cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnp0000231
title: Program of monkey embryogenesis and germ cell formation in vitro

description: Embryo development of post-implantation and gastrulation is a milestone of embryogenesis. However, the fundamental mechanisms underlying this process remain elusive as technological and ethical limitations. Here, we we improved an in vitro culture system that cynomolgus monkey embryos could develop to 20 days without any maternal tissues, which clearly reveal lineage specification, bi-laminar disc generation, amniotic and yolk sac formation, and primordial germ cell like cells (PGCLC). By applying single cell-omics analysis, unsupervised dimensionality reduction and clustering algorithm data show clear, distinct, stepwise development routes for the epiblast, primitive endoderm, trophectoderm and extra-embryonic mesenchyme lineage. We also found development path of PGCLCs, suggesting origin of PGLCs in amnion instead of EPI. Furthermore, signal pathways analysis showed existence of intimate interactions among lineages. By sequencing (scATAC-seq ) assay for transposase-accessible chromatin, we identify transcription factor grammar specifying of each cell type (EPI, PE and TE) and infer potential master transcriptional regulators. Collectively, the results provide the new insight into understanding molecular and cellular dynamics that underlie monkey post-implantation development, especially beyond E13. Our study provides a basic knowledge about regulation of primate pluripotency in vitro for cell replacement therapy.
DOI: 10.26036/cnp0000931
title: The research on mitochondrial DNA in Araneae

description: The mitochondrial genome of Arctosa tanakai (Araneae: Lycosidae) was sequenced. The mitochondrial genome information of it has certain significance for further studies on phylogeny, evolution and environmental adaptability.
DOI: 10.26036/cnp0000892
title: Single cell brain atlas of Parkinson’s disease mouse model

description: Parkinson’s disease (PD) is a neurodegenerative disease leading to the impairment of movement execution. PD pathogenesis has been largely investigated, either restricted in bulk transcriptomic level or at certain cell types, which failed to capture cellular heterogeneity and intrinsic interplays among distinct cell types. To overcome these obstacles, we applied single-nucleus RNA-seq on midbrain, striatum and cerebellum, of α-syn-A53T mouse (a well-established PD model mouse) and matched control, generating the first single cell transcriptomic atlas for PD model mouse brain composed of 46,174 individual cells. Additionally, we comprehensively depicted the dysfunctions in PD pathology, covering the elevation of NF-κB activity, the alteration of ion channel components, the perturbation of protein homeostasis network and the dysregulation of glutamatergic signaling. Notably, we identified a variety of cell types closely associated with PD risk genes. Taken together, our study provides valuable resources to systematically dissect the molecular mechanism of PD pathogenesis at single cell resolution, which could hopefully facilitate the development of novel approaches regarding diagnosis and therapies against PD.
DOI: 10.26036/cnp0000529
title: 香港牡蛎基因组三代测序组装

description: 对香港牡蛎基因组进行测序，组装和注释。
DOI: 10.26036/cnp0000063
title: Whole genome sequencing of 175 Mongolians

description: The genetic variation in Northern Asian populations is currently under-sampled, to address this, we have generated a new genetic variation reference panel by whole-genome sequencing of 175 ethnic Mongolians, representing six tribes. The catalogued variation in the panel reveals strong population stratification among these tribes, which correlates with the diverse demographic histories in the region. Incorporating our results with the 1000 Genomes Project panel reveals shared derived alleles between Finns and Mongolians/Siberians, which suggests that significant gene flow between Northern Eurasian populations has occurred in the past. Furthermore, we highlight that North, East, and Southeast Asian populations are more aligned with each other than these groups are with South Asian and Oceanian populations.
DOI: 10.26036/cnp0000734
title: The Genome of Eggplant

description: Eggplant (Solanum melongena L.), exclusively native to the Old World, is one of the most important Solanaceae crops, which ranks third in total production and economic value in the genus Solanum. Here, we reported a high quality,chromosome-scale eggplant reference genome sequence of 1155.8 Mb with an N50 of 93.9 Mb, which is assembled by combining PacBio long reads and Hi-C sequencing data. Repetitivesequences occupied 70.1%oftheassembly size and 35,018 high-confidence protein-coding genes were annotated based on multiple evidence. Comparative analysis revealed 646 species-specific families as well as 364 positive selection genes in eggplant, conferring the distinguished traits in this plant. We performed genome-wide identification ofdisease resistance genes and discovered an expanded gene family of bacterial spot resistance in eggplant and pepper, compared to tomato and potato.The genes involved in chlorogenic acid synthesis were comprehensively characterized. A highly similar chromosomal distribution pattern of polyphenol oxidases was observed in the eggplant, tomato, and potato genomes. The eggplant reference genome sequence will not only promote the evolutionary studies in Solanaceae,but also facilitate theirbreeding and improvement.
DOI: 10.26036/cnp0000961
title: 关键进化节点鱼类的全基因组测序

description: 收集关键进化节点鱼类进行全基因组测序，提供高质量、高覆盖度的关键鱼类全基因序列。
DOI: 10.26036/cnp0000042
title: update dataset for "a reference human genome dataset of the BGISEQ-500 sequencer"

description: Since new sequence strategy was developed on BGISEQ-500, and two limits in previous data note “A reference human genome dataset of the BGISEQ-500 sequencer”, we updated datasets on BGISEQ-500 PE150 and NovaSeq6000 PE150.
DOI: 10.26036/cnp0000021
title: Metagenome of the female upper reproductive tract

description: BackgroundThe human uterus is traditionally believed to be sterile, while the vaginal microbiotaplays important roles in fending off pathogens. Emerging evidences demonstrate thepresence of bacteria beyond the vagina, but currently there is no support frommetagenomic data.ResultsHere we shotgun-sequence over 50 samples from the cervical canal and the peritonealfluid of Chinese women of reproductive age, who were operated for conditions notknown to involve infection. With 20GB sequences per sample and an average rate of&gt;99% human sequences, vaginal bacteria could be well covered, while a fullcharacterization of bacteria from the upper reproductive tract would require a greateramount of sequences and more samples. Direct annotation of sequencing readsidentified bacteria, archaea, fungi and viruses from the samples, confirming as well asextending results from 16S rRNA gene amplicon sequencing. To further examinetransitions between communities at neighboring sites, another 24 samples from thevagina, the cervical canal, the uterus and the peritoneal fluid were shotgun-sequenced.Samples from the same individual share a large portion of this microbiota.ConclusionsOur metagenomic analysis of the microbiota of the female upper reproductive tractprovides unprecedented data for this unchartered body site and establishes theframework for future studies aimed at understanding the composition and functionalcapacity of this community or its specific members.
DOI: 10.26036/cnp0000016
title: Genome sequencing and assembly of M. charantia Dali-11 and Momordica charantia subsp. Macroloba TR (bitter gourd)

description: M. charantia Dali-11 and Momordica charantia subsp. Macroloba TR were selected for denovo sequencing
DOI: 10.26036/cnp0000017
title: 191 samples of M. charantia / M. charantia var. muricata / Momordica charantia subsp. Macroloba Resequencing

description: 191 samples of M. charantia / M. charantia var. muricata / Momordica charantia subsp. Macroloba Resequencing clean Fq data
DOI: 10.26036/cnp0000050
title: The genomic subreads of wild Sugarcane (Saccharum spontaneum L.) genome

description: The Pacific Biosciences reads of wild Sugarcane (Saccharum spontaneum L.) genome
DOI: 10.26036/cnp0000018
title: Genomic sequencing of Plutella xylostella

description: The diamondback moth is a globally significant pest that currently costs agriculture an estimated US$4-5 billion annually, but for which the origin and invasion patterns are unknown. Here we resolve this challenge by identifying South America as this pest’s origin using genomic sequencing and analysis of 532 individual from 114 sites across 56 countries.
DOI: 10.26036/cnp0001048
title: The draft genome assembly of the critically endangered Chinese tertiary relict tree species species Nyssa yunnanensis

description: The draft genome assembly of the critically endangered Chinese tertiary relict tree species species Nyssa yunnanensis
DOI: 10.26036/cnp0000513
title: Two chromosome level genomes of the Fall armyworm, Spodoptera frugiperda, an alien invasive pest in south China

description: We collected two adult fall armyworms (one male and one female) from Yunnan Province, China. Two chromosome level genomes were finally assembled using stLFR technology with 45 Gb and 37 Gb high-quality raw reads sequenced by the MGI-2000 sequencer, for the male and female individual, respectively. The size of the assembly for the male and female individual was 542 Mbp and 534 Mbp, respectively. Hi-C technology was finally used to concatenate the scaffolds to the chromosome level. Besides, transcriptome data was also sequenced to support the genome annotation.
DOI: 10.26036/cnp0000903
title: mouse olfactory bulb scATAC

description: This project uses single-cell ATAC to study mouse olfactory bulb cells to reveal epigenetic characteristics specific to olfactory bulb cells.
DOI: 10.26036/cnp0000009
title: blueberry degradome

description: degradome cDNA libraries were constructed and sequenced for flowers, young fruits, and ripe fruits
DOI: 10.26036/cnp0000008
title: blueberry sRNA

description: sRNA libraries were constructed and sequenced for flowers, young fruits, and ripe fruits
DOI: 10.26036/cnp0000915
title: 二代测序技术在假体周围感染的准确性研究

description: 利用宏基因组二代测序技术对假体周围感染样本进行病原学诊断研究，促进临床的应用和转化，并形成一系列的科研成果
DOI: 10.26036/cnp0000920
title: 测序仪性能评价用国家参考品测序评估

description: 基于国家参考品进行性能评估，包括但不限于研究建库试剂盒和测序平台的兼容性。
DOI: 10.26036/cnp0000958
title: T. sinensis var. heiyouchun Genome

description: T. sinensis var. heiyouchun was cultivated in Fuyang city in Anhui Province of China. The tender leaves grown from apical buds were collected for DNA isolation
DOI: 10.26036/cnp0000502
title: pylogeny of Bambusoideae based on the chloroplast genome

description: sequecing transcriptome and chloroplast of 387 woody bamboos representing in 15 clades in Asia and a fully resolved phylogenetic tree derived from protein-coding genes and LSC regions.
DOI: 10.26036/cnp0000597
title: Chelmon rostratus genome sequence

description: Chelmon rostratus (Teleostei, Perciformes, Chaetodontidae) is a copperband butterflyfish, living in tropical areas. Just as other coral reef fish, it can be cultivated as an ornamental fish, thus providing genome information for this species might help understanding the genome evolution of Chaetodontidae (without previous genomes available) and adaptation/evolution of coral reef fish.As the first genome for Chaetodontidae family, the genome sequence of Chelmon rostratus increases our understanding of genome content of Chaetodontidae. The information of these data helpfully to improve the essential to the further understanding and exploration of marine ecological environment symbiosis with coral and the genomic innovations and molecular mechanisms contributing to its unique morphology and physiological features.
DOI: 10.26036/cnp0000137
title: 鱇浪白鱼基因组测序

description: 利用二代测序技术对鱇浪白鱼进行基因组测序，并进行组装，注释
DOI: 10.26036/cnp0000887
title: Averrhoa carambola genome project

description: The Whole-genome sequencing of Averrhoa carambola
DOI: 10.26036/cnp0001032
title: Transcriptome of Lasioderma serricorne

description: Transcriptome sequencing was performed for the larvae of Lasioderma serricorne to identify key genes involved in cuticle formation.
DOI: 10.26036/cnp0000971
title: Regulation of anthocyanin synthesis

description: Role of the Arabiodopsis transcription factor in the regulation of anthocyanin biosynthesis
DOI: 10.26036/cnp0000497
title: Assessment of fecal DNA extraction protocols for metagenomic study

description: Aiming at providing an alternative method for human fecal DNA extraction, this study compared 5 DNA extraction protocols (MagPure Stool DNA KF Kit (MP), Macherey-Nagel Nucleospin Soil kit (MN), Zymo Research Quick-DNATM Fecal/Soil Microbe kit (ZYMO), MOBIO DNeasy PowerSoil protocol (PS) and MetaHIT) with a standardized protocol Q using 1 microbial mock community (MMC) (contained 8 bacterial and 2 fungal strains) and fecal samples from 6 individuals via shotgun metagenomics sequencing. For each protocol, six technical replicates were generated on the MMC and each human fecal sample. In total, 233 qualified DNA samples (36 MMC extractions and 197 human fecal DNA extractions) were subjected to shotgun sequencing and further quantitative analyses.
DOI: 10.26036/cnp0000894
title: The genome of largemouth bass

description: Genome sequencing and assembly of large mouthbass (Micropterus salmoides) .
DOI: 10.26036/cnp0000487
title: H1（Penicillium variabile）

description: Penicillium variabile H1 was collected from mangrove forest in fujian province and has activity against colon cancer cell. We sequenced and assembled the genome of Penicillium variabile H1.
DOI: 10.26036/cnp0000959
title: Genome Project of Lytechinus variegatus

description: Lytechinus variegatus is a camarodont sea urchin found widely throughout the western Atlantic Ocean in a variety of shallow-water marine habitats. Here, we present a chromosomal-level genome assembly of L. variegatus generated from a combination of Pacific Biosciences long reads, 10X Genomics sequencing, and HiC chromatin interaction sequencing.
DOI: 10.26036/cnp0000091
title: 二代测序仪行业标准及变异数据库构建

description: 二代测序仪行业标准及变异数据库构建
DOI: 10.26036/cnp0000202
title: LPP_Hoolock tianxing

description: Geneme de novo sequencing of Hoolock tianxing
DOI: 10.26036/cnp0000213
title: Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity

description: Integrative analysis of multi-omics layers at single cell level is critical for accurate dissection of cell-to-cell variation within certain cell populations. Here we report scCAT-seq, a technique for simultaneously assaying chromatin accessibility and the transcriptome within the same single cell. We show that the combined single cell signatures enable accurate construction of regulatory relationships between cis-regulatory elements and the target genes at single-cell resolution, providing a new dimension of features that helps direct discovery of regulatory patterns specific to distinct cell identities. Moreover, we generated the first single cell integrated maps of chromatin accessibility and transcriptome in human pre-implantation embryos and demonstrated the robustness of scCAT-seq in the precise dissection of master transcription factors in cells of distinct states during embryo development. The ability to obtain these two layers of omics data will help provide more accurate definitions of “single cell state” and enable the deconvolution of regulatory heterogeneity from complex cell populations.
DOI: 10.26036/cnp0001033
title: Transcriptome of Ephestia elutella

description: Transcriptome sequencing of the larva of Ephestia elutella.
DOI: 10.26036/cnp0001197
title: sequencing data of spiny head croaker

description: Illumina short reads, PacBio reads, and Hi-C reads of spiny head croaker
DOI: 10.26036/cnp0001025
title: whole genome sequencing of Tetraodon palembangensis

description: The humpback puffer, Tetraodon palembangensis, is a kind of poisonous freshwater pufferfish mainly distributed in Southeast Asian. Despite interesting biological features, such as inactive nature, tetrodotoxin and body expansion mechanisms, molecular research on the humpback puffer is still rare because of the lack of high-quality genome. Here we performed genome assembly, gene annotation and comparative genomics analysis of an adult pufferfish.
DOI: 10.26036/cnp0000963
title: RNA-Seq of gonads of Oryzias curvinotus from sanya population

description: RNA-Seq of gonads of Oryzias curvinotus from sanya population
DOI: 10.26036/cnp0000999
title: Transcriptome profiling of HDF, HDMEC and HEK skin cells under high glucose stimulation by RNA sequencing

description: Diabetes mellitus (DM) is a chronic endocrine disease characterized by hyperglycemia and multiple severe complications. Early research found that the difficulty in healing of diabetic foot ulcers is associated with abnormal proliferation of fibroblasts and vascular endothelial cells, but the specific molecular mechanism is still unclear. In this article, transcriptomics studies were performed on specific cells in diabetic skin to analyze the molecular differences in diabetes from a single skin cell level. and treatment of diabetic foot ulcers.
DOI: 10.26036/cnp0000796
title: TGS-GapCloser datasets and assemblies

description: TGS-GapCloser is gap-closing software tool that uses error-prone long reads generated by third-generation-sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs to fill N-gap in the genome assembly.
DOI: 10.26036/cnp0000186
title: Paradisaea raggiana Genome sequenceing

description: We sequenced Paradisaea raggiana genome of birds-of-paradise to study the evolution of sex chromosomes.
DOI: 10.26036/cnp0000951
title: COVID-19-Project-1-the First Affiliated Hospital of Guangzhou Medical University

description: Eight complete genomes of HCoV-19 which was sequenced directly from clinical samples of COVID-19 patients in Guangzhou by ultra-deep metatranscriptomic sequencing.
DOI: 10.26036/cnp0001050
title: Paris polyphylla genome

description: Paris polyphylla genome and RNA-seq analysis
DOI: 10.26036/cnp0000973
title: Siniperca chuatsi genome

description: Siniperca chuatsi genome assembly raw data and assembly results
DOI: 10.26036/cnp0000751
title: 二代测序在脑炎病原诊断中的准确性研究

description: 研究目标：利用宏基因组测序技术对中枢神经系统感染进行病原学诊断研究，促进临床应用与转化，并形成一系列科研成果。
DOI: 10.26036/cnp0000907
title: gut microbial community of Acipenser dabryanus

description: We experimentally manipulated early life diets in the first 7 months after hatching by using natural diets and formula diets for two experimental groups of Yangtze sturgeon and then introduced some of the individuals from these two groups into the natural environment with labels. We monitored body length and weight and gut microbes, and then, by analyzing the two groups’ growth characteristics and gut microbes, we discussed the mechanisms of how diet training impacts postrelease fitness and survival.
DOI: 10.26036/cnp0001034
title: Narrow leaf lupin pan-genome

description: The lack of sufficient genetic variation in crop varieties due to a domestication bottleneck is an increasing concern for sustaining global food supplies. Countering this concern requires a clear understanding of the domestication process and dynamics of domestication bottlenecks. The long and complicated domestication process in major crops makes it difficult to identify components of the bottleneck. Narrow-leafed lupin (Lupinus angustifolius) has experienced rapid domestication and become the newest crop with key domestication traits being fixed from mutations in natural populations within 50 years. Here, we assemble the third-generation reference genome of narrow-leafed lupin cultivar Tanjil, comprising 20 pseudochromosomes with a total genome size of 772.1 Mb and contig N50 = 5.65 Mb. We identify the key mutation resulting in low seed alkaloid levels that initiated the domestication of narrow-leafed lupin. A comparative analysis of genomic diversity in cultivars and wild types identified an apparent domestication bottleneck, as predicted by the original model of the bottleneck effect on genetic variability in populations. Our findings provide the first direct genomic evidence for a domestication bottleneck and open up the possibility of knowledge-driven de novo domestication of wild plants as an avenue to broaden crop plant diversity to enhance food security and sustainable low-carbon emission agriculture.
DOI: 10.26036/cnp0000505
title: Bird 10,000 Genomes (B10K) Project - Family phase

description: The Bird 10,000 Genomes (B10K) Project is an initiative to generate representative draft genome sequences from all extant bird species. The B10K project will allow the completion of a genomic level tree of life of the entire living avian class, decode the link between genetic variation and phenotypic variation, uncover the correlation of genetic evolutionary and biogeographical and biodiversity patterns across a wide-range of species, evaluate the impact of various ecological factors and human influence on species evolution, and unveil the demographic history of an entire class of organisms. Given all these goals, the B10K project is carried out at hierarchical levels of avian classification. This Family Phase Project aims to achieve the above goals using recently generated reference genomes from 363 species representing most of the 236 avian families. This project will have significant scientific and public impact that will change our understanding of avian biology and evolution, which in turn will affect our understanding of other organisms and open doors to new areas of research.
DOI: 10.26036/cnp0000634
title: 中国长寿之乡肠道微生态平衡研究

description: 本课题是利用第二代高通量测序技术的优势，用深度测序来了解长寿人群和对照组人群的肠道宏基因组组成（包括基因层面和物种层面的组成）的差异，以及这二者间所具有的显著性差异。进而综合多组学的研究手段，在功能层面理解人肠道宏基因组是如何在人体的生命活动中发挥作用的。探讨肠道微生物菌群的变化和长寿之乡的健康长寿现象的潜在关系。
DOI: 10.26036/cnp0000981
title: Thalassaemia gene therapy

description: β-thalassemia is one of the most common genetic diseases in the world, caused by mutations in the human hemoglobin beta(HBB) gene. HBB −28 (A&gt;G) mutations is one of the five most common mutations in China patients with β-thalassemia. However, there are few studies on this mutated of thalassemia, due to the rarity sample and ethics. Genome editing technologies for disease modeling and developing cellular therapies has been extensively documented. Therefore, firstly we combined CRISPR/Cas9 and asymmetric single strand oligo DNA to mutant HBB gene in K562 cell lines and correct the HBB mutation with high efficiency and seamless. Then in order to study how this mutation affected the hemoglobin expression, we use RPMI 1640 medium without glutamine supplemented with 10 % (v/v) FBS and 1 mM sodium butyrate to erythroid differentiation. Finally we see the impact of the mutation at the transcriptome level by RNA-Seq which is the first time to study the HBB(28A&gt;G) differences between the isotype cell lines. The 28(A&gt;G) affects hemoglobin expression, opens the NOTCH pathway, and affects cell morphology and size and so on. Collectively, Our study provides an effective approach to mutation and correct HBB mutations without leaving any genetic footprint in the cells, and we also have the mutation cells can provide the diease model to study the disease without ethics. At the transcriptome level ,we show the difference between the mutation and the wild type which Provide data support for subsequent studies.
DOI: 10.26036/cnp0000715
title: Artocarpus altilis genome

description: 本项目对面包树(也叫面包果)进行了基因组测序，并组装
DOI: 10.26036/cnp0000905
title: Project of the leaf-cutting ants

description: The project is to study the genomes of three species of the leaf-cutting ant genus Acromyrmex that abolished sociality in favor of a socially parasitic life-history.
DOI: 10.26036/cnp0001064
title: Analysis of Soil Microorganisms in Huanghuaihai Region of China

description: The database of soil metagenomics in Huanghuaihai Region of China.
DOI: 10.26036/cnp0000161
title: AOCC chloroplast genome

description: Two chloroplast genome of AOCC species.
DOI: 10.26036/cnp0000750
title: 二代测序在脑膜炎病原诊断中的准确性研究

description: 研究目标：利用宏基因组测序技术对中枢神经系统感染进行病原学诊断研究，促进临床应用与转化，并形成一系列科研成果。