cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0001566
title: Zea mays Transcriptome or Gene expression

description: Most angiosperm nuclear DNA is repetitive and derived from silenced transposable elements (TEs). TE silencing requires substantial resources from the plant host, including the production of small interfering RNAs (siRNAs). Thus, the interaction between TEs and siRNAs is a critical aspect of both the function and the evolution of plant genomes. Yet the co-evolutionary dynamics between these two entities remains poorly characterized. Here we studied the organization of TEs within the maize (Zea mays ssp mays) genome, documenting that TEs fall within three groups based on the class and copy numbers. These groups included DNA elements, low copy RNA elements and higher copy RNA elements. The three groups varied statistically in characteristics that included length, location, age, siRNA expression and 24:22 nucleotide (nt) siRNA targeting ratios. In addition, the low copy retroelements encompassed a set of TEs that had previously been shown to decrease expression within a 24 nt siRNA biogenesis mutant (mop1). To investigate the evolutionary dynamics of the three groups, we estimated their abundance in two landraces, one with a genome similar in size to that of the maize reference and the other with a 30% larger genome. For all three accessions, we assessed TE abundance as well as 22 nt and 24 nt siRNA content within leaves. The high copy number retroelements are under targeted similarly by siRNAs among accessions, appear to be born of a rapid bust of activity, and may be currently transpositionally dead or limited. In contrast, the lower copy number group of retrolements are targeted more dynamically and have had a long and ongoing history of transposition in the maize genome Overall design: We compared TE abundances and siRNA profiles among B73 (maize inbred line) and two additional maize landraces, Palomero Toluqueño (PT) and Olote Colorado (OAXA) using HTS
DOI: 10.26036/cnphis0001567
title: Pinellia ternata transcriptome

description: None
DOI: 10.26036/cnphis0001568
title: GenomeTrakr real-time SE: Minnesota Department of Health

description: Surveillance of Salmonella Enteritidis using SNP based phylogenetic analysis. GenomeTrakr Project: Minnesota Department of Health
DOI: 10.26036/cnphis0001569
title: Glycine max strain:HX3 Transcriptome or Gene expression

description: RNA-seq were performed for 11 soybean tissues,and this data significantly improved soybean gene annotation, and also provide valuable resources for functional genomics and studies of the evolution of duplicated genes from WGDs in soybean.
DOI: 10.26036/cnphis0002245
title: GEO accession GSE74310 is currently private and is scheduled to be released on Mar 01, 2016.

description: If GEO accession GSE74310 has been cited in a publication, please notify us at geo@ncbi.nlm.nih.gov to initiate the public release of associated data.
DOI: 10.26036/cnphis0002246
title: Ceratina calcarata isolate:Rehan_Ccalc_2016 Genome sequencing and assembly

description: Ceratina calcarata (Hymenoptera: Apidae) is a subsocial bee species and important native pollinator in eastern North America (Rehan & Richards 2010a, b). C. calcarata is subsocial, and does not have morphological castes or reproductive division of labor. Unlike highly eusocial, caste-differentiated species, such as honeybees, Ceratina species display behavior thought to be necessary precursors to highly social behaviors, such as maternal care, nest loyalty, cohabitation, and adult longevity. In this study, we present the draft genome and methylome of the facultatively social small carpenter bee, C. calcarata. We will then compare the genome architecture to the previously published Hymenoptera and other social insects genomes to identify genomic regions under selection and help to provide the first evidence for the genetic basis at the onset of sociality.
DOI: 10.26036/cnphis0002247
title: Saskatchewan epidemiological study of Salmonella enterica serovar Typhimurium 14028

description: Laboratory–acquired infections continue to occur despite advances in laboratory design, professional training, and adherence to laboratory standards. In the event of a laboratory-acquired illness, uncovering the source of infection is a prerequisite for identifying and correcting laboratory deficiencies and preventing future LAIs. We investigated suspected cases of laboratory–acquired salmonellosis using a combination of pulsed field gel electrophoresis (PFGE) and whole genome sequencing.
DOI: 10.26036/cnphis0002248
title: Cephalopods raw sequence reads

description: RNA and genomic DNA sequencing of three cephalopod species
DOI: 10.26036/cnphis0002249
title: Red coloration in Birds

description: Comparison of polymorphism in red siskins (Spinus cucullata), common canaries (Serinus canaria), and 30 red factor canaries (hybrid variety produced by crossing red siskins with yellow canaries), to infer regions of the genome responsible for red coloration in birds.
DOI: 10.26036/cnphis0002250
title: Human gut environment Targeted loci environmental

description: Here we associate microbial community membership with distinct phenotypes of colorectal lesion. By performing 16S rRNA gene sequencing on mucosal biopies obtained from colorectal cancer-free patients, patients with adenomatous polyps, and patients with adenocarcinomas, we characterized the taxonomic configurations of microbial community to examine how disease progression is associated with changes in microbial community types.
DOI: 10.26036/cnphis0002251
title: Evaluating genomic divergence and parallelism in replicate ecomorphs from young and old cichlid adaptive radiations

description: Comparative genomic studies of closely related species typically focus on single species pairs at one given stage of divergence. That makes it difficult to infer the continuum of evolutionary process during speciation and beyond. Here, we use whole-genome resequencing to examine genomic patterns of divergence in three sympatric cichlid species pairs with very similar functional and ecological differentiation, but different ages.
DOI: 10.26036/cnphis0002252
title: Variegated Mutant RNA-seq

description: Study Goal: Identify overlapping transcripts from variegated mutants ggps1, crl, and msl2 msl3 double mutants
DOI: 10.26036/cnphis0002253
title: Taenia saginata Genome Sequencing

description: The beef tapeworm, Taenia saginata, is the casual agent of human and bovine cysticercosis. This worm has many similarities with the widely known pork tape worm, Taenia solium, but they act different on the infection procedure. We expect to find out their genomic differences by sequecing and comparing them, and try to find out the key genes that have relations with the infection.
DOI: 10.26036/cnphis0001570
title: Comparative Genomics of Lepidoptera

description: As a ressource for gene mining, we performed the low coverage (5-15x) sequencing of several lepidopteran and trichopteran species using Illumina technology.
DOI: 10.26036/cnphis0001571
title: Transcriptome profiling of siliques at 4 developmental stages in Arabidopsis

description: To search for the differential expressed genes during postferlization and embryonic development in Arabidopsis, We profiled transcriptome of siliques at 4 developmental stages using RNA-seq based on poly(A) selection. Each RNA library yielded 100 million 101-bp paired-end reads.Using Tophat and Cufflinks with the Arabidopsis TAIR10 annotation as reference, we identifed 33,451 assembled transcripts in 4 samples. Of them, 5,608 were up-regulated genes in at least one sample. A group of them are preferentially expressed at mature green-stage of seeds. Overall design: Transcriptome profiling in 0-5 day, 6-10 day, 11-15 day and 16-20 day post-anthesis siliques
DOI: 10.26036/cnphis0001572
title: Genome sequencing of Trichogramma pretiosum and its endosymbiont

description: Whole genome assembly of Parasitic wasp (Trichogramma pretiosum) as part of the BCM-HGSC i5k Pilot Project
DOI: 10.26036/cnphis0001573
title: Esox lucius isolate:CL-BC-CA-002 Genome sequencing

description: The pike (Esox lucius) is a northern hemisphere, circumpolar, fresh water species that is typically the top predator in many lakes. It is an important northern recreational fishery. Pike are morphologically diverse and highly adaptable. Despite their wide distribution, pike populations have low levels of polymorphism and divergence, indicative of a recent common ancestor. Pike often function as sentinel species to monitor pollutants in northern waters. Mitochondrial studies have shown that Escosiformes is the closest living order to Salmoniformes. Esociformes, an old lineage with fossils dating back to 70MYA, contains 10 species (pike, muskellunge and mudminnows) of which most literature concerns pike. The genome size for pike is 1.1pg and its karyotype is 2N=50 NF=50, similar to ancestral karyotypes of many teleosts (2N=48-50, FN=48-50). This compares to the much larger Atlantic salmon karyotype of 2N=56-60, NF=74 and genome size =3.1pg. Recent studies are consistent with the pike having a pre-WGD genome and being much closer to salmon than other fish species (zebrafish, medaka, fugu or stickleback).
DOI: 10.26036/cnphis0001574
title: Bos frontalis strain:Nagaland Genome sequencing

description: Mithun Bos frontalis Whole Genome sequencing in India
DOI: 10.26036/cnphis0001575
title: Melospiza melodia Transcriptome or Gene expression

description: RNA sequencing from auditory forebrain samples.
DOI: 10.26036/cnphis0001576
title: Gerris buenoi Genome sequencing

description: Whole genome assembly of Water strider (Gerris buenoi) as part of the BCM-HGSC i5k Pilot Project.
DOI: 10.26036/cnphis0001578
title: PulseNet Salmonella enterica Genome sequencing

description: Salmonella enterica genomes sequenced as part of PulseNet USA surveillance for foodborne disease
DOI: 10.26036/cnphis0002254
title: Glyceridae (Annelida) Genome and Transcriptome Sequencing

description: This BioProject contains assembled sequences from Next-Generation Sequencing of Glyceridae (Annelida).
DOI: 10.26036/cnphis0002255
title: Codfish genome sequencing

description: Genome sequencing of closely related codfish from North Pacific, Arctic and North Atlantic to study natural selection and speciation.
DOI: 10.26036/cnphis0002256
title: Drosophila melanogaster strain:Gr66aGal4/UAS-H2B YFP (TOG)/ Orco Gal4/UAS-H2B YFP (DOG) Transcriptome or Gene expression

description: examine the differential expression of chemoreceptors in the two main chemosensory organs of the Drosophila larvae
DOI: 10.26036/cnphis0002257
title: Long non-coding RNAs in psoriatic and healthy skin

description: In this study, we used RNA-sequencing to profile the long non-coding RNA (lncRNA) transcriptome in lesional skin from psoriasis patients before (PP) and after treatment (PT) with adalimumab and in normal skin from healthy individuals (NN). For this we sequenced total RNA from 18 psoriasis patients (before and after treatment) and 16 healthy controls. We created our own reference set of long non-coding RNAs by merging three long non-coding RNA reference data sets. The combined reference had 67,157 lncRNA transcripts with no overlaps. We identified differential expression of 971 lncRNAs between PP and NN, 157 between PP and PT, and 377 between PT and NN. Based on differentially expressed (DE) lncRNAs between PP and NN, we identified a molecular lncRNA signature that distinguishes psoriatic skin from healthy skin . Overall design: We recruited 18 psoriatic patients in our study. We took 5 mm punch biopsies from the edge of a psoriatic plaque before treatment and after one month of treatment with adalimumab. The mean improvement in the PASI over this time period was 53.1%. We obtained sixteen normal skin samples (N=16) from healthy control surgical discard specimens.
DOI: 10.26036/cnphis0002258
title: Crotalus pyrrhus Genome sequencing

description: Draft assembly of whole genome sequence data for Crotalus mitchelli pyrrhus (the speckled rattlesnake), a member of the Crotalus mitchellii species complex (Viperidae) distributed throughout southwestern North America.
DOI: 10.26036/cnphis0002259
title: RNA-seq of 9 tissues from an adult male C57BL/6 mouse

description: RNA-editing is a tightly regulated, and essential cellular process for a properly functioning brain. Dysfunction of A-to-I RNA editing can have catastrophic effects, particularly in the central nervous system. Thus, understanding how the process of RNA-editing is regulated has important implications for human health. However, at present, very little is known about the regulation of editing across tissues, and individuals. Here we present an analysis of RNA-editing patterns from 9 different tissues harvested from a single mouse. For comparison, we also analyzed data for 5 of these tissues harvested from 15 additional animals. We find that tissue specificity of editing largely reflects differential expression of substrate transcripts across tissues. We identified a surprising enrichment of editing in intronic regions of brain transcripts, that could account for previously reported higher levels of editing in brain. There exists a small but remarkable amount of editing which is tissue-specific, despite comparable expression levels of the edit site across multiple tissues. Expression levels of editing enzymes and their isoforms can explain some, but not all of this variation. Together, these data suggest a complex regulation of the RNA-editing process beyond transcript expression levels. Overall design: Tissues include: brain, heart, kidney, liver, lung, skin, spleen, testis, thymus mRNA profiles of 9 tissues from an 8 week old, male C57BL/6 mouse were generated by deep sequencing using Illumina HiSeq.
DOI: 10.26036/cnphis0002260
title: GBS sequences from eight species of Grallaria antpittas. raw sequence reads

description: Objectives: to determinte phylogenetic relationships and understand biogeographic history of Grallaria in the Andes
DOI: 10.26036/cnphis0002261
title: A developmental coordinate of the spectrum of pluripotency among mice, monkeys, and humans

description: The epiblast (EPI) is the origin of all somatic and germ cells in mammals, and of the spectrum of pluripotent stem cells (PSCs) in vitro. To explore the ontogeny of human/primate pluripotency, we performed comprehensive single-cell RNA sequencing for pre- and post-implantation EPI development in cynomolgus monkeys. Here we show that after specification in the blastocysts [embryonic day (E)7], cyEPI undergoes major transcriptome changes upon implantation. Thereafter, cyEPI, while generating gastrulating cells (~E13), maintains its transcriptome relatively stably over a week, retaining a unique set of pluripotency genes while acquiring properties for “neuron differentiation.” h/cyPSCs show the highest similarity to post-implantation late cyEPI (~E17), which, despite co-existing with gastrulating cells, bears characteristics of pre-gastrulating mouse EPI (E5.5) and epiblast-like cells (EpiLCs) in vitro. These findings not only reveal divergence/coherence of EPI development, but also identify a developmental coordinate of the spectrum of pluripotency among key species, providing a basis for better regulation of human pluripotency in vitro. Overall design: Single cell transcriptome analysis of cynomolgus monkey embryo E6-17 and mouse embryo E4.5 - E6.5 as well as of cynomogus monkey embryonic stem cells (ESCs) and mouse ESC, epiblast like cells (EpiLCs), using SC3-seq technology.
DOI: 10.26036/cnphis0002262
title: Alligator mississippiensis isolate:KSC_2009_1 Genome sequencing and assembly

description: Long-range and highly accurate de novo assembly from short-read data is one of the most pressing challenges in genomics. Recently, it has been shown that read pairs generated by proximity ligation of DNA in chromatin of living tissue can address this problem. These data dramatically increase the scaffold contiguity of assemblies and provide haplotype phasing information. Here, we describe a simpler approach (“Chicago”) based on in vitro reconstituted chromatin. We generated two Chicago datasets with human DNA and used a new software pipeline (“HiRise”) to construct a highly accurate de novo assembly and scaffolding of a human genome with scaffold N50 of 30 Mbp. We also demonstrated the utility of Chicago for improving existing assemblies by re-assembling and scaffolding the genome of the American alligator. With a single library and one lane of Illumina HiSeq sequencing, we increased the scaffold N50 of the American alligator from 508Kbp to 10Mbp.
DOI: 10.26036/cnphis0001577
title: Loxosceles reclusa Genome sequencing

description: Whole genome assembly of Loxosceles reclusa (Brown Recluse Spider) as part of the BCM-HGSC i5k Pilot Project.
DOI: 10.26036/cnphis0001579
title: Whole genome assembly of Oncopeltus fasciatus using multiple sequencing technologies.

description: Whole genome assembly of Oncopeltus fasciatus using multiple sequencing technologies. Genomic DNA from Carolina Biological Supply (September 2008)
DOI: 10.26036/cnphis0001580
title: Canine gut metagenome Targeted Locus (Loci)

description: The purpose of this study was to evaluate the fecal microbiome in dogs with inflammatory bowel disease. We targeted the 16S rRNA gene for 454-pyrosequencing analysis. Samples from healthy dogs and dogs with inflammatory bowel disease (pre- and post-treatment) were analyzed.
DOI: 10.26036/cnphis0001581
title: Drosophila virilis Genome sequencing

description: 100 bp paired end reads from Blumenstiel lab strains of the Drosophila virilis hybrid dysgenesis syndrome: Strain 9 and Strain 160
DOI: 10.26036/cnphis0001582
title: Lucilia cuprina strain:LS Genome sequencing

description: Whole genome assembly of Sheep blowfly (Lucilia cuprina) as part of the BCM-HGSC i5k Pilot Project.
DOI: 10.26036/cnphis0001583
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001584
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001585
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001586
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001587
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0002263
title: Comparative sequence analyses of genome and transcriptome reveal novel transcripts and variants in the Asian elephant Elephas maximus

description: The study aim is to generate high qulity resource of genomic and transcriptome data for E. maximus. Here, we have carried out genomic and RNA sequencing from total lymphocytes of the captive Asian elephant Jayaprakash from Karnataka. Genome sequences were used to calculate single nucleotide varations (SNVs) in protein coding regions and found a significant enrichment of SNVs in coding regions of genes involved in olfaction function. Poly-A enriched RNA sequences were used to identify novel transcripts and for comparative transcriptome analysis to identify tissue specific genes of total lymphocytes.
DOI: 10.26036/cnphis0002264
title: HX1

description: Various sequencing data sets on HX1.
DOI: 10.26036/cnphis0002265
title: Homo sapiens Genome sequencing

description: The study was designed to compare the whole exome sequencing data between FFPE and frozen samples
DOI: 10.26036/cnphis0002266
title: Rock ptarmigan genome sequencing and assembly

description: Whole genome sequencing of rock ptarmigan (Lagopus muta). A muscle sample from a male collected in november 2012 NE-Iceland. Ref.nr. Icelandic Institute of Natural History LM12-040 male.
DOI: 10.26036/cnphis0002267
title: Phylogeny of grouse genera (Aves: Galliformes: Phasianidae: Tetreoninae). raw sequence reads

description: Raw sequence reads from target capture of ultraconserved elements.
DOI: 10.26036/cnphis0002268
title: Haliotis discus hannai isolate:LJ01 Raw sequence reads

description: transcriptome of digestive gland of Haliotis discus hannai
DOI: 10.26036/cnphis0002269
title: Clione limacina Raw sequence reads

description: whole body transcriptome of vClione limacina
DOI: 10.26036/cnphis0002270
title: Lagopus lagopus Genome sequencing and assembly

description: Whole genome sequencing a male Willow grouse (Lagopus lagopus) collected in Härjedalen in Sweden. Muscle sample is kept at Icelandic Institute of Natural History, Iceland.
DOI: 10.26036/cnphis0002271
title: Zonotrichia querula Raw sequence reads

description: Raw genomic DNA reads of Harris'' Sparrow
DOI: 10.26036/cnphis0001588
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001589
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001590
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001591
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001592
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001593
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001594
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001595
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001596
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0002272
title: Zonotrichia atricapilla isolate:UAM 28053 Raw sequence reads

description: whole genome sequence reads from Golden-crowned sparrow
DOI: 10.26036/cnphis0002273
title: Six species of Darwin''s Finches raw sequence reads

description: Study of genetic variation in Darwin''s Finches
DOI: 10.26036/cnphis0002274
title: Lepidothrix coronata genome sequencing and assembly

description: The blue-crowned manakin (Lepidothrix coronata) is a species of bird in the Pipridae family, which ranges from the Pacific slope of Costa Rica to northwestern Ecuador and in western Amazonia from Venezuela, Colombia, Ecuador, Peru, Brazil to Bolivia. Blue-crowned manakin males aggregate in leks, where they engage in competitive displays that may entice visiting females who are surveying prospective partners for copulation. High reproductive skew among males has led to the question why males join leks when their chances of reproductive success are so low. The genetic changes resulting in plumage variation among closely related taxa as in the blue-crowned manakin subspecies might represent important evolutionary events. The molecular basis of such differences in the blue-crowned manakin is an active area of research.
DOI: 10.26036/cnphis0002275
title: Variation in Onchocerca volvulus

description: Onchocerca volvulus, the filarial nematode that causes onchocerciasis, is widely endemic in sub-Saharan Africa and in partsof Latin America. The pathology ranges from sub-clinical symptoms to dermatitis and ocular disease, and epidemiologicalstudies have shown that blinding onchocerciasis is much more common in dry savannah regions than in rain forest regions ofWest Africa. To develop a comprehensive understanding of the population genetics and structure of O. volvulus, weinvestigated the genomic diversity within and between O. volvulus populations by analyzing whole-genome (nuclear,mitochondrial and Wolbachia) sequences of &gt;30 clinical parasite samples. Of these, 20 were collected from seven countriesin Africa (forest or savanna) and 10 from Ecuador in South America. The study also provides new information on thegenetic variability of potential vaccine, drug, and diagnostic targets.