cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5841603
title: Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding

description: This dataset contains files of the molecular dynamics simulations performed in "Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding" study. Further information in presented in README.md file and the abstract of the study is presented below: "The nucleocapsid (N) protein of the SARS-CoV-2 virus, the causal agent of COVID-19, is a multifunction phosphoprotein that plays critical roles in the virus life cycle, including transcription and packaging of the viral RNA. To play such diverse roles, the N protein has two globular RNA-binding modules, the N- (NTD) and C-terminal (CTD) domains, which are connected by an intrinsically disordered region. Despite the wealth of structural data available for the isolated NTD and CTD, how these domains are arranged in the full-length protein and how the oligomerization of N influences its RNA-binding activity remains largely unclear. Herein, using experimental data from electron microscopy and biochemical/biophysical techniques combined with molecular modeling and molecular dynamics simulations, we showed that, in the absence of RNA, the N protein formed structurally dynamic dimers, with the NTD and CTD arranged in extended conformations. However, in the presence of RNA, the N protein assumed a more compact conformation where the NTD and CTD are packed together. We also provided an octameric model for the full-length N bound to RNA that was consistent with electron microscopy images of the N protein in the presence of RNA. Together, our results shed new light on the dynamics and higher-order oligomeric structure of this versatile protein."
DOI: 10.5281/zenodo.5841602
title: Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding

description: This dataset contains files of the molecular dynamics simulations performed in "Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding" study. Further information in presented in README.md file and the abstract of the study is presented below: "The nucleocapsid (N) protein of the SARS-CoV-2 virus, the causal agent of COVID-19, is a multifunction phosphoprotein that plays critical roles in the virus life cycle, including transcription and packaging of the viral RNA. To play such diverse roles, the N protein has two globular RNA-binding modules, the N- (NTD) and C-terminal (CTD) domains, which are connected by an intrinsically disordered region. Despite the wealth of structural data available for the isolated NTD and CTD, how these domains are arranged in the full-length protein and how the oligomerization of N influences its RNA-binding activity remains largely unclear. Herein, using experimental data from electron microscopy and biochemical/biophysical techniques combined with molecular modeling and molecular dynamics simulations, we showed that, in the absence of RNA, the N protein formed structurally dynamic dimers, with the NTD and CTD arranged in extended conformations. However, in the presence of RNA, the N protein assumed a more compact conformation where the NTD and CTD are packed together. We also provided an octameric model for the full-length N bound to RNA that was consistent with electron microscopy images of the N protein in the presence of RNA. Together, our results shed new light on the dynamics and higher-order oligomeric structure of this versatile protein."
DOI: 10.5281/zenodo.6363016
title: Alexandria Library

description: The Alexandria library is as an open access quantum-chemical database containing optimized molecular structures, frequencies, thermochemistry, polarizability and electrostatic moments for organic and inorganic molecules. The name Alexandria highlights that we aim to collect "all" knowledge in the world, old and new, on molecular properties, just like the legendary library of Alexandria, since availability of data rapidly declines with time. This library will assist systematic development and training of empirical force fields for a broad range of molecules.
description: The Swedish research council is acknowledged for financial support to DvdS (grants 2013-5947, 2020-05059) and for grants of computer time (SNIC2015-16-33, SNIC2016-34-44, SNIC 2020-3-8, SNIC 2021-3-8) through the High Performance Computing Center North in Umeå, Sweden.
DOI: 10.5281/zenodo.1004710
title: Alexandria Library

description: The Alexandria library is as an open access quantum-chemical database containing optimized molecular structures, frequencies, thermochemistry, polarizability and electrostatic moments for organic and inorganic molecules. The name Alexandria highlights that we aim to collect "all" knowledge in the world, old and new, on molecular properties, just like the legendary library of Alexandria, since availability of data rapidly declines with time. This library will assist systematic development and training of empirical force fields for a broad range of molecules.
description: The Swedish research council is acknowledged for financial support to DvdS (grants 2013-5947, 2020-05059) and for grants of computer time (SNIC2015-16-33, SNIC2016-34-44, SNIC 2020-3-8, SNIC 2021-3-8) through the High Performance Computing Center North in Umeå, Sweden.
DOI: 10.6084/m9.figshare.16599317.v2
title: Antibody capture beads

description: examples of Goat anti Rat IgG coupled beads
DOI: 10.25345/c5bn9x61x
title: MassIVE MSV000089075 - One-Pot Exosome Proteomics Enabled by a Photocleavable Surfactant
title: Photocleavable surfactant-based exosome proteomics method.
DOI: 10.6084/m9.figshare.19367174
title: the raw data

description: the raw date of this papar.
DOI: 10.5281/zenodo.6363785
title: Data for the study for total OH reactivity measurements in a suburban site of Shanghai

description: The experimental results of interference corrections in the CRM system in the campaign of the measured total OH reactvity in a suburban of Shanghai. In addition, the time series of NMVOCs, calculated and measured total OH reactvity in a suburban of Shanghai.
DOI: 10.5281/zenodo.6363784
title: Data for the study for total OH reactivity measurements in a suburban site of Shanghai

description: The experimental results of interference corrections in the CRM system in the campaign of the measured total OH reactvity in a suburban of Shanghai. In addition, the time series of NMVOCs, calculated and measured total OH reactvity in a suburban of Shanghai.
DOI: 10.18112/openneuro.ds003887.v1.2.1
title: Capacity for movement is an organisational principle in object representations: EEG data from Experiment 3
DOI: 10.18112/openneuro.ds003885.v1.0.6
title: Capacity for movement is a major organisational principle in object representations: EEG data from Experiment 2
DOI: 10.6084/m9.figshare.19372787
title: La Selva Plots Data 2022

description: Data for experimental community experiment
DOI: 10.6084/m9.figshare.19372787.v1
title: La Selva Plots Data 2022

description: Data for experimental community experiment
DOI: 10.5281/zenodo.6363790
title: Testing what we know about coffee volatiles affecting behaviour of Hypothenemus hampei

description: Raw data about laboratory and field assays of volatile compounds that affects coffee berry borer, <em>Hypothenemus hampei.</em>
DOI: 10.5281/zenodo.6363789
title: Testing what we know about coffee volatiles affecting behaviour of Hypothenemus hampei

description: Raw data about laboratory and field assays of volatile compounds that affects coffee berry borer, <em>Hypothenemus hampei.</em>
DOI: 10.6084/m9.figshare.19291208
title: FSGD Global Data set

description: A dataset of fresh submarine groundwater discharge estimates compiled from peer-reviewed publications.
DOI: 10.6084/m9.figshare.19372790
title: Creep data

description: Dates for Experiments and analysis of the creep behavior of biaxially oriented polymethylmethacrylate: Influence difference between temperature and loading stress.
DOI: 10.26036/cnp0002644
title: RNA-seqs of Rat's muscles

description: Intrauterine growth restriction induces adulthood chronic metabolic disorder and inflammation activity in cardiac and skeletal muscles
DOI: 10.26036/cnp0000775
title: GBS（Genotyping-by-Sequencing） of Triticum urartu

description: The project sequenced 162 T.urartu samples by GBS.
DOI: 10.26036/cnp0002684
title: 河南省农业科学院2个白菜有参全长转 录组建库测序分析任务单 结题报告

description: 两个不同根肿病抗性大白菜的有参全长转录组建库测序分析
DOI: 10.26036/cnp0002688
title: Maize Metabolomics Detection

description: Uncovering the gene regulatory network of maize hybrid ZD309 under heat stress by transcriptomic and metabolomic analysis
DOI: 10.26036/cnp0000699
title: Triticum urartu whole genome resequencing

description: The project sequenced 59 T.urartu samples by whole genome resequencing, aiming at studying the population structure and historical evolutionary status of T.urartu.
DOI: 10.26036/cnp0002706
title: 叶绿体基因组测序分析

description: 为探究牡丹叶绿体基因组特征及其系统进化发育关系，以早花凤丹’、‘凤丹’、‘连鹤’三个品种的牡丹的总DNA为材料，采用高通量测序平台进行牡丹叶绿体基因组测序。
DOI: 10.26036/cnp0002461
title: Transcriptomic profile of the mouse postnatal liver development by single nucleus RNA sequencing

description: The mammalian liver is the major hematopoietic organ during embryonic development, while postnatally its functions change dramatically to support the body metabolism and blood flow, as well as playing important endocrine functions, among others. How the liver adapts to those environmental changes after birth and gradually develops these functions remains elusive. Here, we performed single-nucleus RNA-seq (snRNA-seq) profiling 43,343 nuclei from four key time points of mouse postnatal liver development (P0, P3, P7, P14). We identified 20 clusters of different liver parenchymal and non-parenchymal cell types and analyzed the dynamics in cell composition and biological functions in the developmental processes. By surveying the differentiation trajectory of hepatocytes, we found that several pathways changed significantly in the postnatal liver development, such as glycolysis, bile secretion, and VEGF signaling pathway. Taken together, this study provides a comprehensive single-nuclei transcriptomic atlas of liver cell composition to study the dynamic changes that reshape mouse liver to activate its metabolic functions after birth.
DOI: 10.26036/cnp0001689
title: 胎盘细胞图谱及孕期疾病组学研究

description: 间充质干细胞（mesenchymal stem cells，MSCs）是一类来源于中胚层、在合适的诱导条件下可向成骨、软骨、神经等多种组织细胞分化的成体干细胞。近期研究表明，MSCs细胞本身具有组织修复能力外，还可通过分泌免疫调节因子、细胞生长因子等来响应炎症反应，从而具有免疫调节及赋予组织周围细胞帮助组织修复的能力，其被应用于骨损伤、骨关节炎、老年痴呆等多种疾病的临床研究中。MSCs来源丰富，易于分离、扩增、运输和储存，并易于标准化制备，极具产业化和临床应用前景。然而已有研究发现，MSCs不同组织来源、供体年龄及培养体系等因素均会引入MSCs的生物学活性差异，表现出明显的细胞异质性，也是阻碍进一步临床应用的主要困难之一。 本项目通过单细胞转录组测序技术，对胎盘组织及脐带来源的间充质干细胞P5代细胞进行转录组及表观组的异质性及功能亚群的研究。
DOI: 10.26036/cnp0001454
title: Stepwise rolling back of human pluripotent stem cells to an 8-cell-like stage

description: Human pluripotent stem cells (PSCs) are a good proxy for studying early developmental processes and hold tremendous promise for regenerative medicine. Yet, their spectrum and potency remain less well characterized than in rodents, thwarting application. Particularly, in contrast to their mouse counterparts, human totipotent-like cells corresponding to the time of zygote genome activation (ZGA) or eight-cell (8C) stage have not yet been generated. Here, we report a quick and controllable, exogenous factor-free, methodology for producing cells transcriptionally and epigenetically similar to 8C embryonic cells from human PSCs. Single-cell multiomics characterization identified key molecular events associated with this conversion, including a partial shutdown of the pluripotency network. Loss-of-function experiments also showed fundamental roles for two factors highly enriched in 8C human embryos, DPPA3/STELLA (a master regulator of DNA methylation in oocytes) and TPRX1 (an ETCHbox family transcription factor lacking in mouse). DPPA3/STELLA is necessary for inducing passive DNA demethylation throughout the entire conversion process, whereas TPRX1 is a key regulator of the 8C-like cell (8CLC) conversion. Our approach provides a unique experimental window into the early events of human embryogenesis, which may be instrumental for producing functional artificial blastocysts (blastoids) and high-contribution interspecies chimeras.
DOI: 10.26036/cnp0001756
title: Cycad genome project

description: Cycads are one of the most fascinating seed plant (spermatophyte) groups, they are often referred to as "living fossils".
DOI: 10.26036/cnp0000670
title: Comparative genomics analysis for adaptation of drosophila to climate change

description: The goal of this analysis is to assembly drosophila genomes. These genomes can be used in various comparative genomics study, including the reconstruction of the drosophila phylogeny; discovery and analysis of cis-regulatory modules ; and determining the genetic basis of ecological adaptations.
DOI: 10.26036/cnp0001078
title: Mitochondrial genome of Echinococcus spp.

description: Near-complete mitochondrial genome sequences of Echinococcus spp.
DOI: 10.26036/cnp0001130
title: Whole genome sequence of Brassica oleracea var chinensis Lei

description: Whole genome sequence of Brassica oleracea var chinensis Lei This is the same specie as Brassica oleracea var alboglabra Bailey 这是一个芥蓝的从头组装的项目
DOI: 10.26036/cnp0002351
title: derby_China_pork

description: 分离自猪肉及其生产链的德尔卑沙门菌菌株
DOI: 10.26036/cnp0002309
title: Mechanosensitive lncRNA Neat1 promotes osteoblast function through paraspeckle-dependent Smurf1 mRNA retention

description: Mechanical stimulation plays an important role in bone remodeling. Exercising induced mechanical loading enhances bone strength and mechanical unloading leads to bone loss. Increasing evidence demonstrates that lncRNA plays key roles in diverse biological, physiological and pathological contexts. However, the role of lncRNA in mechanotransduction and its relation with bone formation remains unknown. In this study, we screened the mechanosensing lncRNAs in osteoblasts and identified Neat1, the most obviously decreased lncRNA under simulated microgravity. It is surprising to find that not only Neat1 expression but the specific paraspeckle structure formed by Neat1 are sensitive to different mechanical stimulations, which are closely related with the function of osteoblast. Paraspeckle exhibits small punctate aggregates under simulated microgravity and elongated prolate or larger irregular structures under mechanical loading. Neat1 knockout mice exhibited disrupted bone formation, impaired bone structure and strength, and reduced bone mass. Neat1 deficiency in osteoblasts blunts the response of osteoblasts to mechanical stimulation. In vivo, Neat1 knockout in mice weakened the bone phenotypes in response to mechanical loading and hindlimb unloading stimulation. Mechanistically, paraspeckles promote nuclear retention of E3 ubiquitin ligase Smurf1 mRNA, down-regulation of their translation, thus inhibiting ubiquitination degradation of osteoblast master transcription factor Runx2, one of the Smurf1 targets. Our study revealed that Neat1 plays an indispensable role in osteoblast function under mechanical stimulation, which provides a paradigm for the function of lncRNA assembled structure in response to mechanical stimulation and offers a therapeutic strategy for long-term spaceflight or bedrest induced bone loss and aged osteoporosis.
DOI: 10.26036/cnp0000891
title: 文昌鱼单细胞图谱

description: 基于转座酶的单细胞测序手段已广泛用于诸多物种发育过程中的细胞图谱研究，如小鼠、斑马鱼、爪蟾、线虫和海鞘等。由于在演化历上占据独特地位，文昌鱼是物种演化发展研究的重要物种，然而，其单细胞层面的发育图谱尚未被阐明。本文构建了涵盖文昌鱼胚胎发生各关键时期和成体器官的单细胞图谱。
DOI: 10.26036/cnp0002774
title: 金龙鱼雌雄重测序和转录组

description: 金龙鱼雌雄重测序和转录组
DOI: 10.26036/cnp0002375
title: Genomic adaptations for arboreal locomotion in Asian flying treefrogs

description: Genomic adaptations for arboreal locomotion in Asian flying treefrogs
DOI: 10.26036/cnp0002483
title: Whole Genome Sequencing for profiling canavanine resistance mutation can1-1

description: In Schizosaccharomyces pombe, The the can1-1 mutation has theconfers resistance to the toxic arginine analog canavanine resistance ability in Schizosaccharomyces pombe. This mutation has been assumed to disrupt a gene encoding an arginine transporter. In PomBase, (S. pombe) reported by Kohli et al. in 1977 and the gene SPBC18H10.16 gene is currently named designated can1 on PomBase is thought as an arginine permease same as the CAN1 gene in budding yeast. The exact information about the can1-1 mutation will further promote our understanding about the canavanine resistance mechanism. Here, we sequenced the genomes of three can1-1 strains.use the next-generation sequencing to investigate more details about the N can1-1 mutation and we found that there is no mutations were found in SPBC18H10.16. the gene named can1 in all the strains with the can1-1 mutation. Instead, these strains have all harbor an common R175C mutation in the gene any1/SPBC18H10.20c. any1 encodes an α-arrestin that acts as a trafficking adaptor to down-regulate the basic amino acid transporter Cat1. any1-R175C. Thus, the Our findings indicate that can1-1 is not a loss-of-function mutation in a transporter gene, but rather a likely gain-of-function mutation affecting a trafficking adaptor.SPBC18H10.16 gene annotated as can1 is not the expected gene same with the CAN1 gene in Saccharomyces cerevisiae and the any1-R175C mutation accounts for the canavanine resistance in these strains.
DOI: 10.26036/cnp0002569
title: Chromosome-level genome of Pedinomonas minor project

description: The Pedinophyceae (Viridiplantae) comprise a class of small uniflagellate algae with a pivotal position in the phylogeny of the Chlorophyta as the sister group of the “core chlorophytes”. We present a chromosome-level genome assembly of the freshwater type species of the class, Pedinomonas minor. Although the genome is relatively small (55 Mb), it shares many traits with those of core chlorophytes including number of introns, mRNA lengths, number of protein-coding genes and abundance of repetitive elements. P. minor is a “naked” flagellate, only bound by the plasma membrane, thriving in temporary habitats such as small puddles that frequently dry-out. Gene family innovations and expansions and transcriptomic responses to abiotic stresses have shed light on adaptations of P. minor to its fluctuating environment. Phylogenomic analyses indicated that horizontal gene transfers from fungi and bacteria contributed to the evolution of these traits. We identified a putative endogenization site of a nucleocytoplasmic large DNA virus and hypothesized that endogenous viral elements donated foreign genes to the host genome.
DOI: 10.26036/cnp0002590
title: Spatial transcriptome uncovers the mouse lung architectures and functions

description: Revealing the relationships between the tissue structures and transcriptomic information is significant for understanding the mechanisms and principles underpinning the biological processes in lung development and diseases. The widely transcriptomic technics, including bulk and single-cell RNA sequencing, cannot accurately restore the tissue location of the gene expression. The advanced spatial transcriptomic tools can fill this gap properly with in-situ RNA capturing and spatial barcode labeling and translating. However, the published spatial transcriptome data of lung is rare or low-quality. Here we harnessed the large-view and high-resolution capabilities of Stereo-seq, one of the most advanced spatial transcriptome tools, in a 5-week-old female mouse to uncover the lung functions with their tissue location resolved. We also found a gradient expression of a bunch of genes related to cell proliferation along the axis of the proximal-to-distal trachea. All the data provided by the study pave the way for further studies in lung development and disease in the future.
DOI: 10.26036/cnp0002618
title: The Single-cell Stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves

description: Understanding the complex functions of plant leaves requires a thorough characterization of discrete cell features. Although single-cell gene expression profiling technologies have been developed, their application in characterizing cell subtypes has not been achieved yet. Here, we present scStereo-seq (single-cell SpaTial Enhanced REsolution Omics-sequencing) that enabled us to firstly show the bona fide single-cell spatial transcriptome profiles of Arabidopsis leaves. Subtle but significant transcriptomic differences between upper and lower epidermal cells have been successfully distinguished. Furthermore, we discovered cell-type-specific gene expression gradients from the main vein to the leaf edge, which for the first time led to the finding of distinct spatial developmental trajectories of vascular cells and guard cells. Our study showcases the importance of physical locations of individual cells for exerting complex biologic functions in plants and demonstrates that scStereo-seq is a powerful tool to integrate single cell location and transcriptome information for plant biology study.
DOI: 10.6073/pasta/4bd5b607d82a4cabcd417d451b50bb28
title: MCR LTER: Coral Reef: Population Dynamics: Symbiodinium population initial sampling conditions in corals of Moorea

description: These data consist of sample collection locations and conditions only, not the results of sequencing. These data were an initial collection of an expected time series which was not repeated. Clade data derived from the sample collection described here are archived on GeoSymbio. Coral are symbiotic with photosynthetic dinoflagellates from the genus Symbiodinium. There are eight divergent clades (A-H) within the genus which each contain many genetic varieties. Different types of Symbiodinium have been shown to affect the growth rate and thermal tolerance of the coral. The diversity and population structure of Symbiodinium on a reef and how it changes over time is therefore critical to the stability and resilience of coral reefs. Our research conducted through the MCR LTER project aims at defining the population structure of Symbiodinium present in the corals of Moorea and documenting changes over time.
DOI: 10.25549/pcra-c14-8829
title: Put' = Voie = [The way], no. 4 (June-July 1926)

description: [description english/roman)] Irregular frequency
DOI: 10.15468/dl.ba8mrq
title: Occurrence Download

description: A dataset containing 844 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ruellia erythropus (Nees) Lindau"
 ]
}

 The dataset includes 844 records from 92 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107345-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.