cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0002422
title: CIS is a potent checkpoint in NK cell-mediated tumour immunity

description: Natural killer (NK) cells have evolved to detect and kill aberrant cells with this activity being governed by the cytokine interleukin (IL)-15 and foreign and self-ligands. We have identified CIS (Cytokine-inducible SH2-containing protein; Cish gene) as the critical negative regulator of IL-15 signalling in NK cells. Cish was rapidly induced in response to IL-15 and deletion of Cish rendered NK cells hypersensitive to IL-15, as evidenced by superior proliferation, survival, IFN-? production and cytotoxicity towards tumours. This was associated with enhanced JAK/STAT signalling in Cish-deleted NK cells. Correspondingly, CIS interacted with the tyrosine kinase JAK1, inhibiting its enzymatic activity and targeting JAK for proteasomal degradation. Cish-/- mice were resistant to melanoma, prostate and breast cancer metastasis in vivo, and this was intrinsic to NK cell activity. This study has uncovered a potent checkpoint in NK cell-mediated tumour immunity and holds promise for novel immunotherapies directed at blocking CIS function. Overall design: Transcriptional profiling of ex vivo and in vitro CIS-/- nature killer cells
DOI: 10.26036/cnphis0002426
title: Arabidopsis SAURs Are Critical for Differential Light Regulation of the Development of Various Organs

description: During de-etiolation of Arabidopsis seedlings, light promotes the expansion of cotyledons but inhibits the elongation of hypocotyls. The mechanism of this differential regulation of cell enlargement is unclear. Our organ-specific transcriptomic analysis identified 32 Small Auxin Up RNA (SAUR) genes whose transcripts were light-induced in cotyledons and/or repressed in hypocotyls. We therefore named these SAURs as lirSAURs. Both overexpression and mutation analyses demonstrated that lirSAURs could promote cotyledon expansion and opening and enhance hypocotyl elongation, possibly by inhibiting phosphatase activity of PP2C-Ds. Light reduced auxin levels to down-regulate the expression of lirSAURs in hypocotyls. Further, phytochrome-interacting factors (PIFs) were shown Overall design: Totally eighteen wild type samples, three treatments and two organs, and each has three replicates. Totally six pifq samples, two organs, and each has three replicates.
DOI: 10.26036/cnphis0002429
title: Intoshia linei isolate:Intl2013 Genome sequencing and assembly

description: Intoshia linnei is a member of Orthonectida, enigmatic parasitic worms with extremely reduced morphology. Its genome sequence allows us to place this phylum in animal tree of life and study limits and mechanisms ofa animal genome reduction.
DOI: 10.26036/cnphis0002430
title: Comparing the targets of distinct RNA Directed DNA Methylation mechanisms in Arabidopsis thaliana

description: The diversity of small RNA-directed DNA methylation (RdDM) mechanisms have been underestimated due to the nearly complete transcriptional silencing of transposable elements (TEs) in the wt Col ecotype of Arabidopsis thaliana. In plants mutant for the SWI/SNF2 histone remodeler DDM1, TEs are globally activated due to loss of genome wide heterochromatin condensation. Activated TEs go through additional non-canonical forms of RdDM. However, the global targets of the non-canonical RdDM pathway are unidentified. In an attempt to identify and contrast the targets of canonical and non-canonical RdDM, we sequenced small RNAs from several RdDM mutants in either the TE-silent or the TE-active (ddm1) contexts. Overall design: Examination of unopened flower bud small RNAs from wild type and various single or double mutant combinations, many of which have biological replicates. Small RNA sequences from wt Col, controls and other mutants shown in the study are available at GSE41755 and GSE57191.
DOI: 10.26036/cnphis0002432
title: Heliconius numata arcuella resequence data for qPCR target regions

description: Selection of Valid Reference Genes for Reverse Transcription Quantitative PCR Analysis in Heliconius numata
DOI: 10.26036/cnphis0002433
title: Oobius primorskyensis strain:KRH-2016 | isolate:Oob-CN-2010 Raw sequence reads

description: A new species of egg parasitoid, Oobius primorskyensis Yao & Duan (Hymenoptera: Encyrtidae), was collected from the emerald ash borer Agrilus planipennis Fairmaire (Coleoptera: Buprestidae) near Vladivostok, Russia. Morphological analysis indicate that this taxon is sufficiently distinct from Oobius agrili Zhang & Huang 2005 to merit species status. DNA sequence divergence between O. primorskyensis and O. agrili distinguishes these species. Based on mapping read sequences from one species to genes of the other species, 89 percent of the genes in O. primorskyensis had homologs in O. agrili, and 94 percent of the genes in O. agrili had homologs in O. primorskyensis. When reads from O. primorskyensis were mapped to genes of O. agrili, there were over 2 million sequence variants, including 169 long (=20 nucleotides) insertions/deletions and over 1 million single nucleotide polymorphisms. When reads from O. primorskyensis were mapped to genes of O. agrili, there were over 3 million sequence variants, including 221 long (=20 nucleotides) insertions/deletions and over 1 million single nucleotide polymorphisms. This sequence variation provides ample markers for distinguishing these two species. The new species is a natural enemy of A. planipennis in its native range and may be considered for introduction against A. planipennis in North America.
DOI: 10.26036/cnphis0002437
title: Schmidtea mediterranea Raw sequence reads

description: whole genome sequencing of Schmidtea mediterranea
DOI: 10.26036/cnphis0002438
title: Pieris rapae Raw sequence reads

description: Reference genome of Pieris rapae
DOI: 10.26036/cnphis0001739
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001746
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001751
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001752
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001753
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001754
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001755
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001756
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001757
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001758
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0002428
title: Genome sequencing of the Olympia oyster (Ostrea lurida)

description: High-throughput sequencing of the Olympia oyster genome.
DOI: 10.26036/cnphis0002431
title: Symbiodinium microadriaticum RNAseq

description: Analysis of differential expression and nuclear RNA editing in the coral symbiont Symbiodinium microadriaticum
DOI: 10.26036/cnphis0002434
title: De novo Assembly and Characterization of Swertia japonica Transcriptome for the Identification of Candidate Genes Involved in the Biosynthesis of Therapeutic Metabolites

description: Here, we performed deep transcriptome sequencing for the aerial-tissues and the roots of S. japonica, generating over 2 billion raw reads with an average length of 101 nt by using an Illumina paired-end sequencing by HiSeq2000 platform. Using a combined approach of three popular assemblers, de novo transcriptome assembly for S. japonica was obtained, yielding in 81,729 unigenes with an average length as 884bps and N50-value as 1,452bps, with 46,963 unigenes being annotated based on the sequence similarity against NCBI-nr protein database. Overall design: Transcriptome profiling of the aerial-tissues and the roots of Swertia japonica
DOI: 10.26036/cnphis0002435
title: Propithecus diadema (Diademed Sifaka)

description: Whole genome sequences for 2 Propithecus diadema (Diademed Sifaka) individuals.
DOI: 10.26036/cnphis0002436
title: Target enrichment of thousands of ultraconserved elements sheds new light on early relationships within New World sparrows (Aves: Passerellidae)

description: Sparrows in the nine-primaried oscine family Passerellidae represent an attractive model for studying avian diversification across North and South America. However, the lack of phylogenetic resolution at the base of the New World sparrow tree has hampered the use of the existing sparrow phylogeny to test questions about the evolution of sparrow traits. We generated phylogenomic data from 1,063 ultraconserved elements to estimate phylogenetic relationships among the major clades of New World sparrows. Concatenated and species-tree analyses of 271,830 base pairs of sequence data converged on a well-supported phylogeny that differs from previous estimates. The resolved backbone of the sparrow phylogeny provides new insight into the biogeography of this radiation by suggesting both a tumultuous biogeographic history, with many colonizations of South America, and several independent ecological transitions to different habitat types.
DOI: 10.26036/cnphis0002439
title: The transcriptomes of various invertebrate species for virus discovery

description: This study aims to sequence the total RNA (excluding ribosomal RNA) of various invertebrate samples for the purpose of RNA virus discvoery
DOI: 10.26036/cnphis0002440
title: RNA-seq of Equus Caballus: adult brainstem and spinal cord

description: RNA-sequencing of cervical spinal cord tissue from healthy horses and horses affected with equine neuroaxonal dystrophy.
DOI: 10.26036/cnphis0002442
title: Zaprionus indianus Genome sequencing and assembly

description: Whole genome sequence of Zaprionus has been performed for comparative genomic analysis.
DOI: 10.26036/cnphis0002444
title: Danaus melanippus genome sequencing

description: Danaus melanippus genome sequencing and assembly
DOI: 10.26036/cnphis0001743
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001748
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001759
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001761
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0002441
title: Multi-locus genome-wide association mapping of color polymorphisms in Timema podura

description: Restriction-site associated DNA libraries (generated following the protocol described in Parchman et al. 2012, PMID: 22404645, doi: 10.1111/j.1365-294X.2012.05513.x) of 50 individuals of Timema podura from a phenotypically variable population found on Ceanothus leucodermis (population code: BSC, N33.816°, W116.790°, California). This data was used to carry out GWA mapping analyses to quantitatively describe aspects of the genetic architecture of color in T. podura.
DOI: 10.26036/cnphis0002443
title: Divergent expression and metabolic functions of human glucuronosyltransferases through alternative splicing

description: Purpose: Maintenance of cellular homeostasis and xenobiotics detoxification relies on the glucuronidation pathway mediated by 19 human UDP-glucuronosyltransferase enzymes (UGTs) encoded by 10 highly homologous genes. Recent evidence suggests that alternative splicing largely expands the human UGT transcriptome. Results: we establish the quantitative portrait of the UGT transcriptome in major metabolic organs and characterize cellular functions of selected alternative UGT isoforms with novel in-frame sequences. Targeted RNA sequencing uncovered that AS significantly shapes the UGT transcriptome, with variants quantitatively representing up to 35% and 60% UGT transcripts in normal and tumoral tissues respectively. Novel distinctive in-frame sequences were present in 20% alternative transcripts, which potentially encode UGT isoforms with distinct structural and functional features. Conclusions: This work exposes the important quantitative and biological significance of alternative UGT expression likely creating unparalleled protein diversity evolving from enzymes to regulators of cell metabolism. Overall design: normal and tumoral metabolic tissues by targeted RNA next-generation sequencing; Total RNA was extracted from liver, kidney, intestine and colon from multiple human donors. RNA-sequencing was conducted with a Illumina HiSeq 2500 system
DOI: 10.26036/cnphis0002445
title: Genomic sequences of the carabid beetles Pseudamara arenaria (LeConte, 1848) and Miquihuana rhadiniformis Barr, 1982

description: Miquihuana rhadiniformis Barr, 1982 and Pseudamara arenaria (LeConte, 1847) are enigmatic North American carabid beetles whose tribal-group placement has been in doubt. As these species are relatively rarely collected, neither Miquihuana Barr, 1982 nor Pseudamara Lindroth, 1968 have been sampled in previous phylogenetic studies and attempts to obtain DNA sequences through standard PCR of available specimens failed. We used Illumina sequencing to recover nuclear gene fragments (18S rDNA, 28S rDNA, wingless, and CAD) from pinned M. rhadiniformis and 70%-ethanol-preserved P. arenaria. Combining these data with data from exemplar taxa from putatively closely related tribal-level clades, we examine the tribal relationships of Miquihuana and Pseudamara.
DOI: 10.26036/cnphis0002446
title: The genetics of kinked tail trait in Asian domestic cats

description: The object of this study is to reveal the genetic basis of kinked tail trait in Asian domestic cat and improve the current understanding of vertebrate tail evolution.
DOI: 10.26036/cnphis0002447
title: Double-digest Restriction-site associated DNA sequencing (ddRAD-seq) of wild mouse lemurs (genus Microcebus)

description: We generated ddRAD-seq data from several species of Madagascar's mouse lemurs (genus Microcebus) to investigate their evolutionary histories. ddRAD-seq was conducted with enzymes SphI and MluCIon 30 samples across 6 species within the genus Microcebus (M. berthae, M. lehilahytsara, M. marohita, M. mittermeieri, M. myoxinus, and M. rufus). Previously these species had only been sequenced at a handful of nuclear and mitochondrial loci. Whole genome RAD-seq data will serve to elucidate speciation processes within the genus and will help to elucidate phylogeographic patterns within Madagascar.
DOI: 10.26036/cnphis0002448
title: Human islets contain four distinct subtypes of ß cells

description: The transcriptomes of four subpopulations of beta cells isolated by FACS from five healthy human donors. Populations were defined using cell surface-labeling antibodies, avoiding the need for fixation. Overall design: There are 5 biological replicates of 4 different cell types. Each donor yielded all 4 subtypes.
DOI: 10.26036/cnphis0002449
title: Steinernema carpocapsae genome sequencing project

description: <b><i>Steinernema carpocapsae</i></b>. This species is being sequenced by the Laboratorio Nacional de Genómica para la Biodiversidad.
DOI: 10.26036/cnphis0002450
title: Vigna radiata Genome sequencing

description: Mungbean (Vigna radiata L.) is a fast-growing warm-season legume crop which widelydistributed in Asia. A large amount of self-shading of mungbean plants could reduce itsseed yield. Thus, modification of leaflet type could affect leaf canopy and improve yield.In this study, a classical locus, lobed leaflet margins (lma) in mungbean wasinvestigated, which was controlled by a semi-dominant allele. In order to map the lma,the whole genomes of AL127 carrying lma and another accession Sulu with ovalleaflets were re-sequenced. 236,998 single nucleotide polymorphisms (SNPs) and8,896 Insertion/Deletions (InDels) were identified between the two accessions. Usingthe validated InDel markers, lma was mapped to a syntenic region about 730 kb onchromosome 3 in mungbean.
DOI: 10.26036/cnphis0001760
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001762
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001763
title: Gymnosperms transcriptomes

description: Illumina RNA-seq based transcriptomes from four gymnosperm species
DOI: 10.26036/cnphis0001764
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001769
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0002452
title: Homo sapiens cardiac mitochondrial Genome sequencing

description: This is a collection of sequenced cardiac mitochondrial DNA from individuals with and without Down syndrome. The goal of the study was to compare genomic variation in the heart tissue from those with Down syndrome versus those without Down syndrome
DOI: 10.26036/cnphis0002453
title: Sarotherodon melanotheron Raw sequence reads

description: We used these reads in order to assess the ancestral state of the LG1 XY sex-determination system in the tilapia clade. Previous work on O. niloticus has already begun characterizing sex-determination in this region. However, by using a distant relative we were able to search for shared sex-patterned SNPs in order to elucidate the sex-determination locus in this region.
DOI: 10.26036/cnphis0002457
title: Actias luna Raw sequence reads

description: Genome Sequencing of Actias luna
DOI: 10.26036/cnphis0001765
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001766
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001767
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001768
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001770
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001771
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001772
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001773
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001774
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001775
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001776
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001777
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001778
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0002451
title: RAD sequencing of european brook and river lamprey

description: The major goal of the study was to reconstruct the divergence history of L. fluviatilis and L. planeri using RAD-sequencing data. The objectives were (i) to compare alternative models of demographic divergence history, (ii) estimate the proportion of the genome experiencing reduced gene flow, (iii) identify genomic markers showing particularly high differentiation between ecotypes under the most likely divergence demographic model and (iv) evaluate the extent of parallelism among replicate pairs of ecotypes.
DOI: 10.26036/cnphis0002454
title: Whole genome sequencing of Salmonella Typhimurium illuminates distinct outbreaks caused by an endemic multi-locus variable number tandem repeat analysis type in Australia, 2014

description: This study was to examine the utility of whole genome sequencing in discriminating sporadic and outbreak-linked Salmonella Typhimurium infections within the same endemic MLVA type. This has the potential to improve the accuracy of cluster definitions and timeliness of outbreak response.
DOI: 10.26036/cnphis0002455
title: GenomeTrakr project: Salmonella enterica, MDU PHL, Australia

description: Whole genome sequencing of Salmonella enterica isolates as part of MDU PHL routine surveillance activities
DOI: 10.26036/cnphis0002456
title: Effects of forage type and age at which forage provision is started on bacteria associated with digesta throughout the gastro-intestinal tract of pre-weaned Holstein calves

description: This study investigated the effects of two forage sources supplemented (chopped alfalfa hay or chopped oat hay) either from d 3 or d 15 of age on the composition of the bacteria along the GIT (rumen, cecum, and rectum) of preweaned bull calves using illumina MiSeq sequencing.
DOI: 10.26036/cnphis0002460
title: Coryphaena hippurus Raw sequence reads

description: SNPs discovery via 2bRAd for population genetics
DOI: 10.26036/cnphis0002461
title: Genomic Resources for colour association studies in Philaenus spumarius

description: This project aims to develop genomic resources for research on the genetic basis of colour pattern in the meadow spittlebug Philaenus spumarius.
DOI: 10.26036/cnphis0002462
title: Apple genome resequencing

description: Cultivated apple (Malus × domestica Borkh.), one of the most widely produced and agronomically important fruit crops in temperate regions, has been domesticated from M. sieversii in the Tian Shan Mountains since 4,000-10,000 years ago and dispersed from Central Asia to West Europe along the Silk Route, allowing hybridization and introgression from wild crabapples. Apple domestication is mainly related to two wild species: M. sieversii as the primary progenitor and M. sylvestris as a major secondary contributor. Centuries of human exploitation and selection have produced several thousand apple cultivars with diverse fruit sizes and flavors, the majority of which are maintained in germplasm repositories, leaving only a few dozen elite cultivars grown worldwide for fruit production. Unlike seed-propagated annual crops with intensive artificial selections and selfing peach with recent domestication bottlenecks, apple has a slow, weak, and complex domestication process with intensive wild-introgressions because of their lengthy juvenile phases, self-incompatibility and wide usage of vegetative propagation. Little information is available about genomic responses to the artificial selections in apple. In this study, we performed deep genome sequencing of 97 diverse apple accessions. The large amount of genomic variation resources has allowed us to gain new insights into apple evolution and domestication processes, which may help accelerate the usage of wild species in apple breeding practice.
DOI: 10.26036/cnphis0002463
title: Capra hircus breed:Laoshan dairy goat Raw sequence reads

description: The goal of this project is to identify the functional genes related to the fecundity trait using whole genome resequencing