cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0002744
title: Plenaster craigi Genome sequencing and assembly

description: Data used for assembly of mitochondrial genome, Taboada et al, Marine Biodiversity 2017
DOI: 10.7910/dvn/7zoapg
title: Replication Data for: Do Concepts Matter? Latin America and South America in the Discourse of Brazilian Foreign Policymakers

description: Replication Data for: "Do Concepts Matter? Latin America and South America in the Discourse of Brazilian Foreign Policymakers" as published in BPSR, vol. 12, nº 3, 2018.
DOI: 10.7910/dvn/7zoapg/6oj3vg
title: methodological.apendix.docx
DOI: 10.7910/dvn/7zoapg/a69dwq
title: dataframe_paper_do_concepts_matter.tab
DOI: 10.7910/dvn/7zoapg/nvknri
title: .Rhistory
DOI: 10.7910/dvn/ebt3uz/5x9vf4
title: Internet and Politics studies in Brazil.tab

description: Dataset
DOI: 10.7910/dvn/ln9ekn/pg3kfl
title: HCs_SP_media.tab

description: Dataset
DOI: 10.7910/dvn/nr3dnk/qm3egt
title: Appropriation_of_Legislative_Agenda_1995_2010_Brazil.xlsx

description: Dataset Codebook
DOI: 10.7910/dvn/zqehqq/e5zkwf
title: Banco_Dados.tab

description: Dataset
DOI: 10.7910/dvn/zqehqq/iiy84b
title: Planilhas.tab

description: Tables
DOI: 10.26036/cnphis0002699
title: Identification of HDA15-PIF1 as a Key Repression Module Directing the Transcriptional Network of Seed Germination in the Dark

description: our analysis uncovered the role of histone deacetylation in light-regulated seed germination process and identified that HDA15-PIF1 as a key repression module directing the transcription network of seed germination Overall design: whole genomic transcriptome analysis of wild type(Col) and hda15 mutant in FR(Dark) conditions,in triplicate, using an mRNA Seq Kit (Illumina).
DOI: 10.26036/cnphis0002736
title: Teleopsis dalmanni isolate:2A Raw sequence reads

description: A shotgun genome assembly of the stalk eyed fly Teleopsis dalmanni (inbred strain 2A) was produced using a combination of Pacific Biosciences, Roche 454, and Illumina sequencing data.
DOI: 10.26036/cnphis0002745
title: Oryza sativa Kitaake FN2042-S Resequencing

description: Categorizing rice deletion mutants by re-sequencing
DOI: 10.26036/cnphis0002747
title: Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest

description: The advent of next-generation sequencing allows researchers to use large-scale datasets for species delimitation analyses, yet one can envision an inflection point where the added accuracy of including more loci does not offset the increased computational burden. One alternative to including all loci could be to prioritize the analysis of loci for which there is an expectation of high informativeness, such as those with higher numbers of parsimony-informative sites. Here, we explore the issue of species delimitation and locus selection with species from two anuran genera: Melanophryniscus (Bufonidae) and Brachycephalus (Brachycephalidae). Montane species in these genera have been isolated in sky islands across the southern Brazilian Atlantic Forest, which led to the formation of a number of microendemic species. To delimit species, we obtained genetic data using target enrichment of ultraconserved elements from 32 populations (13 for Melanophryniscus and 19 for Brachycephalus), and we were able to create datasets that included over 800 loci with no missing data. We ranked loci according to their corresponding number of parsimony-informative sites, and we performed species delimitation analyses using BPP in each genus based on the top 10, 20, 40, 80, 160, 320, and 640 loci. We also conducted several additional analyses using 10 randomly sampled datasets containing the same numbers of loci to discriminate the relative contribution of increasing the number of loci from prioritizing those with higher informativeness. We identified three types of node: nodes with either consistently high or low support regardless of the number of loci or their informativeness, and nodes that were initially poorly supported, but whose support became stronger with more data. Adding more loci had a stronger impact on model support than prioritizing loci for their informativeness, although this effect was less apparent in datasets with more than 160 loci. When viewed across all sensitivity analyses, our results suggest that the current species richness in both genera might have been underestimated. In addition, our results show the effects of different sampling strategies on species delimitation using phylogenomic datasets.
DOI: 10.26036/cnphis0002749
title: Brachypodium distachyon strain:Bd21-3 NaN448 Genome sequencing

description: Creating a genome-wide sequence-indexed collection of grass mutants
DOI: 10.26036/cnphis0002727
title: Comparative Transcriptomic Profiling of Normal-Appearing and Scarred Areas of the Lungs Reveals Pathobiological Clues to Idiopathic Pulmonary Fibrosis

description: RATIONALE: Idiopathic pulmonary fibrosis (IPF) is a fatal disease with overtly scarred peripheral and basilar lung regions and macroscopically unaffected central lung areas. OBJECTIVES: To gain better insight into IPF pathobiology by comparing transcriptomic profiles of normal-appearing and scarred regions of IPF lung. METHODS: Lung tissue samples from macroscopically unaffected (normal-appearing, IPFn) and scarred (IPFs) regions of explanted IPF lungs were analyzed by RNASeq and compared with healthy control (HC) lung tissues. RT-qPCR and immunohistochemistry were used to confirm selected findings. MEASUREMENTS AND RESULTS: Numerous previously reported IPF-associated gene expression disturbances as well as additional differentially expressed mRNAs were observed. There were profound transcriptomic changes in IPFn compared with HC tissues, which included elevated expression of extracellular matrix-, immunity- and inflammation-related mRNAs. The magnitude and statistical significance of these changes were comparable or greater than those in the IPFs-to-HC comparison. When directly compared with IPFn, IPFs tissues demonstrated elevated expression of epithelial mucociliary mRNAs. Compared with HC, both IPFn and IPFs tissues demonstrated reduced expression of mRNAs related to solute carrier membrane transport and metabolic processes. Primary fibroblast cultures from IPFn and IPFs tissues were transcriptomically identical. CONCLUSIONS: Macroscopically normal-appearing IPF tissues demonstrate profound disease activity and substantially similar transcriptomic profiles to scarred areas. Differences between these tissues are due to cell types other than fibroblasts and notably include enhanced expression of mucociliary genes in scarred areas. Deranged epithelial homeostasis or possibly non-transcriptomic factors may thus explain the marked architectural differences between normal-appearing and terminally scarred lung in end-stage IPF. Overall design: RNASeq of 26 lung tissue samples from patients with IPF, including affected and unaffected areas of the lung, and from healthy controls
DOI: 10.26036/cnphis0002737
title: Splicing site disruption in the KIT gene as strong candidate for white dominant phenotype in an Italian Trotter

description: Sequencing of a white solid coat foal born in Italy in 2014 from bay parents.
DOI: 10.26036/cnphis0002746
title: Analysis of chromatin landscapes in early human development reveals epigenetic transition during ZGA

description: Upon fertilization, drastic chromatin reorganization occurs during human preimplantation development. However, the global chromatin landscape and its molecular dynamics in this period remain largely unexplored. Deciphering such process is crucial for understanding both early human development and in vitro fertilization. Here, we investigated genome-wide chromatin accessibility in human preimplantation embryos by employing an improved ATAC-seq that uses as few as 20 cells. We found widespread accessible chromatin in early human embryos that overlaps extensively with putative cis-regulatory sequences and transposable elements. Integrative analyses showed both conservation and divergence in regulatory circuitry between human and mouse early development, and between naïve human pluripotency in vivo and human embryonic stem cells. Surprisingly, we also found widespread open chromatin at the 2-cell stage despite its minimal transcription activities. Such accessible chromatin loci are readily found at CpG-rich promoters. Unexpectedly, many others are located in distal regions enriched for transcription factor binding sites and overlap with partially methylated domains (PMDs) in human oocytes. A large portion of these regions then rapidly become inaccessible upon zygotic genome activation (ZGA). Importantly, such drastic transition of chromatin accessibility during ZGA is well conserved in mouse embryos. Furthermore, it strongly correlates with the reprogramming of non-canonical H3K4me3 (ncH3K4me3), a form of histone mark that is uniquely present in oocytes and pre-ZGA embryos and contributes to genome silencing. Finally, both the reprogramming of chromatin accessibility and ncH3K4me3 during ZGA is completely blocked upon transcription inhibition, indicating a critical role of zygotic transcription in shaping early epigenomes. Together, these data revealed conserved chromatin state transition during ZGA in human and mouse early development. Overall design: ATAC-seq and RNA-seq were applied on human pre-implantation embryos and mouse transcription blocked embryos to examine the chromatin state as well as their transcriptome
DOI: 10.26036/cnphis0002750
title: Transcriptome analysis of genetically matched human induced pluripotent stem cells disomic or trisomic for chromosome 21

description: Trisomy of chromosome 21, the genetic cause of Down syndrome, has the potential to alter expression of genes on chromosome 21, as well as other locations throughout the genome. These transcriptome changes are likely to underlie the Down syndrome clinical phenotypes. We have employed RNA-seq to undertake an in-depth analysis of transcriptome changes resulting from trisomy of chromosome 21, using induced pluripotent stem cells (iPSCs) derived from a single individual with Down syndrome. These cells were originally derived by Li et al, who genetically targeted chromosome 21 in trisomic iPSCs, allowing selection of disomic sibling iPSC clones. Analyses were conducted on trisomic/disomic cell pairs maintained as iPSCs or differentiated into cortical neuronal cultures. Overall design: 12 total polyA selected samples. 6 IPSC samples with 3 biological repeats for trisomic samples and 3 biological repeats for disomic samples. 6 IPSC derived neuronal samples with 3 biological repeats for trisomic samples and 3 biological repeats for disomic samples.
DOI: 10.26036/cnphis0002751
title: Drusilla canaliculata Genome sequencing and assembly

description: Drusilla canaliculata
DOI: 10.26036/cnphis0002752
title: Adranes taylori Genome sequencing and assembly

description: Adranes taylori
DOI: 10.5284/1049652
title: Society of Antiquaries Monographs

description: The Society of Antiquaries of London has a long tradition of publishing scholarly research on the archaeological and historic resource in order to encourage knowledge and understanding of human history and development in its physical and cultural environments. As part of the Society's aim to support research and communicate its results as widely as possible, the Society is digitising titles from its extensive backlist and making these accessible via the ADS as a staged process.
DOI: 10.26036/cnphis0002753
title: Aenictocupidus jacobsonorum Genome sequencing and assembly

description: Aenictocupidus jacobsonorum
DOI: 10.26036/cnphis0002754
title: Mimaenictus wilsoni Genome sequencing and assembly

description: Mimaenictus wilsoni
DOI: 10.26036/cnphis0002755
title: Weissflogia rhopalogaster Genome sequencing and assembly

description: Weissflogia rhopalogaster
DOI: 10.26036/cnphis0002758
title: Platyusa sonomae Genome sequencing and assembly

description: Platyusa sonomae
DOI: 10.26036/cnphis0002759
title: Tomocerus minor Genome sequencing and assembly

description: Tomocerus minor
DOI: 10.7910/dvn/7zoapg/iqlzpz
title: .tab
DOI: 10.7910/dvn/cimskq/6xpysb
title: Database Mouron_Urdinez.tab

description: Dataset
DOI: 10.7910/dvn/nujdia/rfowje
title: Codebook_Ligia_Mori.docx

description: Codebook
DOI: 10.7910/dvn/t9xedq/0mlcnm
title: Baird_Fernandes.tab

description: Dataset
DOI: 10.7910/dvn/t9xedq/k8fjrb
title: Codebook Baird_Fernandes.doc

description: Codebook
DOI: 10.26036/cnphis0002740
title: CITE-seq: Large scale simultaneous measuremnt of epitopes and transcriptomes in single cells

description: Recent high-throughput single-cell sequencing approaches have been transformative for understanding complex cell populations, but are unable to provide additional phenotypic information, such as protein levels of cell-surface markers. Using oligonucleotide-labeled antibodies, we integrate measurements of cellular proteins and transcriptomes into an efficient, sequencing-based readout of single cells. This method is compatible with existing single-cell sequencing approaches and will readily scale as the throughput of these methods increase. Overall design: Cord blood mononuclear cells were profiled by CITE-seq using a panel of 13 antibodies.
DOI: 10.26036/cnphis0002756
title: Felis catus testis transcriptome

description: Domestic and hybrid cat testis RNA
DOI: 10.26036/cnphis0002757
title: Sceptobius lativentris Genome sequencing and assembly

description: Sceptobius lativentris
DOI: 10.26036/cnphis0002761
title: Commensal microbiota associated with anti-PD-1 efficacy in metastatic melanoma patients

description: Anti-PD-1-based immunotherapy is having a major impact on cancer outcomes but only benefits a subset of patients. Among the variables that could contribute to inter-patient heterogeneity is differential composition of the commensal microbiota, which preclinically has been shown to affect anti-tumor immunity and immunotherapy efficacy in mice. Baseline stool samples were analyzed from metastatic melanoma patients prior to immunotherapy treatment, through an integration of 16S rRNA sequencing, metagenomic shotgun sequencing, and quantitative PCR for selected bacteria. A significant association between commensal microbial composition and clinical response was observed. Reconstitution of germ-free mice with fecal material from a responding patient led to improved tumor control, augmented T cell responses, and a distinct microbiota compared to a non-responding patient. Our results indicate a mechanistic impact of the commensal microbiota on anti-tumor immunity in human cancer patients.
DOI: 10.26036/cnphis0002764
title: Anas platyrhynchos breed:shaoxing Genome sequencing

description: investigate the casual mutation of blue eggshell of duck
DOI: 10.26036/cnphis0002765
title: Next Generation Sequencing of Wild Type and AtSRT1 transgene plants Transcriptomes

description: To study genome-wide gene expression regulated by AtSRT1, we analyzed transcriptomes of wild type and AtSRT1 RNAi-1 (R) and overexpression OX-SRT1-1(OX) line by RNA-sequencing using the Illumina Hiseq-2000 sequencing system. Three biological replicates for each genotype were tested.The data suggest that AtSRT1 plays an important role in regulation of genes involved in stress responses and in carbon and energy metabolism in Arabidopsis. Overall design: Arabidopsis mRNA profiles of 14-day old wild type (WT) and RNAi-SRT1 and OX-SRT1 were generated by deep sequencing, in triplicate, using Illumina.
DOI: 10.26036/cnphis0002769
title: Nodule RNAseq from M. truncatula NPD knockout lines

description: A nodule-specific subset of PLAT domain proteins (NPDs) expanded to 5 members in the Medicago lineage. In order to characterize NPD gene function, a set of cumulative NPD knockout lines was generated. A two-gene knockout line npd2/4, three-gene knockout lines npd1/2/4 and npd2/4/5, and wild type M. truncatula R108 were inoculated with Ensifer meliloti strain 1021. Plants were grown in a growth chamber at 22C and with a 16 h photoperiod in conetainers arranged in a completely randomized design. Trays were watered with sterile deionized water twice a week and with Fahräeus medium lacking nitrogen once a week. Thirty days post inoculation, roots and nodules were harvested and flash-frozen in liquid nitrogen. Total RNA was extracted with a Qiagen RNeasy Plant Mini Kit and sequenced by the University of Minnesota Genomics Center.
DOI: 10.7910/dvn/cimskq/3d2ijt
title: Script Mouron_Urdinez.docx

description: Script
DOI: 10.7910/dvn/gbcyjr/sjqoah
title: CNEP_Micro_Mapping_

description: Dataset - Micro
DOI: 10.26036/cnphis0002731
title: genome of Hycleus cichorii and Hycleus phaleratus

description: Hycleus cichorii and Hycleus phaleratus are most important blister beetles in Traditional Chinese Medicine due to their ability to biosynthesize cantharidin, which has recently been used for cancer therapy. However, there are lack of genome reference, which hindered to development of studies on biosynthesize cantharidin and other biology. We sequence, assembly and annotate both two genomes using low depth Illumina sequence data (36-38X).
DOI: 10.26036/cnphis0002733
title: Apostasia shenzhenica isolate:ASH160606 Genome sequencing

description: Apostasia shenzhenica has a karyotype of 2N=2X=68 with uniform small-size chromosomes . To completely sequence A. shenzhenica genome, we generated a total of 80.02 Gb of raw reads, with multiple insert libraries ranging in size from 180 bp to 20 Kb. A K-mer analysis estimated the genome size of A. shenzhenica at 471.0Mb. We assembled the sequence using Allpaths-lg (49292) software. The total length of the assembly was 348Mb (scaffold N50 1.196 Mb in length; corresponding contig N50 length 30.1 Kb).
DOI: 10.26036/cnphis0002743
title: Arabidopsis thaliana Raw sequence reads

description: Identify Aarabidopsis MPK3/MPK6 activation-induced genes
DOI: 10.26036/cnphis0002762
title: Measuring gene expression and RNA editing in Drosophila adapting to divergent microclimates

description: We performed RNA-seq to profile gene expression in the heads and whole bodies of 32 isofemale fly lines from two divergent microclimates at ''Evolution Canyon'' in Israel (16 fly lines from each microclimate). We also measured RNA editing levels in the head tissue of these flies. Overall design: For each of the 32 isofemale fly lines from ''Evolution Canyon'', gene expression profiles of whole bodies and heads, along with RNA editing profiles of heads of 3-5 day old male flies through RNA-seq.
DOI: 10.26036/cnphis0002768
title: Ch1 and Ch2 Genes Siberian Cat

description: Ch1 and Ch2 genes sequencing in Siberian Cat to detect genetic mutation
DOI: 10.26036/cnphis0002770
title: whole genome duplications in anggiosperms

description: Wide-spread whole genome duplications contribute to genome complexity and species diversity in angiosperms
DOI: 10.26036/cnphis0002771
title: Epigenetic marks and nuclear transcriptomes of cardiac myocytes

description: Here we report genome-wide maps of CpG methylation, 5-hydroxy-methylcytosine, seven histone marks and nuclear RNA expression of purified cardiac myocyte nuclei from fetal, infantile, adult non-failing and failing human hearts.
DOI: 10.26036/cnphis0002773
title: Puma concolor Genome sequencing and assembly

description: In this study, we used whole-genome sequences from most parental lines of the admixed Florida panthers that resulted from the introduction of Texas pumas into South Florida in order to understand evolutionary and demographic processes occurring in the puma. We assembled a composite genome and identified genes and polymorphisms linked to adaptive traits in pumas.
DOI: 10.26036/cnphis0002776
title: Cultivated Soybean RNA-Seq of salt treatment

description: To obtain a comprehensive understanding of transcriptomic reprogramming under salt stress, we performed whole genome RNA sequencing on salt-treatment soybean seedlings, on two tissues in a time-course experiment (0h, 1h, 2h, 4 h, 24h and 48h). This time series dataset enables us to identify important hubs and connection of gene expressions. We highlighted the analysis of phytohormone signaling pathways and their possible cross-talking. Gene expression regulation also controls adjustment of carbon and nitrogen metabolism. In general, the treated seedlings had turned off the photosynthetic mechanism and enhanced sugar catabolism to provide energy for survival. Primary nitrogen assimilation was shut down while re-distribution of nitrogen resources was activated. Genes for other protective mechanisms were also induced, including structural modification, ion-sequestering, and scavenging of reactive oxygen species.
DOI: 10.26036/cnphis0002778
title: Elysia chlorotica stage-specific gene expression

description: Here we used RNA-Seq analysis to test the idea that plastid sequestration leaves a significant signature on host gene expression during E. chlorotica development
DOI: 10.7910/dvn/gyoqmg/gb2itb
title: Perceptions on justice, the judiciary and democracy.tab

description: Dataset
DOI: 10.7910/dvn/hzpcz2/wpgtlh
title: Banco_dados_Speck_Mancuso.tab

description: Dataset
DOI: 10.26036/cnphis0002742
title: Ctenopharyngodon idella Genome sequencing

description: next generation sequencing of four DNA samples that collected at four early developmental stages of grass carp
DOI: 10.26036/cnphis0002763
title: Whole genome sequencing of Drosophila melanogaster from different microclimates at ''Evolution Canyon''

description: We sequenced the genomes of 32 isofemale fly lines from two divergent microclimates at ''Evolution Canyon'' in Israel (16 fly lines from each microclimate). Overall design: We sequenced the whole genomes of single male flies from each of the 32 isofemale fly lines from ''Evolution Canyon''.
DOI: 10.26036/cnphis0002774
title: Maternal plasma cell-free RNA sequencing for prematurity initiative

description: cfRNA-seq: We used cfRNA-seq to identify differentially expressed gene-specific cfRNA transcripts between women who delivered spontaneous preterm (n=8) and women who delivered at full-term (n=7). Overall design: cfRNA-seq was used for gene-specific cfRNA transcript discovery. RT-qPCR (available through Github link) was used for validation, and the development of a heuristic to predict spontaneous preterm delivery up to two months in advance of labor.