cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0000677
title: Reproducibility of associations between the human gut microbiome and colorectal cancer assessed in a patient population from Washington, DC, USA

description: Accumulating evidence indicates that the gut microbiota affects colorectal cancer development, but previous studies have varied in population, technical methods, and associations with cancer. Understanding these variations is needed for comparisons and for potential pooling across studies. Therefore, we performed whole-genome shotgun metagenomics sequencing on fecal samples from 52 pre-treatment colorectal cancer cases and 52 matched controls from Washington, DC. We compared findings from a previous 16S rRNA study to the metagenomics-derived taxonomy within the same population. In addition, metagenome-predicted genes, modules, and pathways in the Washington, DC cases and controls were compared to cases and controls recruited in France whose specimens were processed using the same platform. Associations between the presence of fecal Fusobacteria, Fusobacterium, and Porphyromonas with colorectal cancer detected by 16S rRNA were reproduced by metagenomics, whereas higher relative abundance of Clostridia in cancer cases based on 16S rRNA was merely borderline based on metagenomics. Considering significant cancer associations with the relative abundance of genes, modules, and pathways in the French population, statistically significant associations in the Washington, DC population were detected for four out of 10 genes, three out of nine modules, and seven out of 17 pathways. In conclusion, metagenomic sequencing results reproduced most, but not all of the major taxonomic associations with colorectal cancer previously observed from 16S rRNA profiles. In addition, colorectal cancer in the Washington, DC study was associated with 39% of the metagenome-predicted genes, modules, and pathways identified from the French study. More within and between population comparisons are needed to identify sources of variation and disease associations that can be reproduced despite these variations. Future studies must have larger sample sizes or pool data across studies to have sufficient power to detect associations that are reproducible and significant after correction for multiple testing.
DOI: 10.26036/cnphis0000678
title: ParaA epidemic Cambodia 2014

description: ParaA epidemic Cambodia 2014
DOI: 10.26036/cnphis0000679
title: Colistin resistance in Salmonella and E. coli isolates from a pig farm in Great Britain

description: Background: The aim of this work was to characterize three colistin resistant bacteria isolated from pigs on a farm in Great Britain. Methods: Antimicrobial susceptibility testing was performed by a broth microdilution method. Whole genome sequencing was used to detect antimicrobial resistance (AMR) and virulence genes. The mcr-1 harbouring plasmid was characterised and conjugations performed. Selected transconjugants were plasmid-profiled and their susceptibility to different antibiotics tested. Findings: Two Escherichia coli and 1 Salmonella Typhimurium var. Copenhagen with phenotypic colistin resistance were shown to be multidrug resistant (MDR), with 1 E. coli (E4) and Salmonella (S3) carrying the mcr-1 gene; all 3 isolates also harboured chromosomal mutations for colistin resistance. The pS3 mcr-1 plasmid was highly similar to pHNSHP45, reported in China, but the pE4 mcr-1 plasmid was distinct with only the ISApII and mcr-1 genes in common. This indicated both plasmid and IS-element mediated dissemination of mcr-1 had occurred. Frequency of mcr-1 plasmid transfer to recipient Enterobacteriaceae from S3 was low, lying between 10-7 to 10-9 colony forming units per recipient colony forming unit, by conjugation; we were unable to demonstrate mcr-1 plasmid transfer from E4 under the conditions tested. Plasmid profiling indicated transfer of multiple plasmids from S3 at conjugation resulting in MDR transconjugants.
DOI: 10.26036/cnphis0000680
title: Oesophageal adenocarcinoma exome sequence data from samples before and after neo-adjuvant chemotherapy

description: How chemotherapy affects carcinoma genomes is largely unknown. Here, we performed whole-exome and deep sequencing of 30 paired oesophageal adenocarcinomas sampled before and after neo-adjuvant chemotherapy. Most, but not all, good responders passed through genetic bottlenecks. Some poor responders also passed through bottlenecks, but re-grew by the time of surgical resection, suggesting a missed therapeutic opportunity. Several cancers showed major changes in driver mutation presence or frequency after treatment, owing to outgrowth or persistence of sub-clones, copy number changes, polyclonality and spatial genetic heterogeneity. The post-treatment samples of good responders or bottleneckers showed a mutation spectrum shift to C&gt;A and TT&gt;CT, and several of these harboured mutations in known cancer driver genes (for example, SF3B1, TAF1 and CCND2) that were absent from the pre-treatment sample. Neo-adjuvant chemotherapy can profoundly affect the EAC genome after two treatment cycles and monitoring molecular changes during treatment may be clinically useful.
DOI: 10.26036/cnphis0000681
title: Pathogen_assembly_pipeline_evaluation

description: Pathogen assembly pipeline evaluation
DOI: 10.26036/cnphis0000682
title: Salmonella genome SCV sequencing

description: Salmonella genome SCV sequencing
DOI: 10.26036/cnphis0000683
title: Salmonella Enteritidis Finland

description: Suspected outbreak of Salmonella Enteritidis
DOI: 10.26036/cnphis0001377
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001378
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001379
title: Ciona savignyi bugeye Genome sequencing

description: Sequencing reads from hundreds of Ciona savignyi bugeye mutant genomes
DOI: 10.26036/cnphis0001380
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001381
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001382
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001383
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001384
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0002062
title: Salmonella enterica subsp. enterica serovar Panama str. SA20030878 Genome sequencing and assembly

description: Genome sequence of Salmonella Panama (serogroup D; 1,9,12:l,v:1,5)
DOI: 10.26036/cnphis0002063
title: Salmonella enterica subsp. enterica serovar Rubislaw str. SA20030553 Genome sequencing and assembly

description: Genome sequence of Salmonella Rubislaw (serogroup F; 11:r:e,n,x)
DOI: 10.26036/cnphis0002064
title: Salmonella enterica subsp. enterica serovar Weslaco str. 247K Genome sequencing and assembly

description: Genome sequence of Salmonella Weslaco (serogroup T; 42:z36:-)
DOI: 10.26036/cnphis0002065
title: Salmonella enterica subsp. enterica serovar Paratyphi A str. SA19950809 Genome sequencing and assembly

description: Genome sequence of Salmonella Paratyphi A (serogroup A; 2,12:a:-)
DOI: 10.26036/cnphis0002066
title: Salmonella enterica subsp. enterica serovar Virginia str. SA19971529 Genome sequencing and assembly

description: Genome sequence of Salmonella Virginia (serogroup C2; 8:d:1,2)
DOI: 10.26036/cnphis0002067
title: Female-limited color dimorphism in Drosophila erecta raw sequence reads

description: Female-limited color dimorphism in Drosophila erecta
DOI: 10.26036/cnphis0002068
title: Stylophora pistillata isolate:CSM Monaco Genome sequencing and assembly

description: CSM Monaco clone, northern Red Sea, holotype #3, clade 4
DOI: 10.26036/cnphis0002069
title: Oryza sativa Transcriptome or Gene expression
DOI: 10.26036/cnphis0002070
title: Salmonella enterica subsp. salamae serovar 56:z10:e,n,x str. 1369-73 Genome sequencing and assembly

description: Genome sequence of Salmonella salamae (serogroup O56; 56:z10:enx)
DOI: 10.26036/cnphis0000684
title: Whole genome sequencing and analysis of invasive Neisseria isolates from Malawi

description: Whole genome sequencing and analysis of invasive Neisseria isolates from Malawi
DOI: 10.26036/cnphis0000685
title: Transcriptome of dermal fibroblasts from healthy human donors differing by donor age, donor gender and UV exposition (Gerontosys).

description: RNA-seq data from short term cultivated fibroblasts were sequenced on an Illumina HiSeq 2000 sequencer. Donors were differentiated by age (Years) and gender (F=female; M=male). Two samples were obtained from each individual from different locations (B=buttock, not UV exposed; S=shoulder, UV exposed).
DOI: 10.26036/cnphis0000686
title: Hypertension is one of the most prevalent cardiovascular diseases worldwide. Recent findings have identified a link between gut microbiota and blood pressure, yet the contributions of gut microbes and bacterial metabolites towards hypertension remain largely uncharacterized. We carried out metagenomic and metabonomics analyses, in combination with faecal microbiota transplantation, and elucidate that dysbiosis of gut microbiome triggers the pathogenesis of hypertension through altering the metabolic effects.

description: Hypertension is one of the most prevalent cardiovascular diseases worldwide. Recent findings have identified a link between gut microbiota and blood pressure, yet the contributions of gut microbes and bacterial metabolites towards hypertension remain largely uncharacterized. We carried out metagenomic and metabonomics analyses, in combination with faecal microbiota transplantation, and elucidate that dysbiosis of gut microbiome triggers the pathogenesis of hypertension through altering the metabolic effects. Notably, we demonstrate similar discrepancy of microbial compositional and functional features in pre-hypertension and hypertension when compared with the controls, highlighting varied intestinal microbiota in prehypertensive populations. The impairment of host metabolism in pre-hypertension and hypertension was identified to be closely linked with dysbiotic gut microbiome. The hypertensive phenotype was transferrable from hypertension patients to germ-free mice by faecal transplant. Overall, our results explicate a novel role for aberrant gut microbiota as key contributor to the pathogenesis of hypertension, and emphasize the significance of early intervention for pre-hypertension.
DOI: 10.26036/cnphis0000687
title: Swiss Comparative Equine Resequencing (SCER)

description: Whole Genome sequences of horse with varied phenotype
DOI: 10.26036/cnphis0000688
title: International Human Microbiome Standards

description: The IHMS EU funded project aimed at coordinate the development of standard operating procedures designed to optimize data quality and comparability in the human microbiome field.
DOI: 10.26036/cnphis0000689
title: The_origin_of_H58_Salmonella_Typhi_

description: This study is a joint undertaking between OUCRU Vietnam and Public Health England (PHE) to study the phylogeography of and emergence of H58 Salmonella Typhi. Phylogeography is studying the evolution of organisms in a defined spatiotemporal window.
DOI: 10.26036/cnphis0000690
title: The_genome_sequence_of_Salmonella_Typhimurium_strain_RS9H8

description: Salmonella enterica MDR epidemic isolate was sequenced for comparative genome analysis and SNP typing for phylogenetic analysis. http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000691
title: Complexity_of_genetic_incompatibility

description: On the molecular level, speciation takes place via accumulation of mutations that lead to genetic incompatibilities. The alleles can be incompatible during meiosis (e.g. chromosome segregation errors due to different karyotypes), or in the gametes (e.g. a complement of loss-of-function alleles that fails to carry out an essential task). There is a veritable debate in the genetic complexity of such incompatibilities. A model due to Orr[1] posits that speciation mainly proceeds via combinations of variants in three or more genes, but this has not been explicitly tested yet. Here, we propose to low coverage sequence a large number of meiotic progeny of all pairwise crosses of four yeast strains in order to explicitly test the Orr model. We are generating 1,500 segregants from each of six crosses between African, Japanese, European, and North American wild yeast strains, and are looking to test for presence of two- and three-allele combinations that are underrepresented in the viable ones. This design also has sufficient power to estimate the variance in spore viability due to interactions of different orders. As four gametes are isolated from the same meiotic event, inviable genotypes can be inferred, and one of the most detailed view of the meiotic recombination landscape is generated as a byproduct. The complete genome sequence of the parental strains will allow to investigate how recombination is affected by both sequence and structural variation. We are looking to sequence genomic DNA of 1,500 meiotic progeny from each of 6 pairwise crosses (9,000 yeast strains total) to up to 10x coverage. The library preparation can take place in high throughput, taking advantage of the single cell facility automation, and low volume protocols. 1. Orr, H. A. (1995). The Population Genetics of Speciation: The Evolution of Hybrid Incompatibilities. Genetics 139(4), 1805-1815.
DOI: 10.26036/cnphis0000692
title: Enteritidis

description: Enteritidis
DOI: 10.26036/cnphis0001385
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001386
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001387
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001388
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001389
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001390
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001391
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001392
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001393
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0002071
title: Salmonella enterica subsp. arizonae serovar 62:z36:- str. 5335/86 Genome sequencing and assembly

description: Genome sequence of Salmonella arizonae (serogroup O62; 62:z36:-)
DOI: 10.26036/cnphis0002072
title: Salmonella enterica subsp. arizonae serovar 63:g,z51:- Genome Sequencing

description: Genome sequence of Salmonella arizonae (serogroup O63; 63:g,z51:-)
DOI: 10.26036/cnphis0002073
title: RNA-seq of tumor-educated platelets enables blood-based pan-cancer, multiclass and molecular pathway cancer diagnostics

description: We report RNA-sequencing data of 283 blood platelet samples, including 228 tumor-educated platelet (TEP) samples collected from patients with six different malignant tumors (non-small cell lung cancer, colorectal cancer, pancreatic cancer, glioblastoma, breast cancer and hepatobiliary carcinomas). In addition, we report RNA-sequencing data of blood platelets isolated from 55 healthy individuals. This dataset highlights the ability of TEP RNA-based ''liquid biopsies'' in patients with several types with cancer, including the ability for pan-cancer, multiclass cancer and companion diagnostics. Overall design: Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing EDTA anti-coagulant by standard centrifugation. Total RNA was extracted from the platelet pellet, subjected to cDNA synthesis and SMARTer amplification, fragmented by Covaris shearing, and prepared for sequencing using the Truseq Nano DNA Sample Preparation Kit. Subsequently, pooled sample libraries were sequenced on the Illumina Hiseq 2500 platform. All steps were quality-controlled using Bioanalyzer 2100 with RNA 6000 Picochip, DNA 7500 and DNA High Sensitivity chips measurements. For further downstream analyses, reads were quality-controlled using Trimmomatic, mapped to the human reference genome using STAR, and intron-spanning reads were summarized using HTseq. The processed data includes 285 samples (columns) and 57736 ensemble gene ids (rows). The supplementary data file (TEP_data_matrix.txt) contains the intron-spanning read counts, after data summarization by HTseq.
DOI: 10.26036/cnphis0002074
title: Active DNA demethylation at enhancers during the vertebrate phylotypic period

description: The vertebrate body plan and organs are shaped during a conserved embryonic phase called the phylotypic stage, however the mechanisms that guide the epigenome through this transition and their evolutionary conservation remain elusive. Here we report widespread DNA demethylation of enhancers during the phylotypic period in zebrafish, Xenopus and mouse. These enhancers are linked to developmental genes that display coordinated transcriptional and epigenomic changes in the diverse vertebrates during embryogenesis. Binding of Tet proteins to (hydroxy)methylated DNA, and enrichment of hydroxymethylcytosine on these regions, implicated active DNA demethylation in this process. Furthermore, loss of function of Tet1/2/3 in zebrafish caused reduced chromatin accessibility and increased methylation levels specifically on these enhancers, indicative of DNA methylation being an upstream regulator of phylotypic enhancer function. Overall, our study reveals a novel regulatory module associated with the most conserved phase of vertebrate embryogenesis and uncovers an ancient developmental role for the Tet dioxygenases. Overall design: MethylC-Seq in zebrafish embryos, MethylC-seq in Xenopus tropicalis embryos, MethylC-seq in mouse embryos, MethylC-seq in zebrafish tissues, MethylC-seq in Xenopus tropicalis tissues, TAB-seq in zebrafish embryos, TAB-seq in Xenopus tropicalis embryos, TAB-seq in mouse embryos, RNA-seq in zebrafish embryos, RNA-seq in mouse embryos
DOI: 10.26036/cnphis0002075
title: Ictalurus punctatus Genome sequencing and assembly

description: Catfish Genome Project
DOI: 10.26036/cnphis0002076
title: Hypothenemus hampei isolate:Beltsville Coffee Borer Beetle colony Genome sequencing and assembly

description: Hypothenemus hampei (Ferrari) commonly known as the coffee berry borer, is considered an important agricultural pest of coffee. This is a draft genome with associated RNA-seq data and predicted proteins. We estimate that the genome is nearly complete with respect to protein coding regions.
DOI: 10.26036/cnphis0002077
title: Octopus bimaculoides isolate:UCB-OBI-ISO-001 Genome sequencing

description: We sequenced the genome and multiple transcriptomes of the California two-spot octopus, Octopus bimaculoides, to investigate the molecular bases of cephalopod brain and body innovations. Coleoid cephalopods (octopus, squid, and cuttlefish) are active, resourceful predators with a rich behavioral repertoire. They have the largest nervous systems among the invertebrates, and present other extremes of morphological innovation including camera-like eyes, prehensile arms, fish-like early embryogenesis, and the most sophisticated adaptive coloration system among all animals.
DOI: 10.26036/cnphis0002078
title: Mylabris cichorii Transcriptome or Gene expression

description: Mylabris cichorii is a well-known traditional Chinese medicine. The sesquiterpenoid cantharidin, which is secreted mostly by adult male beetles, has recently been used as an anti-cancer drug. However, there is currently no genomic information for M. cichorii. The transcriptome data for this species could provide an invaluable resource for the future research for M. cichorii.
DOI: 10.26036/cnphis0000693
title: EURL reference testing

description: EURL reference testing
DOI: 10.26036/cnphis0000694
title: Genome-wide analysis of differential RNA editing in epilepsy

description: The recoding of genetic information through RNA editing contributes to proteomic diversity, but the extent and significance of RNA editing in disease is poorly understood. In particular, few studies have investigated the relationship between RNA editing and disease at a genome-wide level. Here, we developed a framework for the genome-wide detection of RNA sites that are differentially edited in disease. Using RNA-sequencing data from 100 hippocampi from mice with epilepsy (pilocarpine- temporal lobe epilepsy model) and 100 healthy control hippocampi, we identified 256 RNA sites (overlapping with 87 genes) that were significantly differentially edited between epileptic cases and controls. The degree of differential RNA editing in epileptic mice correlated with frequency of seizures, and the set of genes differentially RNA edited between case and control mice were enriched for functional terms highly relevant to epilepsy including “neuron projection” and “seizures”. Genes with differential RNA editing were preferentially enriched for genes with a genetic association to epilepsy. Indeed, we found that they are significantly enriched for genes that harbour non-synonymous de novo mutations in patients with epileptic encephalopathy, and for common susceptibility variants associated with generalized epilepsy. These analyses reveal a functional convergence between genes that are differentially RNA edited in acquired symptomatic epilepsy and those that contribute risk for genetic-epilepsy. Taken together, our results suggest a potential role for RNA editing in the epileptic hippocampus in the occurrence and severity of epileptic seizures.
DOI: 10.26036/cnphis0000695
title: Single cell RNA-sequencing of Spike-ins and Control RNA using 10x Genomics Chromium system

description: In this study, we assess technical differences between commonly used single-cell RNA-Sequencing (scRNA-Seq) methods. In this dataset, we assess the RNA detection rates using high-throughput 10x Genomics Chromium system. We mix equal volume of Control Brain RNA (3µl; FirstChoice Total Brain RNA; #AM7962) and ERCC spikes (3µl 1:4 dilution; #4456653) to make a ‘2x Control RNA+ERCC’ master mix. The ‘2x Control RNA+ERCC’ master mix is diluted with equal volume nuclease-free water to make ‘1x Control RNA+ERCC’ master mix. 3µl of ‘1x Control RNA+ERCC’ master mix is added to Chromium single cell suspension and processed as per Chromium guidelines.
DOI: 10.26036/cnphis0000696
title: Fusobacterium in feces of participants in a colorectal cancer screening program

description: see publication