cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0001876
title: Genetic Model for Oral Cancer

description: Dr. Ravindra Uppaluri, a head and neck surgeon at Washington University, has developed a cell line model of mouse oral squamous cell carcinomas (OSCC) for genetic research. Using these tumors and microarry, his lab identified a molecular signature of metastasis that correlates well with human tumors displaying metastasis. This project contains the exome sequence from those cell lines: 3 indolent tumors and 2 aggressive tumors. This is one of several projects at The Genome Institute to characterize mouse models of human cancer.
DOI: 10.26036/cnphis0001877
title: Whole genome sequencing from a panel of Lake Malawi species. Pools of males and females from each species were sequenced. Genome sequencing

description: This research project considers the genetic mechanisms of vertebrate diversification from two perspectives. The first is that of population genetics. How many genes experience divergent selection during the evolution of new species? How are they distributed across the genome? The second perspective is that of the evolution of development. Which genes are modified to produce new phenotypes? The flock of some 800 closely related cichlids fishes in Lake Malawi are an ideal model system for this study. These species differ in the shape of their jaws and teeth, the color of their skin, and their mechanisms of sex determination.
DOI: 10.26036/cnphis0001878
title: Genetic Variation in Essential Laboratory Primates Rhesus Macaque (Macaca mulatta)

description: HGSC has sequenced both deep (~30X) and shallow (~6X) whole genomes on 198 animals from 8 National Primate Research Centers (NPRCs) and primate research facilities. There are an additional 50 whole exomes that have been sequenced from each of five NPRCs. All of these animals are Macaca mulatta. All sequencing was done on Illumina HiSeq machines. Analysis will pursue characterization of genomic variation between individuals and subspecies (Indian and Chinese).
DOI: 10.26036/cnphis0000482
title: Zootermopsis nevadensis Genome sequencing and assembly

description: Zootermopsis nevadensis whole genome shotgun sequencing.
DOI: 10.26036/cnphis0000484
title: Salix suchowensis Genome sequencing

description: We provide here the draft genome of a shrub willow (Salix suchowensis). S. xuzhouensis is an annual flowering shrub willow, which is amenable for genetic manipulation and its natural populations also display high genetic diversity and are likely to contain many low-frequency alleles that underlie outstanding phenotypes useful to breeders. Especially, it is easy to carry out large scale field trial. It is a desirable species to uncover the genetic factors underlying the woody plants specific traits due to the short juvenile period, the small individual size and the moderate genome size. With genome sequences available both in willows and poplars, these important resources will play fundamental roles in the functional genomics studies for trees in Salicaceae, and especially useful in uncovering the major genes that control the domestication traits for biomass production and wood formation both in willows and poplars.
DOI: 10.26036/cnphis0000485
title: Rattus norvegicus Transcriptome or Gene expression

description: Although considered a pest and major health threat by many, the rat is an important model organism to help understand human physiology and disease. Here, the purpose of this study was to systematically profile the expression of miRNA in PS-induced hepatic fibrosis and further investigated the possible roles of miRNAs played in the fibrogenesis by prediction of the potential target genes of differentially expressed miRNAs.
DOI: 10.26036/cnphis0000486
title: Oryza sativa Indica Group Genome sequencing

description: Hybrid rice Liang-You-Pei-Jiu has a notable contribution toyield improvement. It was derived by crossing different varieties within or between two subspecies, Oryza sativa ssp. indica and ssp. japonica. Here we submitted the resequencing recombinant population of Liang-You-Pei-Jiu.
DOI: 10.26036/cnphis0000487
title: Human gut stool samples Targeted Locus (Loci)

description: Human Gut microbiota changes reveal the progression of glucose intolerance statuses. To investigate the change of human gut microbiome when a person developed to be T2DM, a total of 121 stools samples were collected , including 44 heathy, 64 pre-DM and 13 T2DM subjects, and the microbial structure composition were estimated by 16S rDNA-based high though output sequencing.
DOI: 10.26036/cnphis0000488
title: Oryza sativa Indica Group strain:PA64s Genome sequencing

description: The PA64s rice cultivar has a mixed genetic background of indica and javanica, here, we provide the genome sequence of PA64s in the chromosome scale.
DOI: 10.26036/cnphis0000489
title: Comparative Analysis of two Chinese Clinical Isolates of Super XDR Mycobacterium Tuberculosis

description: -
DOI: 10.26036/cnphis0000490
title: Enterococcus faecium LCT-EF90 Transcriptome or Gene expression

description: Enterococcus faecium is a Gram-positive, alpha hemolytic or nonhemolytic bacterium in the genus Enterococcus. It can be commensal (innocuous, coexisting organism) in the human intestine, but it may also be pathogenic, causing diseases such as neonatal meningitis.
DOI: 10.26036/cnphis0000491
title: Enterococcus faecium LCT-EF258 Transcriptome or Gene expression

description: Enterococcus faecium is a Gram-positive, alpha hemolytic or nonhemolytic bacterium in the genus Enterococcus. It can be commensal (innocuous, coexisting organism) in the human intestine, but it may also be pathogenic, causing diseases such as neonatal meningitis.
DOI: 10.26036/cnphis0001195
title: Transcriptional and Epigenetic Dynamics During Specification of Human Embryonic Stem Cells

description: Differentiation of human embryonic stem cells (hESCs) provides a unique opportunity to study the epigenetic mechanisms that facilitate cellular transitions in a human context. To that end, we performed comprehensive transcriptional and epigenetic profiling of early populations derived through directed differentiation of hESCs representing each of the three embryonic germ layers. Integration of whole genome bisulfite sequencing, chromatin immunoprecipitation-sequencing and RNA-Sequencing reveals unique events associated with specification towards each lineage. While we observe expected dynamics such as loss of DNA methylation and gain of H3K4me1 at distal putative regulatory elements, we frequently found a germ layer specific switch to H3K27me3 at sites of high DNA methylation in the undifferentiated state. By carefully dissecting these initial events, we may be able to devise more faithful differentiation strategies and gain novel insights in to the robust rewiring of regulatory programs during cellular transitions. Overall design: 10 Samples in total, 5 in replicate. To better understand the interplay of epigenetic dynamics and transcription factor binding upon in vitro specification of human embryonic stem cells we profiled OCT4, SOX2 and NANOG in hESC and the endoderm master regulatory factor FOXA2 in in vitro derived endoderm cells (dEN). To gain further insights into the relation of DNA methylation and TF binding, we carried out ChIP-bisulfite sequencing for FOXA2 in dEN. Lastly, we were interested in the fate of genes bound by FOXA2 in dEN upon further differentiation and therefore differentiated dEN further towards a hepatocyte like state and performed RNA-Seq.
DOI: 10.26036/cnphis0001196
title: The sequence of Poecilia latipinna (Sailfin molly)

description: Poecilia latipinna (Sailfin molly) and Poecilia mexicana (Altantic molly) are thought to be the parental species for Poecilia formosa. A mating of these species is believed to have taken place about ~200,000 years ago to create the P. formosa species. This sequence data will help establish the origins of the descendants that arose from this rare hybridization event between two species.
DOI: 10.26036/cnphis0001197
title: The sequence of Poecilia mexicana (Altantic molly)

description: Poecilia latipinna (Sailfin molly) and Poecilia mexicana (Altantic molly) are thought to be the parental species for Poecilia formosa. A mating of these species is believed to have taken place about ~200,000 years ago to create the P. formosa species. This sequence data will help establish the origins of the descendants that arose from this rare hybridization event between two species.
DOI: 10.26036/cnphis0001198
title: Sequencing of Anopheles

description: None
DOI: 10.26036/cnphis0001199
title: Cryptobranchus alleganiensis shotgun sequencing

description: Salamanders have the largest genome among tetrapod vertebrates. Our previous results indicated that LTR retrotransposons contribute to the genomic gigantism of Plethodontid salamanders, however, it is elusive if this is the primarily mechanism underlying genomic expansion at the base of the salamander clade. To answer this question, hellbender, one salamander species from the family of Cryptobranchus, which is phylogenetically distantly related to Plethodontid, was employed in this study to explore its repeat landscape. High-throughput sequencing was used to generate shotgun reads for the hellbender genome, and its repeat content was explored using a pipeline specialized for low-coverage shotgun reads. Results indicated that over 75% of hellbender genome was made up of repetitive sequences, and the vast majority of them were derived from known transposable elements (TEs). Gypsy/Ty3 is the most abundant TE superfamily in hellbender, and compared with other vertebrates, there are much higher level of LTR retrotransposons in hellbender genome, suggesting that the proliferation of LTR elements also contributes to the genomic expansion of Cryptobranchus salamander. When comparing the TE landscape of Cryptobranchus with that of Plethodontid, we found that these two taxa of salamanders harbor similar amount of LTR and DNA elements. In contrast, there was much higher level of non-LTR retrotransposons in Cryptobranchus than in Plethodontid. More specifically, there was an increased proliferation of L1 and Penelope retrotransposons in Cryptobranchus. Taken together, our results indicated that salamanders harbor much higher level of LTR retrotransposon, especially Gypsy/Ty3 elements, in their genome than in other vertebrates, which is the primarily mechanism underlying genomic expansion at the base of the salamander clade. In addition, there is differential TE activity among salamanders. Thus, our results indicate that the balance between TE proliferation and host silencing differs dramatically not only between salamander and other vertebrates but also across salamanders.
DOI: 10.26036/cnphis0001200
title: Transcriptome Analysis of the Guinea Fowl

description: In this project the transcriptome of the guinea fowl pancreas was analyzed. Samples were read on an Illumina HiSeq-2000 sequencer.
DOI: 10.26036/cnphis0001201
title: Bombyx huttoni strain:Kalimpong Genome sequencing and assembly

description: Whole genome shotgun sequencing of Bombyx huttoni, a close relative of the domesticated silkmoth, Bombyx mori.
DOI: 10.26036/cnphis0001202
title: Whole transcriptome RNA-seq of undiseased human prefrontal cortex

description: We report the application of high-throughput RNA sequencing to the human prefrontal cortex. The brain dataset was obtained by sequencing total RNAs extracted from the dorsolateral prefrontal cortex of five deceased human patients with no apparent pathology, followed by depletion of ribosomal RNA to obtain all non-rRNA coding and non-coding RNAs in the human brain transcriptome. Overall design: Five samples were sequenced, four coming from frozen brain tissue (frontal cortex) of deceased female human patients with no remarkable pathology, and one from a male patient with no remarkable pathology.
DOI: 10.26036/cnphis0001203
title: Panthera tigris altaica Genome sequencing and assembly

description: PGI, TBI, and collaborators are working on the Amur tiger whole genome sequencing, assembly, and analysis to provide reference genomes for big-cats. A white tiger is also being sequenced.
DOI: 10.26036/cnphis0001879
title: Genome sequencing of a Buryat patient with X-linked ?ongenital cerebellar ataxia

description: Whole genome sequencing of a Buryat patient with X-linked ?ongenital cerebellar ataxia to identify the genetic cause of the disease.
DOI: 10.26036/cnphis0001880
title: Salmonella enterica subsp. enterica serovar Typhimurium strain:DT170 Genome sequencing

description: Retrospective application of next generation sequencing to outbreak detection of Salmonella enterica serovar Typhimurium
DOI: 10.26036/cnphis0001881
title: Genome sequencing of the hamadryas baboon

description: A high coverage whole genome sequencing of Papio hamadryas using read data produced by the Illumina platform and comparative analysis.
DOI: 10.26036/cnphis0001882
title: Drop-Seq analysis of mixtures of human (HEK) and mouse (3T3) cells (1000/100 STAMPs) at 50 cells per microliter

description: A cell supsension containing an equal mix of HEK and 3T3 cells was used in Drop-Seq, a novel technology for high-throughput single cell mRNAseq. The cells were mixed at a final concentration of 50 cells per microliter. Overall design: An estimated 1000 STAMPs and 100 STAMPs were separately selected for sequencing to obtain both high coverage and broad coverage data
DOI: 10.26036/cnphis0001883
title: Characterization of global loss of imprinting in overgrowth syndrome induced by assisted reproduction

description: Embryos generated with the use of assisted reproductive technologies (ART) can develop overgrowth syndromes. In ruminants, the condition is referred to as large offspring syndrome (LOS) and exhibits variable phenotypic abnormalities including overgrowth, enlarged tongue, and abdominal wall defects. These characteristics recapitulate those observed in the human loss-of-imprinting (LOI) overgrowth syndrome Beckwith-Wiedemann (BWS). We have recently shown LOI at the KCNQ1 locus in LOS, the most common epimutation in BWS. Although the first case of ART-induced LOS was reported in 1995, studies have not yet determined the extent of LOI in this condition. Here, we determined allele-specific expression of imprinted genes previously identified in human and/or mouse in day 105 Bos taurus indicus X Bos taurus taurus F1 hybrid control and LOS fetuses using RNAseq. Our analysis allowed us to determine the monoallelic expression of 20 genes in tissues of control fetuses. LOS fetuses displayed variable LOI when compared to controls. Biallelic expression of imprinted genes in LOS was associated with tissue-specific hypomethylation of the normally methylated parental allele. In addition, a positive correlation was observed between bodyweight and the number of biallelically expressed imprinted genes in LOS fetuses. Further, not only was there loss of allele-specific expression of imprinted genes in LOS, but we also observed differential transcript amounts of these genes between control and overgrown fetuses. In summary, we characterized previously unidentified imprinted genes in bovine and identified misregulation of imprinting at multiple loci in LOS. We concluded that LOS is a multi-locus loss-of-imprinting syndrome, as is BWS. Overall design: Imprinted gene expression in kidney, skeletal muscle, liver, and brain of four control and large offspring syndrome(LOS) fetuses were studied using RNAseq
DOI: 10.26036/cnphis0001884
title: A three-dimensional map of the human genome at kilobase resolution reveals prinicples of chromatin looping

description: We use in situ Hi-C to probe the three-dimensional architecture of genomes, constructing haploid and diploid maps of nine cell types. The densest, in human lymphoblastoid cells, contains 4.9 billion contacts, achieving 1-kilobase resolution. We find that genomes are partitioned into local domains, which are associated with distinct patterns of histone marks and segregate into six subcompartments. We identify ~10,000 loops. These loops frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species. Loop anchors typically occur at domain boundaries and bind CTCF. CTCF sites at loop anchors occur predominantly (&gt;90%) in a convergent orientation, with the asymmetric motifs ‘facing’ one another. The inactive X-chromosome splits into two massive domains and contains large loops anchored at CTCF-binding repeats. Overall design: in situ Hi-C and dilution Hi-C were used to probe the three-dimensional structure of the genome in eight diverse human cell types and one mouse cell type. Detailed information about all files (and file formats) uploaded to GEO for this study can be found in the supplementary file 'GSE63525_OVERALL_README.rtf'.
DOI: 10.26036/cnphis0001885
title: Gobio acutipinnatus Transcriptome or Gene expression

description: Gobio acutipinnatus is an endemic fish of the Irtysh River basin in Sinkiang, northwest China. The wide distribution of the species makes it an ideal model for ecological analyses in this area, which has been rarely performed before. However, at present the available molecular markers for this species are very scarce. Transcriptomes from brains and livers of six individuals, which were collected from up-, mid- and down- streams of the river located in China, were sequenced using Illumina paired-end sequencing technology.
DOI: 10.26036/cnphis0001886
title: De novo Sequencing and Assembly of the Egyptian Water Buffalo Genome

description: Production of a high resolution draft genome of Egyptian buffalo. Partial annotation of the genome to identify genetic features within the sequenced of genes, regulatory elements, and repeat families. genomes: These features include, but not limited to, identification genes, regulatory elements, and repeat families.
DOI: 10.26036/cnphis0000492
title: Multi_sequencing_of_2P2cell_HCC.SRP026600

description: We sequenced the WGS/transcriptome of 2 HCC patients and 2 Cellline.
DOI: 10.26036/cnphis0000493
title: Multi_sequencing_of_2P2cell_HCC.SRP026601

description: We sequenced the WGS/transcriptome of 2 HCC patients and 2 Cellline.
DOI: 10.26036/cnphis0000494
title: Oryza sativa Indica Group strain:93-11 Genome sequencing

description: The 93-11 rice cultivar is one of important strains in Oryza sativa indica group, here, we provide more NGS raw data including genomic data and transcriptome.
DOI: 10.26036/cnphis0000495
title: Ursus maritimus Genome sequencing and assembly

description: The polar bear (Ursus maritimus) is one of the largest land carnivores, second only to the Alaskan brown bear. In an effort to adapt to the extremely cold Arctic environment, it has evolved many unique characteristics. However, ecological pressures pose a grave threat to the survival of polar bears. The polar bear genome provides significant contributions to research concerning evolution, biodiversity and climate change.
DOI: 10.26036/cnphis0000496
title: Chaetura pelagica Genome sequencing and assembly

description: The whole genome de novo sequencing of Chaetura pelagica.
DOI: 10.26036/cnphis0000497
title: Haplotype-based noninvasive prenatal testing of monogenic disease by maternal plasma sequencing

description: This study aims to realize the noninvasive prenatal testing of monogenic disease in spontaneous sample, and prove the feasibility and potential of clinical integration.
DOI: 10.26036/cnphis0000498
title: Haplotype-based noninvasive prenatal diagnosis of congenital adrenal hyperplasia by maternal plasma sequencing

description: The aim of this study was to demonstrate the feasibility of the haplotype-based noninvasive method for prenatal diagnosis of congenital adrenal hyperplasia
DOI: 10.26036/cnphis0000499
title: Calypte anna Genome sequencing and assembly

description: The whole genome sequencing of Calypte anna.
DOI: 10.26036/cnphis0001204
title: Nasonia vitripennis laboratory outbred population HVRx genome sequencing

description: Pooled genome sequencing of a genetically variable laboratory population (HVRx), originating from lines collected at the Hoge Veluwe in the Netherlands.
DOI: 10.26036/cnphis0001205
title: The sequence of HCC1395 (ATCC CRL-2324) and HCC1395BL (ATCC CRL-2325) human cell lines

description: This project contains whole genome, exome and transcriptome sequence from the HCC1395 (ATCC CRL-2324) breast carcinoma and corresponding HCC1395BL (ATCC CRL-2325) B lymphoblastoid cell lines of a 43 year old white female with a TNM stage I, grade 3 primary ductal carcinoma and a prior history of cancer.
DOI: 10.26036/cnphis0001206
title: Ceratitis capitata Genome sequencing

description: Whole genome assembly of Mediterranean fruit fly (Ceratitis capitata) as part of the BCM-HGSC i5k Pilot Project
DOI: 10.26036/cnphis0001207
title: Athalia rosae isolate:CS-ADULT Genome sequencing

description: Whole genome assembly of Athalia rosae (Turnip sawfly) as part of the BCM-HGSC i5k Pilot Project.
DOI: 10.26036/cnphis0001208
title: P&G gingivitis Targeted Locus

description: Gingivitis is the most common gum infection, yet its etiology remains elusive. We designed a retrogression-progression model (RPM) to simulate the development and reoccurrence of gingivitis. Fifty adults underwent a controlled transition from naturally occurring gingivitis (NG) to healthy gingivae (Baseline), then back to experimental gingivitis (EG). Within-subject temporal dynamics in taxonomic structure (for the 150 plaque microbiota samples) and functional profiles (for 18 of them) were observed via 16S rRNA gene and shotgun metagenomic sequencing respectively. 16S barcoded pyrosequencing for 273 oral plaque samples.
DOI: 10.26036/cnphis0001209
title: P&G gingivitis Metagenome

description: Here we report the within-subject changes in microbial functional profile related to human gingivitis occurrence via shotgun metagenomic sequencing.
DOI: 10.26036/cnphis0001210
title: Anopheles melas Genome sequencing project

description: None
DOI: 10.26036/cnphis0001211
title: Anopheles arabiensis Dongola Genome sequencing project

description: None
DOI: 10.26036/cnphis0001212
title: Anopheles quadriannulatus SANGWE Genome sequencing project

description: None
DOI: 10.26036/cnphis0001887
title: Sarcoptes scabiei isolate:Arlian Lab Genome sequencing and assembly

description: The genome sequence data will enable research on the biology, culture, host specificity and antigens of the scabies mite, Sarcoptes scabiei.
DOI: 10.26036/cnphis0001888
title: Whole-genome sequencing of several dipteran insects Genome sequencing

description: The genomes of several insect species were sequenced and their X-chromosomes characterized.
DOI: 10.26036/cnphis0001889
title: Alectoris rufa gene expression

description: The purpose of this study is to investigate the transcriptional profiles underlying the different ability of red-legged partridges (Alectoris rufa) to cope with pathogens and external aggressions.
DOI: 10.26036/cnphis0001890
title: Tachysurus fulvidraco Genome sequencing

description: This is the whole genome sequence dataset. The samples are sequenced by Illumina Hiseq platform.