cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0002557
title: Transcriptome profiling of five solanaceous species.

description: The extensive diversity for floral branching systems is an excellent example of morphological evolution in plants. This study seeks to advance our understanding of the relationship between floral system complexity and the developmental progression or maturation of plant stem cells, meristems. This was accomplished through transcriptome profiling of sequential meristem developmental stages in five nightshade species representing a continuum of floral branching architectures. Through comparative transcriptome analyses, we demonstrate that altering the rate of meristem developmental progression explains the range of floral system phenotypes. We further show that heterochronic shifts in expression of a relatively small number of genes, many of which are transcription factors, are responsible for modulating meristem maturation schedules, and that the mid-development transition is a critical window for these changes. This study demonstrates that evolutionary diversity for floral branching systems is determined by subtle modifications of transcriptional programs during a critical window of meristem maturation.
DOI: 10.26036/cnphis0002558
title: Epigenome maps of time-resolved monocyte to macrophage differentiation and innate immune memory (ATAC-Seq)

description: Innate immune memory is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to microbial components such as LPS. We apply an integrated epigenomic approach to characterize the molecular events involved in LPS-induced tolerance in a time dependent manner. ChIP-seq, RNA-seq, WGBS and ATAC-seq data were generated. This analysis identified epigenetic programs in tolerance and trained macrophages, and the potential transcription factors involved. Overall design: Time-course in vitro culture of human monocytes. Two innate immune memory states can be induced in culture through an initial exposure of primary human monocytes to either LPS or BG for 24 hours, followed by removal of stimulus and differentiation to macrophages for an additional 5 days. Cells were collected at baseline (day 0), 1 hour, 4 hour, 24 hour and 6 days.
DOI: 10.26036/cnphis0002560
title: Tropilaelaps mercedesae isolate:Wuxi-XJTLU Raw sequence reads

description: T. mercedesae is one of major prevalent ectoparasitic mite infesting honey bees in Asia. We sequenced the genome and transcriptomes of T. mercedesae to provide insights into the ensory system, development, sex determination/differentiation, reproduction, and the capability to acquire miticide (for example, tau-fluvalinate and flumethrin) resistance and understand how the mite has evolved under a very specialized environment - inside the honey bee colony by depending on the honey bee as the sole host.
DOI: 10.26036/cnphis0002561
title: Tapinoma melanocephalum Raw sequence reads

description: develop the microsatellite loci
DOI: 10.26036/cnphis0002562
title: Dalotia coriaria genome sequencing

description: None
DOI: 10.26036/cnphis0002565
title: A longitudinal analysis of the developing gut microbiome in infants from Finland, Estonia, and Russian Karelia

description: This is a longitudinal collection of stool samples from infants at risk for disease. Approximately 1,000 newborns were recruited to the birth cohort as part of the international DIABIMMUNE Study (http://www.diabimmune.org/) for which the consent rate was 80% in Tartu, Estonia, 59% in Espoo, Finland, and 24% in Petrozavodsk, Russia. Recruitment took place between September 2008 and May 2010 in Estonia and Finland, and between September 2008 and July 2011 in Russia. Follow-up was completed in April 2013 in Estonia and Finland, and in October 2013 in Russia. The final number of children included in the present study was 74 from each country. Inclusion criteria included positive cord blood testing for HLA DR-DQ alleles conferring increased risk for autoimmunity. The participating children were monitored prospectively for infections, use of drugs including antibiotics, and other life events.
DOI: 10.26036/cnphis0002566
title: Genomic sequencing of tule elk

description: Genomes from four individual tule elk, a species endemic to California, were sequenced. The goal of this study was to identify single nucleotide polymorphisms (SNPs) in the genome to develop assays to track tule elk population movement. The species underwent a major genetic bottleneck in the 1870s but today has grown to over 3,000 individuals. However, tule elk populations are stratified by human development such as roads, bridges, and building development.
DOI: 10.26036/cnphis0002563
title: Coproporus ventriculus genome sequencing

description: None
DOI: 10.26036/cnphis0002564
title: Ecitophya simulans genome sequencing

description: None
DOI: 10.26036/cnphis0002568
title: Papilio memnon Genome sequencing and assembly

description: Papilio memnon genome sequencing and assembly
DOI: 10.26036/cnphis0002567
title: Delias oraia Genome sequencing and assembly

description: Delias oraia genome sequencing and assembly
DOI: 10.26036/cnphis0002569
title: Diploeciton nevermanni genome sequencing

description: None
DOI: 10.26036/cnphis0002570
title: Tetradonia laticeps genome sequencing

description: None
DOI: 10.26036/cnphis0002571
title: Papilio gigon Genome sequencing and assembly

description: Papilio gigon genome sequencing and assembly
DOI: 10.26036/cnphis0002572
title: Population structure and local selection yield high genomic variation in Mimulus guttatus

description: Population structure and local selection of Mimulus guttatus (IM, Iron Mountain Oregon population)
DOI: 10.26036/cnphis0002573
title: Graphium evemon Genome sequencing and assembly

description: Graphium evemon genome sequencing and assembly
DOI: 10.26036/cnphis0002575
title: Graphium doson Genome sequencing and assembly

description: Graphium doson genome sequencing and assembly
DOI: 10.26036/cnphis0002577
title: Physcomitrella patens Kaskaskia genome sequencing

description: None
DOI: 10.26036/cnphis0002574
title: Hypolimnas misippus Genome sequencing and assembly

description: Hypolimnas misippus genome sequencing and assembly
DOI: 10.26036/cnphis0002576
title: Proctacanthus coquilletti de novo genome and transcriptome

description: Sequencing the first complete genome of an assassin fly (Diptera: Asilidae).
DOI: 10.26036/cnphis0002579
title: Lateolabrax maculatus LS_HS Raw sequence reads

description: To find the potential pathways when daptation to high salinity
DOI: 10.26036/cnphis0002581
title: Alternative Splicing Within and Between Drosophila Species, Sexes, Tissues, and Developmental Stages

description: Alternative pre-mRNA splicing (“AS”) greatly expands proteome diversity, but little is known about the evolutionary landscape of AS in Drosophila and how it differs between embryonic and adult stages or males and females. Here we study the transcriptomes from several tissues and developmental stages in males and females from four species across the Drosophila genus. We find that 20-37% of multi-exon genes are alternatively spliced. While males generally express a larger number of genes, AS is more prevalent in females, suggesting that the sexes adopt different expression strategies for their specialized function. While the number of total genes expressed increases during early embryonic development, the proportion of expressed genes that are alternatively spliced is highest in the very early embryo, before the onset of zygotic transcription. This indicates that females deposit a diversity of isoforms into the egg, consistent with abundant AS found in ovary. Cluster analysis by gene expression (“GE”) levels show mostly stage-specific clustering in embryonic samples, and tissue-specific clustering in adult tissues. Clustering embryonic stages and adult tissues based on AS profiles results in stronger species-specific clustering, suggesting that diversification of splicing contributes to lineage-specific evolution in Drosophila. Most sex-biased AS found in flies is due to AS in gonads, with little sex-specific splicing in somatic tissues.
DOI: 10.26036/cnphis0002583
title: Salmonella enterica subsp. enterica serovar Enteritidis Raw sequence reads

description: Genome sequencing to aid in the investigation of a multi-provincial Salmonellosis outbreak related to newly hatched chicks and poults
DOI: 10.26036/cnphis0002578
title: Sequence capture and next-generation sequencing of ultraconserved elements in a large-genome salamander

description: Amidst the rapid advancement in next-generation sequencing (NGS) technology over the last few years, salamanders have been left behind. Salamanders have enormous genomes – up to 40 times the size of the human genome – and this poses challenges to generating NGS data sets of quality and quantity similar to those of other vertebrates. However, optimization of laboratory protocols is time-consuming and often cost prohibitive, and continued omission of salamanders from novel phylogeographic research is detrimental to species facing decline. Here, we use a salamander endemic to the southeastern US, Plethodon serratus, to test the utility of an established protocol for sequence capture of ultraconserved elements (UCEs) in resolving intraspecific phylogeographic relationships and delimiting cryptic species. Without modifying the standard laboratory protocol, we generated a data set consisting of over 600 million reads for 85 P. serratus samples. Species delimitation analyses support recognition of seven species within P. serratus sensu lato, and all phylogenetic relationships among the seven species are fully resolved under a coalescent model. Results also corroborate previous data suggesting non-monophyly of the Ouachita and Louisiana regions. Our results demonstrate that established UCE protocols can successfully be used in phylogeographic studies of salamander species, providing a powerful tool for future research on evolutionary history of amphibians and other organisms with large genomes.
DOI: 10.26036/cnphis0002582
title: A genome-wide map of polyadenylation sites in primary human breast tissue

description: We used a modified PAS-Seq protocol to map sites of polyadenylation genome-wide in primary breast tissue. Here, we present a map of breast poly(A)-sites derived from six ER+ tumors, six ER- tumors, and adjacent normal tissue from each of the 12 tumor donors. Overall design: Modified PAS-seq in 12 pairs of matched patient tumor/normal tissue samples (6 ER-, 6 ER+).
DOI: 10.26036/cnphis0002584
title: Human gut microbiome with bacterial pathogen challenge

description: This project takes advantage of challenge studies with an important human pathogen, enterotoxigenic Escherichia coli, the etiological agent of severe diarrhea in the developed countries and traveler’s diarrhea in individuals from developed countries. The goal of this study is to understand the dynamic interactions between the host, pathogen and microbiota and how these interactions play a role in determining the pathogen population in the host, the development of an immune response, and the diversity and ecology of the microbiota. The project uses a combination of genomic, transcriptomic and metagenomic technologies together with human challenge studies to generate new insights into the interaction of host, pathogen, and microbiota.
DOI: 10.26036/cnphis0002585
title: RAD-seq of Galapagos Sea Lion

description: RADseq data used to test for the impact of bioinformatic data processing on downstream population genetic inferences in Galapagos Sea lions.
DOI: 10.26036/cnphis0002587
title: Gene expression profiling associated with knockdown of RNF20 in human normal and malignant lung epithelial cell lines

description: The experiment was designed to display differential gene expression profiling in one lung epithelial cell BEAS2-B, and three lung cancer cell lines A549, H1299, H460 cells upon knockdown of RNF20, by using RNAseq technology. Overall design: RNF20 was first attenuated in duplicated normal lung epithelial cell BEAS2-B, and three lung cancer cell lines A549, H1299, H460 by siRNA-mediated knockdown. Total RNA was extracted from duplicated cancers cells transfected with two independent control siRNA (Ctrl1/2) and RNF20 specific siRNAs (RNF1/2) at 72h post-transfection for RNAseq analysis. Differentially expressed genes in RNF20-attenuated lung epithelial cells were identified in comparison to that in cells transfected with control siRNA.
DOI: 10.26036/cnphis0002588
title: Chrysaora quinquecirrha Raw sequence reads

description: The purpose of this study was to identify the prey species of the jellyfish Chrysaora quinquecirrha in Barnegat Bay, New Jersey
DOI: 10.26036/cnphis0002591
title: Identification of novel equine (Equus caballus) tendon markers using RNA sequencing

description: Although several tendon-selective genes exist, they are also expressed in other musculoskeletal tissues. As cell and tissue engineering is reliant on specific molecular markers to discriminate between cell types, tendon-specific genes need to be identified. In order to accomplish this, we have used RNA sequencing (RNA-seq) to compare gene expression between tendon, bone, cartilage and ligament from horses. We identified several tendon-selective gene markers, and established eyes absent homolog 2 (EYA2) and G-protein regulated inducer of neurite outgrowth 3 (GPRIN3) as specific tendon markers using RT-qPCR. Equine tendon cells cultured as three dimensional spheroids expressed significantly greater levels of EYA2 than GPRIN3, and stained positively for EYA2 using immunohistochemistry. EYA2 was also found in fibroblast-like cells within the tendon tissue matrix and in cells localized to the vascular endothelium.We have identified EYA2 and GPRIN3 as specific molecular markers of equine tendon as compared to bone, cartilage and ligament, and provide evidence for the use of EYA2 as an additional marker for tendon cells in vitro.
DOI: 10.26036/cnphis0002586
title: Melittobia australica - Raw sequence reads

description: DNA sequencing project on a pool of 20 females from a laboratory culture of Melittobia australica. Goal of this project was the identification of microsatellites for further study.
DOI: 10.26036/cnphis0002589
title: Jaguar Genome Project

description: The Jaguar Genome Project is a multi-national effort led by the Carnivore Genetics Research Group at PUCRS, Brazil. It aims to characterize the genome of the jaguar (Panthera onca) using a diverse array of approaches, and to employ the resulting genomic resources to perform comparative analyses with other mammals, as well as in-depth population-level studies. As the latter analyses advance, the project aims to continuously provide useful information to improve ongoing conservation and management strategies on behalf of endangered jaguar populations.
DOI: 10.26036/cnphis0002590
title: Cis-regulatory evolution in primates - RNA-seq

description: Cis-regulatory evolution has played a critical role in shaping animal and plant phenotypic diversity. We include data of five primate species (excluding human samples) used to study the evolution of promoters and enhancers in the livers of six species selected from all major clades of the primate lineage. We produced ChIP-seq data for two different histone modifications to profile active and poised regulatory elements, and performed RNA-seq on the same samples to produce corresponding transcriptional profiles.
DOI: 10.26036/cnphis0002594
title: Caenorhabditis elegans Hawaiian Strain CB4856 Genome Assembly

description: Among the many wild isolates of C. elegans, one of the most genetically divergent and most heavily studied is CB4856, which was isolated in 1972 by Linda Holden from a pineapple field on the Hawaiian island of Maui (under the name HA8) (HODGKIN AND DONIACH 1997). It shows multiple phenotypic differences with N2, including production of a copulatory plug, aggregation (social) behavior, a lack of temperature-size dependence, growth rate, fecundity and RNAi insensitivity by feeding and drug resistance (DE BONO AND BARGMANN 1998; KAMMENGA et al. 2007; GHOSH et al. 2012; POLLARD AND ROCKMAN 2013; ANDERSEN et al. 2014) as well as gene expression differences (CAPRA et al. 2008; VINUELA et al. 2012; VOLKERS et al. 2013). We have undertaken the construction of a C. elegans Hawaiian strain CB4856 reference genome sequence.
DOI: 10.26036/cnphis0002595
title: Atkinsonella texensis B6155 Genome sequencing and assembly

description: Atkinsonella texensis is a systemic parasite of the grass, Nassella leucotricha (Texas needlegrass), and reproduces in fruiting bodies (stromata) that choke immature host inflorescences, preventing seed production. This fungus is a close relative of mutualistic symbionts (endophytes) such as the Epichloe species.
DOI: 10.26036/cnphis0002593
title: Phylogenomics of non-core Caryophyllales

description: None
DOI: 10.26036/cnphis0002596
title: University of Missouri Animal Genomics: Bubalus genome sequencing

description: Whole genome re-sequencing of Bubalus
DOI: 10.26036/cnphis0002602
title: trancriptomic analyses of the turbot Scophthalmus maximus

description: The goal of this study is to figure out what potential stressing effects would happen in the immunostimulated turbot when facing stressful high temperature, based on the information of differentially expressed genes high and low temperature
DOI: 10.26036/cnphis0002592
title: Cell fixation and preservation for droplet-based single cell transcriptomics

description: Background: Recent developments in droplet-based microfluidics allow the transcriptional profiling of thousands of individual cells, in a quantitative, highly parallel and cost-effective way. A critical, often limiting step is the preparation of cells in an unperturbed state, not compromised by stress or ageing. Another challenge are rare cells that need to be collected over several days, or samples prepared at different times or locations. Results: Here, we used chemical fixation to overcome these problems. Methanol fixation allowed us to stabilize and preserve dissociated cells for weeks. By using mixtures of fixed human and mouse cells, we showed that individual transcriptomes could be confidently assigned to one of the two species. Single-cell gene expression from live and fixed samples correlated well with bulk mRNA-seq data. We then applied methanol fixation to transcriptionally profile primary single cells from dissociated complex tissues. Low RNA content cells from Drosophila embryos, as well as mouse hindbrain and cerebellum cells sorted by FACS, were successfully analysed after fixation, storage and single-cell droplet RNA-seq. We were able to identify diverse cell populations, including neuronal subtypes. As an additional resource, we provide 'dropbead', an R package for exploratory data analysis, visualization and filtering of Drop-seq data. Conclusions: We expect that the availability of a simple cell fixation method will open up many new opportunities in diverse biological contexts to analyse transcriptional dynamics at single cell resolution. Overall design: Mixtures of human and mouse cells, either live or fixed, or fixed and stored for several weeks were used for droplet-based single cell mRNA transcriptome profiling. The methods were also successfully applied to primary cells isolated from Drosophila embryos and newborn mouse hindbrain/cerebellum.
DOI: 10.26036/cnphis0002597
title: Epigenetic analysis of tumor-specific CD8 T cells in murine and solid tumors

description: ATACseq analysis of dysfunctional CD8 T cells in progressing tumors. The overall goal of this study was to elucidate chromatin states associated with functional unresponsiveness in tumor-specific CD8 T cells in the context of mouse and human tumors. As comparison we also investigated chromatin state dynamics associated with CD8 T cells differentiation to functional effector and memory T cells during an acute listeria infection. Overall design: CD8 T cells were sorted by flow cytometry and ATAC-seq was performed.
DOI: 10.26036/cnphis0002598
title: Nippostrongylus brasiliensis Genome & Transcriptome sequencing and assembly

description: Providing a high-quality reference genome, transcriptome and predicted proteome for Nippostrongylus brasiliensis. The assembly process uses MinION long reads for initial contig generation, with Illumina reads for subsequent error correction.
DOI: 10.26036/cnphis0002599
title: Gallus gallus Ovarian Raw sequence reads

description: In order to screen differential expressed genes between transcriptome of high and low egg production chicken ovaries, RNA sequencing was carried out. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups of proteins (COG) were performed on new genes and DEGs. 13 DEGs were randomly selected to conduct RT-PCR to verify the RNA-seq results. Our study can not only provided a theoretical basis for regulatory mechanism research of egg production, but also provided candidate genes for genetic improvement of egg production.
DOI: 10.26036/cnphis0002600
title: exome sequencing of a family of congenital contractural arachnodactyly

description: The aim of this study is to identify the mutation which caused congenital contractural arachnodactyly
DOI: 10.26036/cnphis0002605
title: The Shc1 Scaffold protein simultaneously balances Stat1 and Stat3 activity in breast cancer to promote immune suppression and resistance to immunotherapy.

description: Receptor and cytoplasmic tyrosine kinases are key signal integrators in poor outcome breast cancers that are central to the establishment of an immunosuppressive microenvironment. Immunotherapies represent an emerging approach within the armament of anti-cancer agents. Although the efficacy of tyrosine kinase inhibitors relies, in part, on their ability to augment adaptive immunity, the increased heterogeneity and functional redundancy of the tyrosine kinome in poor outcome breast cancers represents a significant hurdle to achieving durable responses to immunotherapies. We previously identified the Shc1 (ShcA) scaffold protein, a central regulator of tyrosine kinase signaling, as essential for promoting immune suppression. Here we show that the ShcA pathway simultaneously activates STAT3 immunosuppressive signals and impairs STAT1-driven immune surveillance in breast cancer cells. Impaired phosphorylation of Y239/Y240 residues on ShcA potently and selectively reduces STAT3 activation in breast tumors, profoundly sensitizing them to immune checkpoint inhibitors and tumor vaccines. Finally, the ability of diminished tyrosine kinase signaling to initiate STAT1-driven immune surveillance in breast tumors can be overcome by a compensatory hyper-activation of STAT3. Our data indicates the development of pharmacological inhibitors that prevent pY239/240-ShcA dependent STAT3 signaling may represent an attractive therapeutic strategy to sensitize breast tumors to multiple immunotherapies.