cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0000044
title: The Pig’s other genome: a reference gene catalogue of the gut microbiome

description: Pig is a main species for livestock and biomedicine. The pig genome sequence was recently reported. To boost research, we established a catalogue of the genes of the gut microbiome based on faecal samples of 287 pigs from France, Denmark and China. More than 7.6 million non-redundant genes representing 719 metagenomic species were identified by deep metagenome sequencing, highlighting more similarities with the human than with the mouse catalogue. The pig and human catalogues share only 12.6 and 9.3 % of their genes, respectively, but 70 and 95% of their functional pathways. The pig gut microbiota is influenced by gender, age and breed. Analysis of the prevalence of antibiotics resistance genes (ARGs) reflected antibiotics supplementation in each farm system, and revealed that non-antibiotics-fed animals still harbour ARGs. The pig catalogue creates a resource for whole metagenomics-based studies, highly valuable for research in biomedicine and for sustainable knowledge-based pig farming.
DOI: 10.26036/cnphis0000045
title: Herbal Formula-3 modulated intestinal microbiota in BALB/c mice

description: Formula-3, a modified Chinese herbal medicine, has been demonstrated to inhibit food allergy in rats by stabilizing mast cells through modulating calcium mobilization. In this study, we explored whether Formula-3 could modulate the composition of the gut microbiota. 13 mice were randomly allocated to two groups, receiving phosphate buffer saline and Formula-3 for 5 weeks. Sequencing of the V4-V5 regions of bacterial 16S rRNA genes from fecal samples revealed a change of microbial community structure. Mice received Formula-3 was characterized by distinct and less diverse gut microbial compositions with lower levels of Prevotella, Blautia, and higher levels of Tannerella and Rikenella. In addition, Formula-3 could alter the metabolic pathways Lipopolysaccharide biosynthesis and decrease some infectious diseases. Our data provide insight into the integrated responses of the host microbiome to Formula-3, and the methodology presented in this study can be adapted to assess other host-commensal and host-pathogen interactions.
DOI: 10.26036/cnphis0000046
title: Gut microbial dysbiosis in young adults with obesity

description: Obesity has become a global epidemic as a high risk factor for type 2 diabetes, cardiovascular diseases and cancer. Besides human genetics, our gut microbiome is another contributor to human obesity. Here we perform metagenome-wide association studies (MGWAS) on fecal samples from a case-control cohort including 95 Chinese young adults with obesity and 105 normal-weight controls, and 23 obese patients after weight-loss treatment. We discover and validate microbial species deregulated in obesity, and show the changes of gut microbial composition after weight-loss treatment.
DOI: 10.26036/cnphis0000047
title: Gut microbiome-dependent stratification of patients for anti-diabetic treatment

description: Dysbosis of intestinal microbiota could contribute to the pathogenesis of Type 2 Diabetes. It is yet to be known whether intestinal flora could be related to differential responds to antidiabetic therapies. This study, herein for the first time, metagenomic sequenced fecal samples from a randomized clinical trial on new onset untreated Type 2 Diabetes patients applied two treatment arms, Acarbose and Glipizide (Sulfonylurea) and analyzed the differential responses of intestinal flora in different groups. Results showed substantial impact of Acarbose on gut microbiota community but minor of Glipizide. Enterotypes with similar baseline clinical characteristics, had significant different pharmacologic respond to Acarbose on insulin resistance, gut hormones, bile acids and cardiovascular risks, indicating that different pattern of intestinal microbiota component could determine different responses of Type 2 Diabetes to antidiabetic pharmacological therapies.
DOI: 10.26036/cnphis0000048
title: Roux-en-Y gastric bypass surgery of morbidly obese patients shows swift and persistent changes of the individual gut microbiota

description: Roux-en-Y gastric bypass (RYGB) is an effective means to achieve sustained weight loss for morbidly obese individuals. Besides rapid weight reduction, patients achieve major improvements of insulin sensitivity and glucose homeostasis. Dysbiosis of gut microbiota has been associated with obesity and some of its co-morbidities like type 2 diabetes, and major changes of gut bacterial communities have been hypothesized to mediate part of the beneficial metabolic effects observed after RYGB. This study we describe changes in gut microbial taxonomic composition and functional potential following RYGB.
DOI: 10.26036/cnphis0000793
title: Ostrinia nubilalis laboratory population gut metagenome project

description: Total DNA extracted from bacterial cells from the midgut of a field population of the European Corn Borer Ostrinia nubilalis was sequenced with the 454 GS FLX system in order to evaluate their taxonomic and functional profile in comparison with a population of the same insect specie reared under laboratory conditions Total DNA extracted from midgut of laboratory and field populations of the lepidopteran Ostrinia nubilalis.
DOI: 10.26036/cnphis0000794
title: GSE28078: mRNA-Seq of whole flies from Drosophila

description: Summary: We sequenced mRNA from whole flies of females and male of Drosophila melanogaster, D. simulans, D. yakuba, D. ananassae, D. pseudobscura, D. mojavensis, and D. virilis as part of the modENCODE project to validate novel gene models found in D. melanogaster, identify genes differentially expressed between the sexes and sex-specific alternative splicing events, and examine the evolution of gene expression. Overall Design: Comparison of expresssion profiles in female and male whole flies. These are the same samples used to generate the array data found in GSE6640.
DOI: 10.26036/cnphis0000795
title: Camptotheca acuminata Transcriptome or Gene expression

description: Illumina RNA Sequencing (RNA-Seq) of Camptotheca acuminata for the Medicinal Plants Consortium
DOI: 10.26036/cnphis0000796
title: Lottia scutum Project

description: none provided
DOI: 10.26036/cnphis0000797
title: Comparative analysis of bacterial communities in a potato field as determined by pyrosequencing

description: Background: Plants selectively attract particular soil microorganisms, in particular consumers of root-excreted compounds. It is unclear to what extent cultivar type and/or growth stage affect this process. Methodology / Principal Findings: DNA-based pyrosequencing was used to characterize the structure of bacterial communities in a field cropped with potato. The rhizospheres of six cultivars denoted Aveka, Aventra, Karnico, Modena, Premiere and Desiree, at three growth stages (young, flowering and senescence) were examined, in addition to corresponding bulk soils. Around 350,000 sequences were obtained (5,700 to 38,000 per sample). Across all samples, rank abundance distributions best fitted the power law model, which indicates a community composed of a few highly dominant species next to numerous rare species. Grouping of the sequences showed that members of the Actinobacteria, Alphaproteobacteria, next to as-yet-unclassified bacteria, dominated. Other groups that were consistently found, albeit at lower abundance, were Beta-, Gamma- and Deltaproteobacteria and Acidobacteria.
DOI: 10.26036/cnphis0000798
title: High through put screen of small RNA in parental, hybrid and allopolyploid wheat

description: Speciation via interspecific or intergeneric hybridization and polyploidization triggers genomic responses Overall design: Examination of small RNA of diploid Parent, Tetraploid parent, F1 hybrid and hexaploid amhiploid. Four pools of plants for each sample
DOI: 10.26036/cnphis0000799
title: Bankia setacea genome sequencing

description: None
DOI: 10.26036/cnphis0000800
title: Study of WASP

description: study of 454_PMETRICUS_CDNA_TRACE
DOI: 10.26036/cnphis0000041
title: a whole genome sequencing (WGS) study of 88 matched HCC tumour/normal pairs

description: This study to identify genetically altered genes and pathways implicated in HBV-associated HCC
DOI: 10.26036/cnphis0000049
title: Integrated metabolomics and metagenomics analysis of plasma and urine identified microbial metabolites associated with coronary heart disease

description: Coronary heart disease (CHD) is top risk factor for health in modern society, causing high mortality rate each year. However, there is no reliable way for early diagnosis and prevention of CHD so far. So study the mechanism of CHD and development of novel biomarkers is urgently needed. In this study, metabolomics and metagenomics technology are applied to discover new biomarkers from plasma and urine of 59 CHD patients and 43 healthy controls and trace their origin. We identify GlcNAc-6-P which has good diagnostic capability and can be used as potential biomarkers for CHD, together with mannitol and 15 plasma cholines. These identified metabolites show significant correlations with clinical biochemical indexes. Meanwhile, GlcNAc-6-P and mannitol are potential metabolites originated from intestinal microbiota. Association analysis on species and function levels between intestinal microbes and metabolites suggest a close correlation between Clostridium sp. HGF2 and GlcNAc-6-P, Clostridium sp. HGF2, Streptococcus sp. M143, Streptococcus sp. M334 and mannitol. These suggest the metabolic abnormality is significant and gut microbiota dysbiosis happens in CHD patients.
DOI: 10.26036/cnphis0000050
title: Digital gene expression analysis reveals two sets genes associated with hexythiazox resistance in Panonychus citri (Acari: Tetranychidae)

description: We compared a miticides resistant strain and a susceptible strain's gene expression profile to reveal genes associated with miticide resistance in Panonychus citri.
DOI: 10.26036/cnphis0000051
title: Updated raw reads from the YH (Homo sapiens) genome (version SOAPdenovo2). The genomic DNA used in this study came from an anonymous male Han Chinese individual who has no known genetic diseases.

description: The SOAPdenovo2 version YH genome was assembled based on 2.1 billion reads using the Illumina HiSeq2000. We achieved 202G nucleotides data and the genome was sequenced to 67.5-fold average coverage. By aligning the short reads with SOAP, 177G nucleotides were mapped onto the NCBI reference genome and 99.99% of the genome was covered.
DOI: 10.26036/cnphis0000052
title: The gut microbiome in Crohn's disease and modulation by exclusive enteral nutrition

description: AbstractBackgroundInflammatory bowel diseases (IBD), with Crohn’s disease (CD) being one of the primary types, have been extensively studied for genetic and gut microbial factors leading to its epidemic in the modern world. However, limited information using metagenomic shotgun-sequencing to pinpoint the gut microbial species and functions involved. Exclusive enteral nutrition (EEN) is a nutritional therapy used for disease-modifying treatment of CD, but its impact on the gut microbiome remains unclear. ResultsWe collected 123 stool samples from 49 CD patients, 14 of whom were resampled after 2 weeks of EEN, and 56 subjects with no disease. Metagenomic shotgun sequencing and analyses confirmed a decreased diversity in the gut microbiota of CD patients, and identified microbial species and potential functions altered in CD, most notably an increased ratio of hexa- to penta-acylated lipopolysaccharide (LPS). Some co-abundance gene groups (CAGs) including Parabacteroides distasonis, Bacteroides intestinalis, Ruminococcus sp. showed strong correlation with clinical indicators such as hs.CRP, Prealbumin, platelets and BMI. The entire cohort could be divided into three types according to their species composition, with Type A largely consisting of healthy controls and Type C containing exclusively CD or after EEN samples. Although compositional changes were generally mild after 2 weeks of EEN, remodeling of the gut microbial network could be observed.ConclusionsOur metagenomic dataset unlock the gut microbiome in CD for functional investigations. Microbiome-based stratification of CD patients before EEN might help optimize the therapy for wider applications.
DOI: 10.26036/cnphis0000053
title: Sequence reads of HBV integration sites in HCC

description: annotation of read to hbv
DOI: 10.26036/cnphis0000054
title: BGISEQ-500 RNA-seq demo FASTQ data

description: BGISEQ-500 RNA-seq demo FASTQ data
DOI: 10.26036/cnphis0000055
title: BGISEQ-500 WGS demo FASTQ data

description: BGISEQ-500 WGS demo FASTQ data
DOI: 10.26036/cnphis0000801
title: Whole genome shotgun sequence of the roundworm,Caenorhabditis remanei

description: <i>Caenorhabditis remanei</i> genome sequencing project at the Washington University School of Medicine is part of the roundworm comparative genomics project that will add three more species (Caenorhabditis remanei, Caenorhabditis japonica, CB5161-Caenorhabditis sp. 1) to the two species (Caenorhabditis elegans, Caenorhabditis briggsae) that are already in public database (Read more about sequencing proposal). <br> Sequencing strategy - a combination of large insert clone mapping and whole genome shotgun (WGS) assembly.
DOI: 10.26036/cnphis0000802
title: Gymnogyps californianus

description: The California condor (Gymnogyps californianus) is the largest North American flying bird, part of the nature''s cleanup crew, and a flagship species for conservation. Over the 20th century, there was a rapid decline in the condor population. In 1985, only nine birds remained in the wild and in about 1980 a California condor rescue and restoration program was created. The last bird was removed from the wild in 1987. Captive breeding was successful and condors were reintroduced to central California (Los Padres National Forest), Grand Canyon area in Arizona, Monterey County, California, and in Baja, Mexico. The California condor is among the first endangered avian species under captive management for which genetic and genomic investigation technologies are being developed and used. The condor genome project targets creation of novel genomic resources for this species. A blood sample from a 14 year old female condor was used as the DNA source for clone-based sequencing using selected clones from a BAC library and a microsatellite-enriched library. In 2006, the Washington University Genome Sequencing Center generated almost 440,000 cDNA sequences from a condor fibroblast cell line using the 454 technology. Their total length is over 43 Mb. 78% transcripts were homologous to chicken genes. After assembly and clustering, around 15,000 contigs were built that contain roughly 190,000 reads. These data provide information about the condor transcriptome.
DOI: 10.26036/cnphis0000803
title: Drosophila melanogaster Whole Genome Sequencing Study

description: Drosophila melanogaster whole genome Sequencing Project.
DOI: 10.26036/cnphis0000804
title: Widespread regulated alternative splicing of single codons accelerates proteome evolution

description: Thousands of human genes contain introns ending in NAGNAG motifs (N any nucleotide), where both NAGs can function as 3' splice sites, yielding isoforms differing by inclusion/exclusion of just three bases. However, the functional importance of NAGNAG alternative splicing is highly controversial. Using very deep RNA-Seq data from sixteen human and eight mouse tissues, we found that approximately half of alternatively spliced NAGNAGs undergo tissue-specific regulation and that regulated events have been selectively retained: alternative splicing of strongly tissue-specific NAGNAGs was ten times as likely to be conserved between species as for non-tissue-specific events. Further, alternative splicing of human NAGNAGs was associated with an order of magnitude increase in the frequency of exon length changes at orthologous mouse/rat exon boundaries, suggesting that NAGNAGs accelerate exon evolution. Together, our analyses show that NAGNAG alternative splicing constitutes a major generator of tissue-specific proteome diversity and accelerates evolution of proteins at exon-exon boundaries. Overall design: mRNA-Seq of sixteen human and eight mouse tissues. Supplementary files: human.nagnag.junctions.gff and mouse.nagnag.junctions.gff are the annotation files (in GFF3 format) corresponding to the 'bwtout' mapped reads files linked to the Sample records. Raw data files provided for Samples GSM742937-GSM742952 only.
DOI: 10.26036/cnphis0000805
title: The evolution of gene expression levels in mammalian organs

description: Changes in gene expression are thought to underlie many of the phenotypic differences between species. However, large-scale analyses of gene expression evolution were until recently prevented by technological limitations. Here we report the sequencing of polyadenylated RNA from six organs across ten species that represent all major mammalian lineages (placentals, marsupials and monotremes) and birds (the evolutionary outgroup), with the goal of understanding the dynamics of mammalian transcriptome evolution. We show that the rate of gene expression evolution varies among organs, lineages and chromosomes, owing to differences in selective pressures: transcriptome change was slow in nervous tissues and rapid in testes, slower in rodents than in apes and monotremes, and rapid for the X chromosome right after its formation. Although gene expression evolution in mammals was strongly shaped by purifying selection, we identify numerous potentially selectively driven expression switches, which occurred at different rates across lineages and tissues and which probably contributed to the specific organ biology of various mammals. Our transcriptome data provide a valuable resource for functional and evolutionary analyses of mammalian genomes. Overall design: To study mammalian transcriptome evolution at high resolution, we generated RNA-Seq data (~3.2 billion Illumina Genome Analyser IIx reads of 76 base pairs) for the polyadenylated RNA fraction of brain (cerebral cortex or whole brain without cerebellum), cerebellum, heart, kidney, liver and testis (usually from one male and one female per somatic tissue and two males for testis) from nine mammalian species: placental mammals (great apes, including humans; rhesus macaque; mouse), marsupials (gray short-tailed opossum) and monotremes (platypus). Corresponding data (~0.3 billion reads) were generated for a bird (red jungle fowl, a non-domesticated chicken) and used as an evolutionary outgroup. Important note: Fluorophore intensity files were processed with the Ibis base caller (version 1.11). As illustrated in Supplementary Note Table 1 and Supplementary Note Figure 1 of Brawand et al. (Nature 2011), we found that Ibis significantly increased the number of usable reads and drastically reduced the error rate. However, Ibis quality values are not comparable to those from Illumina values, which should be taken into account when using our data and interpreting their quality relative to data established using other base calling approaches.
DOI: 10.26036/cnphis0000806
title: GSE30567: Long RNA-seq from ENCODE/Cold Spring Harbor Lab

description: None
DOI: 10.26036/cnphis0000807
title: Transposon-mediated gene regulatory network rewiring contributed to the evolution of pregnancy in mammals

description: We report the gene expression profile of human endometriual stromal cells and armadillo endometrial samples Overall design: We report the gene expression profile of human endometriual stromal cells and armadillo endometrial samples generated with Illumina GA2
DOI: 10.26036/cnphis0000808
title: A Hybrid Mechanism of Action for BCL6 in B Cells Defined by Formation of Functionally Distinct Complexes at Enhancers and Promoters

description: BCL6 is crucial for B-cell activation and lymphomagenesis. We used integrative genomics to explore BCL6 mechanism in normal and malignant B-cells. Surprisingly, BCL6 assembled distinct complexes at enhancers vs. promoters. At enhancers BCL6 preferentially recruited SMRT, which mediated H3K27 deacetylation through HDAC3, antagonized p300 activity and repressed transcription, but without decommissioning enhancers. This provides a biochemical basis for toggling enhancers from the active to poised state. Virtually all SMRT was bound with BCL6 suggesting that in B-cells BCL6 uniquely sequesters SMRT from other factors. In promoters BCL6 preferentially recruited BCOR, but most potently repressed promoters where it formed a distinctive ternary complex with SMRT and BCOR. Promoter repression was associated with decreased H3K36me3, H3K79me2 and Pol II elongation, linking BCL6 to transcriptional pausing. Overall design: We identified the binding patterns of BCL6, SMRT, NCOR and BCOR corepressors in normal germinal center B cells and a DLBCL cell line (OCI-Ly1) using ChIP-seq. Additionally we treated lymphoma cells with siRNA against BCL6 and a non-targeted siRNA (NT control) and performed RNA-seq to identify the genes bound and repressed by BCL6. RNA-seq experiments were performed at 24h and 48h after siRNA treatments. Additional biological triplicate RNA-seq experiments were performed at 48h after BCL6 knockdown. Furthermore, a series of histone mark ChIP-seq and RNA polymerase ChIP-seq (total, Ser5-P and Ser2-P) were preformed to capture the chromatin states associated with the formation of BCL6 corepressor complexes.
DOI: 10.26036/cnphis0000809
title: Genome sequencing of a Fusobacterium nucleatum colon cancer tumor isolate

description: A strain of Fusobacterium nucleatum, which we named CC53, was cultured from a colon cancer tumor surgical section and its genome sequenced.
DOI: 10.26036/cnphis0000056
title: We systematically sample the microbiota in the female reproductive tract from a large cohort of Chinese women of reproductive age using 16S rRNA gene sequencing, conventional bacterial culture and real-time PCR, and demonstrate a continuity of the vagino-uterine microbiome.

description: Human fetuses are long believed to grow in a sterile environment until birth, when they receive their mothers’ vaginal microbiota. Bacteria have been detected in umbilical cord, amniotic fluid and placenta, which is as yet not viewed as a normal condition. Here we systematically sample the microbiota throughout the female reproductive tract, and uncover diverse microbes from the cervix, uterus, fallopian tubes and peritoneal fluid, which are distinct from the vaginal microbiota but mirror their anatomical contingency with each other. Microbial taxa and potential functions correlated with menstrual cycle, or over-represented in subjects with adenomyosis, and infertility due to endometriosis are identified. Correlations between urine metabolites and microbiota components were also found. The study presents a framework for future endeavors in understanding the relationship between the vagino-uterine microbiome and the health of women and infants, and in the development of novel tests for the microbiome-related conditions.
DOI: 10.26036/cnphis0000057
title: KCL_twins2

description: KCL_twins2
DOI: 10.26036/cnphis0000058
title: GD_MGS_title

description: GD_MGS_describe
DOI: 10.26036/cnphis0000059
title: The performance of BGISEQ-500 for whole exome sequencing

description: The source DNA is a reference sample - NA12878, a WES library of this sample was constructed and sequenced by BGISEQ-500 (2 x 100 bp). Since the Genome in a Bottle (GIAB) has released a high-confidence calls set of this sample, precision and sensitivity of WES application can then be estimated.
DOI: 10.26036/cnphis0000060
title: The performance of BGISEQ-500 for whole genome sequencing.

description: The source DNA is a reference standard sample - NA12878. A WGS library of this sample was constructed and sequenced by BGISEQ-500 (2 x 100 bp). Since the Genome in a Bottle (GIAB) has released a high-confidence calls set of this sample, precision and sensitivity of WGS application can then be estimated