution of isolates by the epidemiological typing methods applied (mainly PFGE). The main goal of this study is therefore to evaluate whether application of whole genome sequence based analysis can improve the resolution of isolates in a way where the outbreak investigation on S. Choleraesuis is strengthened.
DOI: 10.26036/cnphis0000627
title: Bacterial_Long_Range_Paired_End_Tests

description: http://www.sanger.ac.uk/resources/downloads/bacteria/
DOI: 10.26036/cnphis0000628
title: Potential of fecal microbiota for early stage detection of colorectal cancer

description: Several bacterial species have been implicated in the development of colorectal carcinoma (CRC), but CRC-associated changes of fecal microbiota and their potential for cancer screening remain to be explored. Here we used metagenomic sequencing of fecal samples to identify taxonomic markers that distinguished CRC patients from tumor-free controls in a study population of 156 participants. Accuracy of metagenomic CRC detection was similar to the standard fecal occult blood test (FOBT) and when both approaches were combined, sensitivity improved &gt;45% relative to the FOBT while maintaining its specificity. Accuracy of metagenomic CRC detection did not differ significantly between early and late-stage cancer and could be validated in independent patient and control populations (N=335) from different countries. CRC-associated changes in the fecal microbiome at least partially reflected microbial community composition at the tumor itself, indicating that observed gene pool differences may reveal tumor-related host-microbe interactions. Indeed, we deduced a metabolic shift from fiber degradation in controls to utilization of host carbohydrates and amino acids in CRC patients accompanied by an increase of lipopolysaccharide metabolism.
DOI: 10.26036/cnphis0000629
title: Sequencing_Salmonella_Paratyphi_A_samples

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000630
title: Sequencing_of_Salmonella_Dublin_isolates_from_2006_2011

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0001323
title: H. saldiasi Genome sequencing

description: Whole genome sequencing of H. saldiasi DNA for the examination of the effects of library preparation
DOI: 10.26036/cnphis0001324
title: Zonotrichia albicollis Transcriptome or Gene expression

description: White-throated sparrow transcriptome
DOI: 10.26036/cnphis0001325
title: Ciona Chongmague Genome sequencing

description: Sequencing reads from hundreds of ciona intestinalis chongmague mutant genomes
DOI: 10.26036/cnphis0001326
title: Drosophila yakuba strain:multiple Genome sequencing

description: Aligned genomic sequences for 20 isofemale lines derived from natural populations of D. yakuba from Nguti, Cameroon and Nairobi, Kenya.
DOI: 10.26036/cnphis0001327
title: Branchiostoma belcheri Genome sequencing and assembly

description: The current whole-genome shotgun (WGS) assembly was sequenced from an single male of the Chinese amphioxus Branchiostoma belcheri. The draft diploid assembly was generated from a total of ~73X raw shotgun and paired-end reads which included both 454 FLX titanium reads (~23X) and Illumina 2x115bp reads (~50X). Both the assembler Newbler and the assembler CABOGv6.1 were used in this task. The initial diploid assembly is fragmented and highly polymorphic (~4% heterozygosity). We developed novel algorithms (HaploMerger) to reconstruct a reference haploid assembly from the original diploid assembly. The details and programs of HaploMerger are available here (http://mosas.sysu.edu.cn/genome/download_softwares.php). The new reference assembly (version: bbv18h27) were created by using an pipeline that combines hierachical scaffolding, a hybrid assembly method (both Illumina and 454 reads were used for de novo assembly), the HaploMerger algorithms for error correction and haploid assembly reconstruction. The new reference assembly has a size of ~426Mb, with scaffold and contig N50 sizes at 2.3Mb and 46 Kb, respectively. An alternative haploid assembly is also provided, which contains all other alleles not included in the reference assembly.
DOI: 10.26036/cnphis0001328
title: GenomeTrakr Project: Technology and Food Safety Services, Mexico

description: GenomeTrakr Project: Epidemiological Research Center at Sinaloa, Mexico
DOI: 10.26036/cnphis0001329
title: RNA-seq transcriptomes of term not in labour and term in labour human myometrial tissue

description: Purpose: To chart the human myometrial transcriptomes before and after the onset of labour. Methods: Tophat splice junction mapping of paired-end reads, HTSeq to generate counts, cufflinks to track transcripts, DESeq, edgeR and baySeq to detect differentially expressed genes and principal component analysis for clustering analyses. Results: We mapped on average 14 million paired-end reads per sample (counting each end individually) to the human genome (build hg19) and covered the expressed transcriptome about 13 times with a TopHat-HTSeq workflow. We performed a comparative analysis with an analogous microarray study (Mittal et al., 2010) and found some overlap between the RNA-seq and the microarray data. Conclusions: Our study is the first RNA-seq study of the human myometrium before and after the onset of labour. We show that while microarray and RNA-seq studies may complement each other, RNA-seq has a much greater resolution. Overall design: At term with and at term without labour human myometrial mRNA profiles were generated by deep sequencing, using Illumina GAIIx (five biological replicates each).