cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnp0001301
title: The transcriptome project of Fusarium graminearum PH-1

description: Functional characterization of calcineurin-responsive transcription factors Fg01341 and Fg01350 in Fusarium graminearum. To this end, we performed RNA-sequencing of the wild-type PH-1, ΔFg01341 and ΔFg01350 mutant strains, and their respective complemented strains.
DOI: 10.26036/cnp0000517
title: genome sequencing and assembly of Areca catechu

description: we present a high quality genome of Areca catechu using Illumina HiSeq and PacBio sequel data.
DOI: 10.26036/cnp0001287
title: Chromosome-level reference genome assembly provides insights into aroma biosynthesis in passion fruit (Passiflora edulis)

description: Passion fruit, native to tropical America, is an agriculturally, economically and ornamentally important fruit plant that is well-known for its acid pulp, rich aroma and distinctive flavor. Here, we present a chromosome-level genome assembly of passion fruit by incorporating PacBio long HiFi reads and Hi-C technology.
DOI: 10.26036/cnp0001299
title: Epigenetic therapy targeting SARS-CoV-2 viral RNA to treat COVID-19

description: we reported a way of epigenetic therapy by regulating methylation on viral RNA to overcome the problems associated with polymerase fidelity, in which azacytidine was applied to efficiently replace cytidine (C) and meanwhile reduce the robust m5C methylation identified on viral RNA to inhibit SARS-CoV-2 replication
DOI: 10.26036/cnp0001290
title: 肠道菌群通过SCFAs调控巨噬细胞对肺炎克雷伯菌的吞噬的机制研究

description: 肺炎克雷伯菌肺炎是影响人类健康的重要感染性疾病。研究表明肠道菌群增强了呼吸道疾病的防御能力，然而其机制尚不清楚。预实验结果表明Lamtor2基因在肠道菌群耗竭小鼠的肺泡巨噬细胞中异常表达，补充短链脂肪酸后，表达水平趋于正常；肺炎克雷伯菌感染小鼠巨噬细胞RAW264.7后Lamtor2基因表达上调，短链脂肪酸受体基因表达水平降低。由此，我们推测肠道菌群通过SCFAs/FFAR调控肺泡巨噬细胞的LAMTOR2信号通路进而增强其对病原体的吞噬能力。为此，我们拟采用不同类型的肺炎克雷伯菌感染不同肠道菌群背景的小鼠，运用多组学联合的方法阐明肠道菌群与小鼠细菌性肺炎固有免疫的关系；拟构建Lamtor2基因敲除的RAW264.7细胞系和条件性基因敲除小鼠，进一步明确该基因在“肠-肺”轴中的功能。本项目拟从肠道菌群这个新视点出发，探究细菌性肺炎的固有免疫机制，为开发细菌性肺炎的新型疗法提供重要的理论基础。
DOI: 10.26036/cnp0001243
title: HiSeq data of Mitra chinensis

description: Tissue samples of M. chinensis from six individuals were collected from GuangXi province, raw data were sequenced (2×150bp paired-end) using HiSeq platform at BGI Company.
DOI: 10.26036/cnp0001739
title: gilts fecal and vagina 16S rRNA raw data

description: Identification of Gut and Vaginal Microbiota and Serum Metabolite Associated with Sow Non-return of estrus After Weaning
DOI: 10.26036/cnp0001484
title: leaf growth in bamboo

description: By detecting more than 7,500 parenchymal cells length, we discover that the linear growth leaf of Pseudosasa japonica could be divided into three growth modules.The next PacBio and Illumina transcriptome sequencing finds 21,933 unigenes that are expressed in these zones.
DOI: 10.26036/cnp0001325
title: Aegilops tauschii Genome sequencing and assembly

description: Aegilops tauschii sequencing and assembly. Provide genetic resources for wheat breeding.
DOI: 10.26036/cnp0001311
title: Callithrix jacchus (common marmoset) Genome , mCalJac1, maternal haplotype

description: The common marmoset (Callithrix jacchus) is a small, social monkey native to Brazil. With numerous attributes making it advantageous to study in the laboratory, the marmoset has become a prominent model in biomedical research. Sponsored by Guojie Zhang of the University of Copenhagen, a trio of samples were collected from a male juvenile and its parents by Stephanie Marcus of Erich Jarvis’ Lab in the colony of the Winrich Freiwald Lab at The Rockefeller University, and were used to generate a high-quality reference genome as part of the G10K-VGP.
DOI: 10.26036/cnp0001314
title: Comprehensive analysis of Transcriptome and Metagenomic in two agricultural pests (Spodoptera frugiperda and Spodoptera litura)

description: We collected Spodoptera frugiperda and Spodoptera litura in the field in Xindu District, Chengdu, Sichuan, China. They were artificially propagated to sample their first-generation by the Institution of plant protection, Sichuan Academy of Agricultural Sciences. We sampled 5th instar larvae, 6th instar larvae, chrysalis, female adult and male adult. In total, Each species had 15 individuals from four developmental stages, containing 5th instar larvae stage, 6th instar larvae stage, chrysalis stage, and adult stage. Larvae removed intact intestinal tissues and the whole bodies from the chrysalis and adult individuals.The intestinal tissue and the whole body were sequenced by metagenomics and transcriptome respectively.
DOI: 10.26036/cnp0001332
title: A chromosome-level genome assembly of Vibrio diabolicus R-31 isolated from saline-alkaline soil

description: Vibrio is a large genus containing many highly problematic pathogens common in aquaculture. In this study, a strain of Vibrio diabolicus, named R-31, was isolated from radiation-tolerant soil in Xinjiang Uyghur Autonomous Region, China, and characterized via single-tube long fragment read (stLFR). The genome of V. diabolicus R-31 was calculated to contain 5,262,922 base pairs with a G+C content of 45.82%. And 4,702 open reading frames (ORFs) were predicted in the whole genome, genomic analysis revealed that the organism contains multiple genes (catB, tlh) are related to its virulence gene and drug resistance. This is the first time that V. diabolicus R-31 has been found in a non-aquatic ecosystem. The V. diabolicus R-31 genomic sequence data analyzed in this study is of great significance for us to redetermine the scope of Vibrio, and will help to further understand he characteristics of V. diabolicus.
DOI: 10.26036/cnp0001336
title: Four Ardisia chloroplast genomes

description: 四个紫金牛属植物（走马胎、朱砂根、雪下红、虎舌红）叶绿体双向测序数据
DOI: 10.26036/cnp0000758
title: 17 Marine mammals Genome sequencing and assembly

description: to perform the whole genome sequencing of 17 marine mammals
DOI: 10.26036/cnp0000974
title: Genomes of silver carp and bighead carp

description: The silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis) are edible fishes among “Four Domesticated Fishes” originated from China and disseminated intensively worldwide. Here, we report the genomes of the two fishes and the sequencing data.
DOI: 10.26036/cnp0000757
title: 弓背青鳉幼鱼转录组数据

description: 弓背青鳉初孵仔鱼 在雌雄激素暴露后转录组数据
DOI: 10.26036/cnp0001334
title: HiSeq data of Antigona lamellaris

description: Tissue samples of Antigona lamellaris from six individuals were collected from GuangXi province, raw data were sequenced (2×150bp paired-end) using HiSeq platform at BGI Company.
DOI: 10.26036/cnp0001371
title: Topping

description: 烟草打顶刺激
DOI: 10.26036/cnp0001379
title: Efficient construction of mega diverse single domain antibody libraries from multiple non-immunized camels

description: 抗体药是目前最激动人心的抗癌药之一，目前人们常用的传统抗体来源大多为小鼠和人类，但传统抗体的不足限制了其应用范围，寻找和发现小型化抗体是当前主要的研究趋势。驼类动物来源的重链抗体（Heavy-chain antibodies, HCAbs）可产生一种新型单域抗体VHH（Variable domain of the H chain of Heavy Chain Antibody），这种单域抗体又称为纳米抗体，是目前所发现的具有完整功能的最小分子抗体片段，分子量约为12-15kDa，具有分子量小、可溶性强、稳定性高、可逆折叠、识别隐蔽抗原表位，组织渗透性强等优势。 本研究采集了76投未免疫的驼科动物包括羊驼（alpaca）、美洲羊驼（llama）和双峰骆驼（bactrian camel）外周血淋巴细胞和脾脏组织，构建了一个mega级库容的天然纳米抗体的噬菌体展示文库，并利用该展示库和经过优化的负向筛选技术，获得了靶向不同抗原的多种不同的VHH候选分子。本研究建立了一个快速高效的纳米抗体开发平台，可极大的节约抗体研发时间和成本，具有巨大的市场价值。
DOI: 10.26036/cnp0001387
title: Coral reef invertebrates and their associated microbial communities

description: Host-controlled microbial community structuring can often lead to patterns of coevolution and vertical inheritance. In a community of many bacteria with no a priori hypotheses of symbiosis, taxa that display patterns of coevolution with their hosts are more likely to be relevant to host fitness. This project will 1) reveal the complexity of marine invertebrate sysmbioses through elucidating patterns of host/microbiome associations; 2) characterize the influence of microbiome on the biodiversity, distribution, adaptation and health of marine invertebrates. We propose to sample 100 invertebrate taxa selected based on their ecological importance and role in reef ecosystem function. Selected species will focus on scleractinian coral species, the subclass of Octocorallia, members of the Porifera and phylum Mollusca. The microbiome of each marine invertebrate will be characterized to establish diversity patterns. The associated metabolic potentials of these communities will be assessed through metagenomic sequence analysis and the active component of the microbial community members addressed through metatranscriptomic analysis.
DOI: 10.26036/cnp0000352
title: genome assembly and genome-wide Hi-C analysis

description: The three-dimensional architecture of chromosome is an important factor in response to environmental and developmental cues. To investigate the chromatin organization features of sesame (Sesamum indicum), we firstly achieved a chromosome-level sesame assembly using Pacific Biosciences (PacBio) long-read data combined with a genome-wide chromosome conformation capture (Hi-C) approach. Based on the high quality reference genome, we interrogated the chromatin architecture features of sesame genome. The substructure units, such as A/B compartments, topologically associated domains (TADs) and chromatin loops were presented in sesame genome, similar to several other plant species. Moreover, we detected the alterations of chromatin organization of sesame seedlings in response to dark-treatment or between two varieties with different morphological properties. The conspicuous changes of chromatin architectures in both two cases suggested that chromatin organization was associated with the adaptation to environmental cues regardless of the short-time stimuli, such as dark-treatment or long-time adaptiveness as different characters between varieties (“Zhongzhi 13” and “Zhouhei 1”). A great number of significant differential contacts with a false discovery rate (FDR) of ≤ 0.05 were identified from pairwise normal growth vs. dark-treated sesame seedlings, or “Zhongzhi 13” vs. “Zhouhei 1” varieties. However, the promoter of differentially expression genes (DGEs) were not obvious enrichment in the differential contact regions compared to background genes, implying that there should be an unknown relationship between DGEs and differential contact regions. These resources facilitate to unveil biological processes and improve agricultural technologies in sesame.
DOI: 10.26036/cnp0000069
title: Technical replicates reveal a sequencing batch effect among eight Illumina MiSeq runs on soil fungal communities

description: evaluating the impact of sequencing run on the data by designing to use three soil samples for repeated sequencing, namely technical replicates
DOI: 10.26036/cnp0001410
title: tetraploid peanut genome

description: We de novo assembled the fourth chromosomal level peanut cultivar (Arachis hypogaea cv. Haihua1) genome using Nanopore and Hi-C platform(CNP0001330)
DOI: 10.26036/cnp0001473
title: 基于线粒体Cytb和D-loop的中华蟾蜍两野生种群遗传背景分析

description: We evaluated the host genetic divergence of two wild populations of Bufo gargarizans by using mitochondrial DNA (mtDNA: cytb and D-loop). The mtDNA and SSR markers were amplified by using the primers designed in previous studies.
DOI: 10.26036/cnp0001417
title: High-quality chromosome-level genome assembly and full-length transcriptome analysis of the pharaoh ant Monomorium pharaonis

description: We de novo assembled a chromosome-level genome for Monomorium pharaonis, with a scaffold N50 of 27.2 Mb, by hybridizing Illumina, PacBio, and Hi-C sequencing technologies.
DOI: 10.26036/cnp0000665
title: Genome sequencing and assembly of Plectropomus leopardus

description: to perform the whole genome sequencing of Plectropomus leopardus
DOI: 10.26036/cnp0001408
title: 寿光鸡快慢羽全基因组关联分析和转录组分析

description: 寿光鸡一共56个重测序数据和12个转录组数据，其中28个快羽芯片数据，28个慢羽芯片数据，6个快羽转录组数据，6个慢羽转录组数据。
DOI: 10.26036/cnp0001421
title: 蓖麻蚕病蚕病原物检测

description: 利用MinION对蓖麻蚕病蚕全基因组进行纳米孔测序
DOI: 10.26036/cnp0001419
title: Next-generation sequencing data of 16 Rhode Island Red chickens

description: The project of next-generation sequencing data of 16 Rhode Island Red chickens is pair-end sequencing, 150 bp, 50X, Illumina HiSeqTM 4000.
DOI: 10.26036/cnp0001405
title: the whole-genome of five Erysipelotrichaceae strains

description: Isolation and whole genome sequencing unveiling five novel strains of the Erysipelotrichaceae family
DOI: 10.26036/cnp0001429
title: DNBSEQ-T20测序系统和全自动样品加载

description: 研发高通量低成本的DNBSEQ-Tx测序系统
DOI: 10.26036/cnp0001445
title: An ATAC-seq dataset uncovers the regulatory landscape during axolotl limb regeneration

description: Axolotl (Ambystoma mexicanum) is a tetrapod species with extraordinary power to regenerate its body parts when lost entirely, thus serves as an illustrious model for regeneration research. Even though several previous studies have investigated the transcriptomic patterns, axolotl regeneration’s epigenetic regulations remain elusive. To identify critical regulatory elements during axolotl limb regeneration, we report an ATAC-seq dataset with 24 ATAC-seq profiles from axolotl upper forearm tissues at the homeostatic stage and seven regenerative stages. 342,341 regulatory elements were identified from the dataset, of which 33,604 exhibited transient dynamic changes. We also performed transcription factors enrichment analysis to examine the occupancy by key transcription factors that drive specific regeneration events. Our results provide an unprecedented resource on the axolotl epigenome, which will enhance the comprehension of the underlying mechanisms for axolotl regeneration and further boost the development of regeneration research.
DOI: 10.26036/cnp0001439
title: Whole genome sequencing of pika samples

description: We collected 81 pika samples and performed whole genome sequencing for them, the obtained data were used for phylogenetic and morphology analysis.
DOI: 10.26036/cnp0001440
title: pan-genome of cultivated and wild sorghum

description: Sorghum is a drought tolerant staple crop for half a billion people in Africa and Asia, an important source of animal feed throughout the world and a biofuel feedstock of growing importance. Cultivated sorghum and its inter-fertile wild relatives constitute the primary gene pool for sorghum. Understanding and characterising the diversity in the primary gene-pool is fundamental for its effective utilisation in crop improvement activities. Here, we report the first sorghum pan-genome comprising cultivated sorghums and its wild relatives to explore the diversity within the sorghum primary gene pool. With 13 genomes de novo assembled using a combination of short-read and long-read sequencing, we have generated a pan-genome of 51,349 gene families (35% of which are core genes), and identified 185.29 Mb sequence absent from the reference genome.
DOI: 10.26036/cnp0000794
title: Inter-determination of blood metabolite levels and gut microbiome supported by Mendelian randomization

description: BACKGROUND:The gut microbiome has been implicated in a variety of physiological states. Controversy over causality, however, has always haunted microbiome studies. Here, we utilized the bidirectional Mendelian randomization (MR) approach to address questions that are not yet mature for more costly randomized interventions. From a total of 3,432 Chinese individuals with shotgun sequencing data for whole genome and whole metagenome, as well as anthropometric and blood metabolic traits, we identified 58 causal relationships between the gut microbiome and blood metabolites, and replicated 43 out of the 58. Gut microbiome could determine features in the blood. For example, increased fecal relative abundances of Oscillibacter and Alistipes were causally linked to decreased triglyceride concentration, and fecal microbial module pectin degradation might increase serum uric acid. On the other hand, blood features may determine gut microbial features, e.g. glutamic acid appeared to decrease Oxalobacter, and a few members of Proteobacteria were unidirectionally influenced by cardiometabolically important metabolites such as 5-methyltetrahydrofolic acid, alanine, as well as selenium. This study illustrates the value of human genetic information to help prioritize gut microbial features for mechanistic and clinical studies. The results are consistent with whole-body cross-talks of the microbiome and the circulating molecules. Data Access:Summary statistics that support the findings of this study including the associations between host genetics and microbiomes, host genetics and metabolites are publicly available. The release of the data was approved by the Ministry of Science and Technology of China (Project ID: 2020BAT1137). Sequencing data are available via application on request.
DOI: 10.26036/cnp0001188
title: Cell-free Echinococcus spp. DNA changes before and after chemotherapy.

description: Cell-free Echinococcus spp. DNA changes before and after chemotherapy.
DOI: 10.26036/cnp0001443
title: Construction of a chromosome-level genome for the Pacific oyster Crassostrea gigas

description: Here we report a high-quality chromosome-level genome assembled by Pacific Bioscience long reads and Hi-C-based and linkage-map-based scaffolding technologies for the Pacific oyster (Crassostrea gigas) .
DOI: 10.26036/cnp0000716
title: The Chinese mitten crab genome research

description: This project first sequenced the Chinese metten crab genome and assembled the genome on chromosome level.
DOI: 10.26036/cnp0001452
title: MTB diagnosis by mNGS on BALF

description: Metagenomic Next-generation Sequencing (mNGS) has been shown as an effective diagnostic method for infectious diseases, but its potential clinical utility for tuberculosis (TB) diagnosis remains to be demonstrated. The diagnostic performance of mNGS with conventional detection methods for Mycobacterium tuberculosis complex (MTBC) and other pathogens in BALF were compared
DOI: 10.26036/cnp0001442
title: Fuxian Lake 20m freshwater Hi-C sample

description: Hi-C data for 20m depth freshwater. Kit was from USA Phasegenomics and enzyme used in this study was Sau ^GATC
DOI: 10.26036/cnp0001509
title: High-resolution single-molecule long-fragment rRNA gene amplicon sequencing for uncultured bacterial and fungal communities

description: This dataset is currently public only for peer review. The abstract and other details will be released after it is accepted.
DOI: 10.26036/cnp0001470
title: An ATAC-seq atlas of chromatin accessibility in rat tissues

description: The Norway rat (Rattus norvegicus) serves as a valuable model for many complex disorders and social behavior researches due to its remarkably stable. Therefore, a comprehensive study of epigenetic regulation of rats is essential for a deeper understanding of diseases and social behaviors. Here, we globally profiled chromatin accessibility using ATAC-seq (Assay for Transposase-Accessible Chromatin coupled with next-generation sequencing) in the 10 body tissues and 12 brain regions from adult female rats with a comprehensive, replicated datasets. The open chromatin landscape of the rat tissues consisted of 187,930 accessible elements, from which 24,238 tissue specific peaks are detected by comparing the open chromatin landscapes of different tissues. Furthermore tissue-specific transcription factors and their transcription factors are correlated with tissue characteristics, indicating that our study may pave the way for diseases and social behaviors researches on rat.
DOI: 10.26036/cnp0001474
title: Assembly of P. chinensis

description: Assembly of P. chinensis
DOI: 10.26036/cnp0001471
title: Single-cell chromatin accessibility landscape reveals diversity in regulatory regions across distinct adult rat cortex

description: The rat has been used widespread as an experimental animal for modelling human disease and toxicology and for psychological, medical and biological research especially in neurological disease. To discover regulatory elements driving the specificity of gene expression in different cell type and regions of the adult rat brain. We applied a single-cell ATAC-seq assay, DNBelab C Series, to generated a profile of open chromatin from four dissected areas of adult SD rat brain. High-quality ATAC-seq data was obtained for 59,023 single cells and identified 16 distinct cell types with marker gene. We found that different regions have differences in the proportion of excitatory neuron cells and gene expression We further found that some interesting transcription factors have great guiding significance in the exploration and treatment of the pathogenesis of various neurological diseases. For example, the reductions in SPI1 contribute to a delayed onset of Alzheimer’s disease and KLF4 may be a potential therapeutic target for neurodegenerative diseases. Mutations of the KLF6 gene play a role in the pathogenesis of astrocytic gliomas and NEUROD2 pathogenic mutations caused ASD and intellectual disability. Thus, this cortex altas serves as a resource for understanding the chromatin regulatory landscape of diverse rat brain cell types and interpreting the key of regulatory network of neuropathogenesis.
DOI: 10.26036/cnp0001491
title: Assemble plant mitochondrial genome with short reads - insights into the mitochondrial genome evolution of Fagales

description: The nonconservation and uncertain structure of plant mitochondrial genomes make the assembly a big challenge. So far, in angiosperms, the known mitochondrial genomes are much less than plastid genomes. For many species, the mitochondrial genome becomes the last genome in the cell that undeciphered, e.g. in Fagales, more than 20 nuclear genomes and 150 plastid genomes are known but no more than two mitochondrial genomes were formally published. To close the gap and improve the quality of plant mitochondrial genome assemblies, we developed a reliable workflow and assembled 23 complete and high-quality mitochondrial genomes of Fagales by using short Illumina sequencing reads.
DOI: 10.26036/cnp0001464
title: NOTCH3 is a prognostic factor and is correlated with immune tolerance in gastric cancer

description: 论文发表, 信息平台共享，平台网址：https://db.cngb.org/cnsa
DOI: 10.26036/cnp0001313
title: African arowana genome project

description: The African arowana genome sequences provides insights on the ancient teleost evolution
DOI: 10.26036/cnp0001498
title: Siganus canaliculatus ATAC-seq

description: Siganus canaliculatus ATAC-seq data
DOI: 10.26036/cnp0001450
title: Improvement of Pulmonary Infection Diagnosis with Metagenomic Next Generation Sequencing

description: Improving Pulmonary Infection Diagnosis with Metagenomic Next Generation Sequencing
DOI: 10.26036/cnp0001535
title: whole-genome resequencing of moso bamboo

description: Moso bamboo (Phyllostachys edulis) is an economically important species, widely naturalized in subtropical areas. Further developing of this species for sustainable bamboo resource has been hindered due to a lack of its population genome information. Here, we performed the whole-genome resequencing of 427 individuals covering all fifteen major moso bamboo production areas in China.
DOI: 10.26036/cnp0001525
title: plant evolution

description: Raw sequence data from mangroves
DOI: 10.26036/cnp0001527
title: Long Term Microgravity Effect on Macaca mulatta

description: 15 Rhesus macaques (Macaca mulatta) were subjected to -6° head-down tilted bed rest (HDBR) for 6 weeks.skeletal muscle tissue was collected for metabolomic analyses.Metabolite detection was carried out by ultrahigh-performance liquid chromatography (UPLC)-MS.