cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0001539
title: Calanus glacialis Genome sequencing

description: Genome sequencing of Calanus glacialis for development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification
DOI: 10.26036/cnphis0001540
title: Staphylococcus aureus subsp. aureus Genome sequencing

description: Community associated methicillin resistant Staphylococcus aureus (CA-MRSA) has emerged as a major public health problem around the world. In Australia, ST93-IV[2B] is the dominant CA-MRSA clone and displays significantly greater virulence than other S. aureus. Here we have examined the evolution of ST93 via genomic analysis of 12 MSSA and 44 MRSA ST93 isolates, collected from around Australia over a 17-year period.
DOI: 10.26036/cnphis0001541
title: Malus baccata var. xiaojinensis Transcriptome or Gene expression

description: Describe genes expression after iron starvation in Malus xiaojinensis
DOI: 10.26036/cnphis0001542
title: Whole genome capture of mammoth DNA

description: Pre- and post-enrichment sequencing of whole genome-captured mammoth DNA
DOI: 10.26036/cnphis0002218
title: Discovery of progenitor signatures by time series synexpression analysis during Drosophila cell immortalization [RNA-Seq]

description: To characterize the sequence of events associated with RasV12 immortalization of Drosophila embryonic cells, we generated transcriptional time series during cell line establishment, from primary cultures until passage (P) 19. Overall design: We generated three transcriptional time series from three cell lines (R1, R4 and R5) by sampling the cultures at successive stages, early (P2-4), intermediate (P4-11), and late (P16-19), characterized by different passage times. Time points for the R1 time-series were: P2, P3, P4, P5, P7, P8, P10, P11, P16, P17 and P19; for the R4 time-series: P2, P3, P4, P5, P6, P7, P9, P11, P12, P16, P17 and P19; and for the R5 time-series: P2, P3, P4, P6, P7, P8, P16, P17 and P19
DOI: 10.26036/cnphis0002219
title: Single cell sequencing identifies clonal stasis and punctuated copy number evolution in triple negative breast cancer patients

description: We sequenced 1000 single cells from 12 triple negative breast cancer patients for copy number profilings. All samples were collected from primary tumors before treatments.
DOI: 10.26036/cnphis0002220
title: Coenagrion scitulum Raw sequence reads

description: We studied the genomic signature of range expansion in the damselfly Coenagrion scitulum using 4950 newly developed genomic SNPs and linked this to the rapidly evolved phenotypic differences between core and (newly established) edge populations.
DOI: 10.26036/cnphis0002221
title: Endometrial cancer microbiome

description: None
DOI: 10.26036/cnphis0002222
title: Intestinal microbiota dynamics in hospitalized patients

description: Using whole-metagenome shotgun sequencing, we examined the diversity and composition of the fecal microbiota in a prospective cohort study of 98 hospitalized patients.
DOI: 10.26036/cnphis0002223
title: Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes

description: We report the single-cell RNA-seq based identification of 6 known human islet cell types (alpha cells, beta cells, delta cells, pp cells, acinar cells and duct cells) based on the expression of known marker genes. We further assess cell type specific gene expression and suggest novel marker genes for several cell types. Overall design: Transcriptional dissection of human pancreatic islets of one donor using single-cell RNA-seq
DOI: 10.26036/cnphis0002224
title: Cottus genome sequencing and assembly

description: De novo assembly and analysis of two Cottus species.
DOI: 10.26036/cnphis0002225
title: Total RNA sequencing in multiple Sus Scrofa tissues reveals novel long non-coding RNAs functioning in skeletal muscle development

description: Long non-coding RNAs (lncRNAs) play important roles in diverse biological processes. However, the landscape of lncRNAs is largely unclear in Sus scrofa. Here we performed stranded RNA-seq on total RNA libraries from over 100 samples of Sus scrofa tissues. We identified 10,813 lncRNAs in Sus scrofa, of which 9,075 are novel. 57% of these lncRNAs were conserved in both human and mouse. These conserved lncRNAs tend to be more tissue-specific than pig-specific lncRNAs, and enriched in reproducible organs (i.e. testis and ovary). We characterized a group of lncRNAs potentially involved in the skeletal muscle development. One such lncRNA, a homolog of maternally expressed gene 3 (MEG3), was specifically expressed in the skeletal muscle at early developmental stage. And its expression pattern is conserved in pig and mouse. By over-expressing and knocking down MEG3 in mouse myoblast cell lines, we demonstrated its novel function as a myoblast proliferation suppressor. Overall design: A comprehensive lncRNA profile in pig by total RNA sequencing Please note that ''TCONS_000nnnn'' identifiers in the *RPKM.txt processed data files are the new lncRNAs we identified in our study and that the ''sus_lncRNA.fa'' contains the sequence information for each feature.
DOI: 10.26036/cnphis0002226
title: Ptilocercus lowii Raw sequence reads

description: Whole genome sequence of Ptilocerucus lowii generated to establish phylogenetic relationships among euarchontans and mammals and explore evolution of sensory genes.
DOI: 10.5284/1049649
title: Land adjacent to 173 Watling Street, Towcester, Northamptonshire. Archaeological Evaluation (OASIS ID: kdkarcha1-201140)

description: In February 2015, an archaeological evaluation was undertaken on land adjacent to 173 Watling Street, Towcester, Northamptonshire, in order to inform development proposals for the site. A 2m2 test pit was excavated close to the north western boundary of the site. The upper fills of this test pit comprised layers of post medieval and modern made ground. These overlay a layer of dark soil, which was still present c.2.5m below the modern ground level. The natural stratum was not reached within the test pit. This deep layer of dark soil may represent a post Roman build-up of material, which has been seen elsewhere within Towcester town centre. While no significant archaeological remains were encountered during the evaluation, it is possible that they may survive below this layer, or elsewehere within the development site.
DOI: 10.26036/cnphis0001543
title: RNAseq Analysis of Formalin-Fixed Paraffin-Embedded Prostate Cancer Tissues

description: In an effort to identify biomarkers of recurrence, we have performed global RNA-sequencing on 106 formalin-fixed, paraffin-embedded (FFPE) prostatectomy samples from 100 patients at three independent sites, and identified a new set of biomarkers of biochemical recurrence composed of a 24-gene panel. We validated this 24-gene panel on an independent publicly available dataset of 140 patients and this new panel outperformed previously published markers based on cell proliferation gene sets in terms of prediction of biochemical recurrence (BCR). In addition we identified differences in gene expression between Gleason Pattern 4+3 and Gleason Pattern 3+4 tumors. Overall design: 106 samples from 100 patients were sequenced. Six samples were sequenced from two independent RNA preps and libraries. All samples were taken from FFPE Radical Prostatectomies. Samples were obtained from Atlanta VA Medical Center, U. Toronto Sunnybrook Research Centre, and Moffitt Cancer Center.
DOI: 10.26036/cnphis0001544
title: Centrocercus minimus Genome sequencing

description: The goal of this study was to assemble a high-quality genome sequence for Centrocercus minimus. Furthermore, using relatively low sequencing coverage and a distantly-related guide genome (Gallus gallus) we empirically compared de novo and reference-guided assembly techniques.
DOI: 10.26036/cnphis0001545
title: Nucifraga columbiana Genome sequencing

description: Empirical comparison of assembly approaches in Clark''s Nutcracker (Nucifraga columbiana)
DOI: 10.26036/cnphis0001546
title: Zea mays Transcriptome or Gene expression

description: Maize is one of the most important crops in the world and serves as an excellent model for seed development research. Despite the important role of the transcriptome in development, genome-wide expression throughout the process of maize seed development has not been characterized. Using RNA-seq, we developed a spatio-temporal transcriptome atlas of B73 maize seed development from fertilization to maturity for embryo, endosperm, and whole seed tissue.
DOI: 10.26036/cnphis0001547
title: Zea mays Transcriptome or Gene expression

description: We explored the expression profile among the development of maize embryo and endosperm
DOI: 10.26036/cnphis0001548
title: Honey Bee Genome sequencing

description: Whole genome sequences for Apis mellifera scutellata, Apis mellifera jemenitica, Apis mellifera monticola, and Apis mellifera litorea
DOI: 10.26036/cnphis0001549
title: Tigriopus californicus strain:San Diego Genome sequencing

description: This project aims at sequencing the genome of the marine copepod Tigriopus californicus. This species has served as an excellent model for studies of speciation, adaptation, and physiology.
DOI: 10.26036/cnphis0001550
title: Pleurobranchaea maculata Genome sequencing

description: Pleurobranchaea maculata is a native species to New Zealand coastal water. This poorly understood organism was found to contain high concentrations of tetrodotoxin. There is no molecular markers available for P. maculata. We sequenced the organism''s genome to develop microsatellite markers markers for further use to study the population genetics of this organism and to reveal any association between different toxicity levels and genetic structure. Here, we submit the sequences that were used for developed microsatellite merkers.
DOI: 10.26036/cnphis0002227
title: Microbiome in Cowpat Targeted Locus (Loci)

description: Project aims to study the aging process dynamics of fecal microbiomes in intact cowpats exposed to natural environments. Fresh cowpats were sampled at multiple time points for 57 days under field conditions; half the samples were exposed to sunlight (unshaded) while the other half was protected from sunlight (shaded). The 16sRNA hypervariable region 4 was amplified from each sample and sequenced on an Illumina MiSeq Platform.
DOI: 10.26036/cnphis0002228
title: Anolis carolinensis Raw sequence reads

description: Raw sequence reads from formalin-fixed museum specimen
DOI: 10.26036/cnphis0002229
title: Haliotis tuberculata Transcriptome or Gene expression

description: Transcriptome of the European abalone Haliotis tuberculata, comprising larval tissue exposed to two pHs and two temperatures and adult tissue deriving from two populations, exposed or unexposed to bacterial infection.
DOI: 10.26036/cnphis0002230
title: Nothura darwinii Genome sequencing

description: SSR discovery using Illumian MiSeq data
DOI: 10.26036/cnphis0002231
title: Nothoprocta ornata Raw sequence reads

description: Search for microsatellites markers using Illumina MiSeq data.
DOI: 10.26036/cnphis0002232
title: Mesocentrotus franciscanus Genome sequencing and assembly

description: Sea urchins are marine invertebrates of extreme diversity of life span. Red sea urchin S. franciscanus is among the longest living creatures of the Ocean. Its lifetime is estimated to exceed a century, while the green sea urchin L. variegatus hardly survive more than 3 years. We sequenced and compared the genomes of these animals aiming at determination of the genetic basis of their longevity difference. List of genes related to the longevity of other animal species was created and used for homology search among the genomic data obtained in this study. Aminoacid sequences of longevity related proteins of S. fransciscanus and L. variegatus as well as from a set of model species, were aligned and grouped on the basis of the species lifespan. Aminoacid residues specific for a longevity group were identified. Proteins containing aminoacids whose identity correlated with the lifespan were clustered on the basis of their function.
DOI: 10.26036/cnphis0002233
title: Ruditapes philippinarum Transcriptome or Gene expression

description: Transcriptome of the Japanese clam Ruditapes philippinarum, comprising larval tissue exposed to two pHs and two temperatures
DOI: 10.26036/cnphis0002234
title: Salmonella enterica subsp. enterica serovar Heidelberg Genome sequencing and assembly

description: Develop molecular sub typing scheme based on whole genome sequencing data of Salmonella Heidelberg
DOI: 10.26036/cnphis0002235
title: Caenorhabditis elegans Genome sequencing

description: During the first meiotic division, crossovers (COs) between homologous chromosomesensure their correct segregation. COs are produced by homologous recombination(HR) mediated repair of programmed DNA double strand breaks (DSBs). As moreDSBs are induced than COs, mechanisms are required to establish a regulatednumber of COs and to repair remaining intermediates as non-crossovers (NCOs). Weshow that the Caenorhabditis elegans RMI homolog RMH-1 functions during meiosis topromote both CO and NCO HR at appropriate chromosomal sites. RMH-1 accumulatesat CO sites, dependent on known pro-CO factors, and acts to promote CO designationand enforce the CO outcome of HR-intermediate resolution. RMH-1 also localizes atNCO sites and functions in parallel with SMC-5 to antagonize excess HR-basedconnections between chromosomes. Moreover, RMH-1 also has a major role inchanneling DSBs into a NCO HR outcome near the centers of chromosomes, therebyensuring that COs form predominantly at off-center positions.
DOI: 10.26036/cnphis0001551
title: Angiosperm species Genome sequencing

description: Highly Effective Sequencing Whole Chloroplast Genomes of Angiosperms by Nine Novel Universal Primer Pairs
DOI: 10.26036/cnphis0001552
title: A rat RNA-Seq transcriptomic Bodymap across eleven organs and four developmental stages

description: The rat has been used extensively as a model for evaluating chemical toxicities and for understanding drug mechanisms. However, its transcriptome across multiple organs, or developmental stages, has not yet been reported. Here we show, as part of the SEQC consortium efforts, a comprehensive rat transcriptomic BodyMap created by performing RNASeq on 320 samples from 11 organs of both sexes of juvenile, adolescent, adult and aged Fischer 344 rats. We catalogue the expression profiles of 40,064 genes, 65,167 transcripts, 31,909 alternatively spliced transcript variants and 2,367 non-coding genes/non-coding RNAs (ncRNAs) annotated in AceView. We find that organ-enriched, differentially expressed genes reflect the known organ-specific biological activities. A large number of transcripts show organ-specific, age-dependent or sex-specific differential expression patterns. We create a web-based, open-access rat BodyMap database of expression profiles with crosslinks to other widely used databases, anticipating that it will serve as a primary resource for biomedical research using the rat model. Overall design: We constructed a comprehensive RNA-Seq data set for studying the dynamics of the rat transcriptome using 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old). Four biological replicates were used for each of the 80 sample groups.
DOI: 10.26036/cnphis0001553
title: Cuscuta reflexa Transcriptome or Gene expression

description: RNA-Seq in order to determine host mobile transcripts in C. reflexa.
DOI: 10.26036/cnphis0001554
title: Sponge treated by PBDE-47 Metagenome

description: To study the effect of PBDE-47 on the microbial community in sponge
DOI: 10.26036/cnphis0001555
title: Whole genome sequencing, assembly and annotation of Agrilus planipennis

description: Whole genome sequencing, assembly and annotation of Emerald Ash Borer
DOI: 10.26036/cnphis0001556
title: Haliaeetus leucocephalus Genome sequencing and assembly

description: The American bald eagle experienced a population decline due to environmental pollutants that at one point could have led to extinction. The bald eagle genome now allows scientists to study the effects of this population bottleneck and monitor genetic diversity to better manage conservation efforts.
DOI: 10.26036/cnphis0001557
title: Centruroides sculpturatus isolate:CEXI.00-Female Genome sequencing

description: Whole genome assembly of Bark scorpion (Centruroides sculpturatus) as part of the BCM-HGSC i5k Pilot Project
DOI: 10.26036/cnphis0001558
title: Felis catus Genome sequencing and assembly

description: In September 2011, The Genome Institute at Washington University School of Medicine, in collaboration with Agencourt Bioscience Corporation and the Broad Institute, submitted an updated <i>Felis catus</i> assembly. The DNA source for this assembly, Felis_catus-6.2, is a female Abyssinian cat named Cinnamon. The assembly is a combination of WGS sequence and 454 sequencing, for a combined genome coverage of 14x. Details on the assembly process are described in the WGS project accession AANG00000000.
DOI: 10.26036/cnphis0001559
title: Sus scrofa scrofa strain:Nong Da Xiang Transcriptome or Gene expression

description: provide a resource for pluripotent stem cell engineering and for understanding pig development
DOI: 10.26036/cnphis0001560
title: 1000 Bull Genomes Run 2, Bovine Whole Genome Sequence

description: Whole genome sequence data (BAM format) of 234 bovine individuals aligned to UMD3.1. The aim of the study was to identify genetic variants (SNPs and indels) for downstream analysis such as imputation, GWAS, and detection of lethal recessives. Additional sequences for later 1000 bull genomes runs can be found at partners individual projects including PRJEB9343, PRJNA176557, PRJEB18113, PRNJA343262, PRJNA324822, PRJNA324270, PRJNA277147, PRJEB5462.
DOI: 10.26036/cnphis0002236
title: Pecten maximus Transcriptome or Gene expression

description: Transcriptome of the great scallop Pecten maximus, comprising larval tissue exposed to two pHs and two temperatures.
DOI: 10.26036/cnphis0002237
title: Mytilus chilensis sequence reads

description: raw illumina data obtained using RAD-seq from 190 individual of Chilean blue mussel form six location from southern Chile
DOI: 10.26036/cnphis0002238
title: Daphnia magna strain:Xinb3 Genome sequencing and assembly

description: The waterflea Daphnia magna is used to explore gene x environment interactions, central to the food web of lentic aquatic habitats and a model for environmental health. This study develops a genome assembly of Daphnia magna
DOI: 10.26036/cnphis0002239
title: Ailuropoda melanoleuca Genome sequencing and assembly

description: Sequence and analysis of the giant panda genome to understand the genome structure and genome evolution
DOI: 10.26036/cnphis0002240
title: Folsomia candida strain:VU population Genome sequencing and assembly

description: The genome of the Folsomia candida
DOI: 10.26036/cnphis0002241
title: Acinonyx jubatus Genome sequencing

description: Six cheetah samples were sequenced with 5-6x coverage. Three from Tanzania and three from Namibia.
DOI: 10.26036/cnphis0002242
title: Acinonyx jubatus Genome sequencing and assembly

description: High coverage whole genome sequencing and draft genome assembly of African cheetah, Acinonyx jubatus.
DOI: 10.26036/cnphis0002243
title: Trachinotus blochii Transcriptome or Gene expression

description: The transcriptome of Trachinotus blochii pituitary and liver under high and low temperature
DOI: 10.26036/cnphis0002244
title: A collection of grey wolves and dogs Genome sequencing

description: Large scale sequencing of dogs and wolves.
DOI: 10.26036/cnphis0001561
title: Salmonella enterica subsp. enterica serovar enteritidis Genome sequencing

description: develop molecular sub typing scheme based on whole genome sequencing data
DOI: 10.26036/cnphis0001562
title: Gallus gallus Transcriptome or Gene expression

description: The goal of this project is to identify the differently expressed genes.
DOI: 10.26036/cnphis0001563
title: Unbiased Capture Hi-C reveals the potential targets of breast cancer susceptibility loci

description: Genome-wide association studies have identified over 70 common variants that are associated with breast cancer risk. Most of these variants map to non-protein-coding regions; several map to gene deserts, regions of several hundred kb lacking protein-coding genes. We hypothesized that gene deserts harbour long-range regulatory elements that can physically interact with target genes to influence their expression. To test this, we developed Capture Hi-C (CHi-C), which by incorporating a sequence capture step into a Hi-C protocol, allows high-resolution analysis of targeted regions of the genome. We used CHi-C to investigate long-range interactions at three breast cancer gene deserts mapping to 2q35, 8q24.21 and 9q31.2. We identified interaction peaks between putative regulatory elements ("bait fragments") within the captured regions and "targets" that included both protein-coding genes and long non-coding (lnc)RNAs, over distances of 6.6 kb to 2.6 Mb. Target protein-coding genes were IGFBP5, KLF4, NSMCE2 and MYC; target lncRNAs included DIRC3, PVT1 and CCDC26. For two gene deserts we were able to define a set of SNPs that were correlated with the published risk variant and that clustered within the bait end of an interaction peak. Preliminary functional analyses implicate one SNP (rs12613955; 2q35) as a potentially functional variant. Overall design: Capture Hi-C was carried out in BT483, SUM44, and GM06990 cell lines to investigate breast cancer risk loci 2q35, 8q24.21 and 9q31.2.
DOI: 10.26036/cnphis0001564
title: Trichuris suis Genome sequencing and assembly

description: The intestine whipworm Trichuris suis, is commonly found in porcine intestinal track, causing diarrhea, anorexia, anemia, poor growth, dehydration, and emaciation. Following these initial symptoms, secondary infections can set in and cause death. The whipworm can colonize humans but after a limited time is cleared from the individual without causing infection. Trichuris suis ova have been studied as a potential treatment for auto-immune disease such as Crohn''s disease through the repression of Th1 response.
DOI: 10.26036/cnphis0001565
title: Microphysogobio brevirostris Transcriptome or Gene expression

description: Microphysogobio brevirostris, perch in shallow, is one of the endemic species in Taiwan. Microphysohobio brevirostris take the seaweed and other organic scrap under the water for food. Thus, the tissue of Microphysohobio brevirostris could be taken to deeply sequence for water heavy metals detection. Due to the ecological importance of Microphysogobio brevirostris, genomic data are eagerly needed. However, there is still no sufficient data available. Thus, this project is to sequence transcriptome deeply and provide well-assembled transcriptome sequences and annotation for Microphysohobio brevirostris research.