cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnp0001242
title: Assembly of the Baylisascaris schroedari genome

description: This project is mainly used for assembly and resequencing analysis of the genome of a Baylisascaris schroedari at the near chromosome level.
DOI: 10.26036/cnp0001584
title: The raw sequencing data of Buddleja lindleyana

description: The raw sequencing data of Buddleja lindleyana
DOI: 10.26036/cnp0000149
title: Camelus bactrianus

description: Camelus bactrianus and Camelus bactrianus ferus RAD sequencing
DOI: 10.26036/cnp0000214
title: A Swedish PID patient

description: 利用目标区域捕获测序，发现一例瑞典患者致病基因，及早发现致病基因有望改善疗效。
DOI: 10.26036/cnp0000221
title: Precise genome editing via one homology-arm mediated gene integration

description: Establishment of precise targeted gene knock-in technology
DOI: 10.26036/cnp0000906
title: DNBelab Series Single-Cell Sequencing data and Reference Database

description: 此项目包含液滴微流控的高通量单细胞转录组测序系列产品的分析数据库，以及两个的Demo（人和鼠混合的细胞系单细胞测序数据、鼠细胞系单细胞测序数据），分析方法及流程脚本下载详见https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_scRNA-analysis-software。
DOI: 10.26036/cnp0000251
title: Evolution and Adaptation of Mandrill Revealed by Genome Sequencing

description: Mandrillus sphinx Raw sequence reads
DOI: 10.26036/cnp0001046
title: eDNA sequences in Qinghai Lake basin

description: We proposed the concept of watershed biological information flow (WBIF) and defined it as the path, processes and control of biological information transport, exchange, interaction and feedback among different space and system along with watershed ecosystem processes. We chose the Qinghai Lake basin, which had relative simple watershed ecosystem and relative weak human disturbance, as a natural simplified model to study WBIF. We studied the WBIF in Qinghai Lake basin according to analyze the Operational Taxonomic Units (OTU) assemblages detected in riverine water eDNA samples, riparian soil eDNA samples and fish gut eDNA samples.
DOI: 10.26036/cnp0000748
title: Sequencing data for YYC codec demonstration

description: This is a supplementary data for the paper entitled 'Towards the practical and robust DNA-based data archiving by codec system named 'Yin-Yang''. This is the sequencing raw data of the synthesized oligo pool for storage of three digital file collections including Tao-Te-Ching, Shakespeare's Sonnet and a scientific image, the sequencing result was obtained from BGI-seq.
DOI: 10.26036/cnp0001066
title: Co-infections with COVID-19

description: The global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused sharply increased cases and deaths worldwide. Between January 27 and February 26, 2020, we collected 68 clinical specimens (sputum, nasal and throat swab, anal swab and feces) from 24 patients hospitalized with SARS-CoV-2 infection, in Guangdong, China. We extracted total RNA, applied ultra-deep metatranscriptomic sequencing in combination with laboratory technologies, and uncovered co-infection rates, the prevalence and abundance of viruses, bacteria and fungi in these SARS-CoV-2 patients. Compared to mild cases, severe cases with ICU admission had much higher co-detection rates of respiratory viruses (30.8% vs 0%) and fungi (15.4% vs 0%), and greater expression levels of clinically relevant bacterial pathogens including Burkholderia cepacia complex (BCC), Staphylococcus epidermidis and Mycoplasma spp. More importantly, we demonstrated a time-dependent secondary and systemic infection of B. cenocepacia with expressions of multiple virulence genes in one ventilated patient, which might be the primary cause of his death after 1-month ICU admission. Our findings characterized a comprehensive spectrum of co-infections with SARS-CoV-2 and multiple respiratory pathogens that were distinct between hospitalized patients with different disease severity. Detection and tracking of BCC-associated secondary infections are recommended to inform the pre-emptive treatment regimen and prevent fatal outcomes of hospitalized patients during the current SARS-CoV-2 pandemic.
DOI: 10.26036/cnp0000835
title: Detecting off-target mutations in genome-editing by nuclear transfer and sequencing

description: detecting the off-target mutations in genome-editing in any clonal cells
DOI: 10.26036/cnp0000908
title: Whole genome sequencing of Streptococcus suis

description: To study the virulence genes and genetic evolution of two streptococcus suis strains
DOI: 10.26036/cnp0000311
title: colorectal tumor transcriptome

description: The RNA-seq based data were derived from 5 AOM/DSS induced CRC tumors and paired normal adjacent tissues from mice. The sequencing was carried out with Illumina HiSeq 4000, in paired-ends mode (100 bp read length).
DOI: 10.26036/cnp0001018
title: Transcripts of red claw crayfish (Cherax quadricarinatus) by single-molecule long-read sequencing

description: Analysis of transcripts and splice isoforms in red claw crayfish (Cherax quadricarinatus) using single-molecule long-read sequencing
DOI: 10.26036/cnp0001002
title: flax RNA-seq

description: Transcriptome analysis of flax related to stem fiber development
DOI: 10.26036/cnp0000884
title: The genome assembly and annotation of Magnolia biondii

description: 本项目对望春玉兰进行了基因组测序及组装
DOI: 10.26036/cnp0001042
title: Whole genome sequencing of Panax notoginseng

description: The genetic architecture of disease resistance and economic traits of Panax notoginseng
DOI: 10.26036/cnp0001047
title: Pathogenic Detection by Metagenomic Next-Generation Sequencing in Osteoarticular Infections

description: The project is to evaluate metagenomic next-generation sequencing (mNGS) as a diagnostic tool in detecting pathogens from osteoarticular infection (OAI) samples.
DOI: 10.26036/cnp0000868
title: Candidate cell-free Echinococcus spp. DNA reads from negative individuals

description: Candidate cell-free Echinococcus spp. DNA reads from negative individuals after human reads removing
DOI: 10.26036/cnp0001082
title: A high-quality genome of taro (Colocasia esculenta (L.) Schott)

description: Taro (Colocasia esculenta (L.), Schott), from the Araceae family, is one of the oldest crops with important edible, medicinal, nutritional and economic value. A high‐quality chromosomal-level genome of C. esculenta was assembled using Illumina, PacBio and Nanopore sequencing data. The genome database obtained for the first time using long-read whole-genome sequencing will provide valuable resources for further genetic, ecological and evolutionary analysis of taro or other species in the Araceae.
DOI: 10.26036/cnp0000051
title: The PacBio transcriptome sequencing of of wild Sugarcane (Saccharum spontaneum L.)

description: The PacBio transcriptome sequencing of of wild Sugarcane (Saccharum spontaneum L.) Results of the study provided a high-quality full-length transcriptome dataset for future studies of wild Sugarcane (Saccharum spontaneum L.)
DOI: 10.26036/cnp0000354
title: Medicago truncatula cultivar:R108 Transcriptome or Gene expression

description: The different expression between wild-type R108 and cra2 mutant inoculated with rhizobia Sm1021 for 5 day.
DOI: 10.26036/cnp0000559
title: NRT1.1B contributes to the host-dependent variation and functional divergence of the root microbiome between rice subspecies

description: The root microbiome extends the functional repertoire of the plant genome and is essential for plant growth and health in natural environments. Variation and functional divergence in the root microbiome among a population of plants and the corresponding host genetic basis remain to be ascertained. We find that two rice subspecies, indica and japonica, recruit distinct root microbiomes with robust biomarker taxa under field conditions. Many indica-enriched bacteria are related to the nitrogen cycle. Notably, NRT1.1B, a nitrate transporter and sensor, regulates a substantial proportion of indica-specific bacterial taxa. Metagenomic sequencing reveals that the ammonification pathway is dramatically impaired in the root microbiome of the nrt1.1b mutant. We establish comprehensive root bacterial culture collections representing more than 70 percent of bacterial species that are reproducibly detectable by culture-independent sequencing. With the synthetic community approach, we found that indica-enriched bacteria have stronger ability to promote rice growth under the organic nitrogen condition than bacteria enriched in japonica. Our results provide insights into the integration of the root microbiome, soil nutrient cycles, host genetic regulation, and plant traits, which could thus facilitate microbiome-based improvements in sustainable agriculture.
DOI: 10.26036/cnp0000803
title: Cell competition between human and mouse primed PSCs

description: Cell competition entails an evolutionarily conserved fitness-sensing process during which fitter cells eliminate their neighboring less-fit but otherwise viable cells. Cell competition has been proposed as a surveillance mechanism to ensure normal development and maintain tissue homeostasis, and also been suggested to act as a barrier to interspecies chimerism. To date, however, cell competition has not been examined in an interspecies context during early development due to lack of in vitro model. Here, we develop an interspecies pluripotent stem cell (PSC) co-culture strategy and uncover a previously unknown mode of cell competition. Interspecies PSC competition occurs during primed but not naive pluripotency, and between evolutionarily distant species. We identified genes related to P53 and NF-κB signaling pathways, among others, were upregulated in loser cells and genetic inactivation of either TP53 or RELA, a core component of canonical NF-κB pathway, could overcome interspecies PSC competition. We further showed that MYD88 innate immune signal transduction adaptor was also involved in promoting loser PSC elimination. Suppressing interspecies PSC competition via genetic perturbation of MYD88, P65, or TP53 improved engraftment of human cells in early post-implantation mouse embryos. Our study discovers a new paradigm of cell competition and paves the way for studying evolutionarily conserved cell competition mechanisms during early mammalian development. Strategies developed here to overcome interspecies PSC competition may facilitate the xeno-generation of human tissues in animals.
DOI: 10.26036/cnp0001337
title: Complete Chloroplast Genome of eleven Ficus species

description: Complete Chloroplast Genome of eleven Ficus species
DOI: 10.26036/cnp0000810
title: Transcriptome of Cinnamomum burmanni

description: Transcriptome of Cinnamomum burmanni
DOI: 10.26036/cnp0000411
title: metagenomic sequencing of Indian ocean surface water

description: Characterization of microbial composition and functional genes in Indian Ocean
DOI: 10.26036/cnp0000770
title: A direct link between Prss53, hair curvature, and skeletal dysplasia

description: Prss53基因的功能研究并不是很清楚，利用Crispr/Cas9技术在模式动物兔子上进行Prss53基因的完全缺失。卷毛和骨骼异常被发现。并用过RNA-SEQ测序发现，其钙离子代谢可能被影响。并利用流式技术对Flu-3处理后的细胞验证。
DOI: 10.26036/cnp0000737
title: The Reproductive Development Regulation in Pine

description: 油松基因表达数据
DOI: 10.26036/cnp0000946
title: 甜樱桃

description: 甜樱桃重测序
DOI: 10.26036/cnp0001019
title: Transcripts in red claw crayfish (Cherax quadricarinatus) using Illumina sequencing

description: Transcripts in gills of red claw crayfish (Cherax quadricarinatus) using Illumina sequencing
DOI: 10.26036/cnp0000997
title: Intra-host Variation and Evolutionary Dynamics of SARS-CoV-2 Population in Patients with COVID-19

description: Ultra-deep sequencing reveals intra-host variation of SARS-CoV-2 in patients with COVID-19.
DOI: 10.26036/cnp0000924
title: Prasinoderma coloniale

description: The genome of Prasinoderma coloniale provides insights into the dawn of green plant evolution
DOI: 10.26036/cnp0000818
title: The genome sequencing of Limnodynastes dumerilii

description: 1. Genomic DNA was extracted from the whole body of an adult animal Limnodynastes dumerilii . 2. Four libraries with short-insert sizes (170 bp × 1,250 bp × 1, 500 bp × 1, and 800 bp × 1) were constructed according to the standard protocol provided by Illumina (San Diego, CA, USA). 3.Ten mate-paired libraries with long-insert sizes (2 kb × 3, 5 kb × 3, 10 kb × 2, 20 kb × 2) were constructed according to the standard protocol provided by Illumina (San Diego, CA, USA). 4. Paired-end sequencing was performed for the fourteen libraries on the HiSeq 2000 platform according to the manufacturer’s instructions.
DOI: 10.26036/cnp0000110
title: The genome sequencing of Elysia chlorotica

description: 1. Genomic DNA was extracted from the whole body of an adult animal. Six libraries with short-insert sizes (170 bp × 2, 500 bp × 2, and 800 bp × 2) were constructed according to the standard protocol provided by Illumina (San Diego, CA, USA). Paired-end sequencing was performed for the six libraries on the HiSeq 2000 platform according to the manufacturer’s instructions. 2. Genomic DNA was extracted from a pool of ~1000 larvae (whole organisms). Five mate-paired libraries with long-insert sizes (2.5 kb × 2, 5 kb × 2, 10 kb × 1) were constructed according to the standard protocol provided by Illumina (San Diego, CA, USA). Paired-end sequencing was performed for the five libraries on the HiSeq 2000 platform according to the manufacturer’s instructions. 3. Genomic DNA was extracted from whole organisms of multiple adult Elysia chlorotica. Sequencing was performed on the PacBio RS platform.
DOI: 10.26036/cnp0000260
title: The whole transcriptome of Davidia involucrata

description: The whole transcriptome datasets of Davidia involucrata, including the raw data and the annotations of small RNA and mRNA from mutiple tissues.Yang H, Zhou C, Li G, et al. Reference gene set and small RNA set construction with multiple tissues from Davidia involucrata Baill. [J].
DOI: 10.26036/cnp0000953
title: 薛氏海龙RADseq揭示其谱系地理格局

description: 本研究涉及薛氏海龙三个群体（黄海YS, 东海ECS, 南海SCS）的RADseq测序，本数据为RADseq测序后经过质控的Clear data
DOI: 10.26036/cnp0001004
title: Intra-host Variation and Evolutionary Dynamics of SARS-CoV-2 Population in Patients with COVID-19 (assembly data)

description: Ultra-deep sequencing reveals intra-host variation of SARS-CoV-2 in patients with COVID-19.
DOI: 10.26036/cnp0001357
title: HiSeq data of Matuta victor

description: Tissue samples of Matuta victorfrom six individuals were collected from GuangXi province, raw data were sequenced (2×150bp paired-end) using HiSeq platform at BGI Company.
DOI: 10.26036/cnp0001020
title: Whole genome sequencing of the fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), an alien invasive pest in China

description: The fall armyworm, Spodoptera frugiperda (J.E. Smith) is a severely destructive pest native to the Americas, but now becomes an alien invasive pest in China. It is urgent to understanding its genetic background to help make effective management strategies. In this study, the resequencing analysis of 8 populations in 6 locations is performed, which demonstrated the Chinese fall armyworm was most likely invaded from Africa.
DOI: 10.26036/cnp0000847
title: Draft genome of water moss Fontinalis antipyretica

description: Fontinalis antipyretica is a species of submerged aquatic moss belonging to the subclass Bryidae. Here, we generated a draft genome of Fontinalis antipyretica using 10X technology. Our genomic resources are thus vital towards addressing the age-old question of the evolution of mosses and ultimately the land plants.
DOI: 10.26036/cnp0000732
title: Genome sequencing of a giant panda

description: We sequenced a giant panda with DIPSEQ T1 sequencing platform and the age of this individual is about 100 years old.
DOI: 10.26036/cnp0000723
title: DNB-Based On-Chip Motif Finding (DocMF): a High-Throughput Method to Profile Different Types of Protein-DNA Interactions

description: DNA-protein interactions play pivotal roles in many cellular activities, such as replication, development, and DNA repair. Here we report a DNB-based on-chip Motif Finding (DocMF) system that utilizes next-generation-sequencing chips to profile protein binding or cleaving activity toward several hundred millions or billions of DNA sequences. Using DocMF, we successfully identified a variety of endonuclease recognition sites and the protospacer-adjacent motif (PAM) sequences of different CRISPR effector proteins. Compared with the widely used PAM depletion assay, our DocMF platform can simultaneously screen both 5’ and 3’ sequences adjacent to the protospacer to identify PAMs with high coverage using the same DNB library pool. For the well-studied SpCas9, our DocMF platform not only identified its common PAMs, 5’-NGG-3’, but also revealed a small proportion (~5%) of noncanonical 5’-NAG-3’ PAMs. We also used the DocMF to assay two uncharacterized Cas endonucleases, VeCas9 and BvCpf1. VeCas9 PAMs were not detected by the conventional PAM depletion method. However, DocMF revealed that VeCas9 requires the PAM sequences 5’-NNNRR-3’, whereas BvCpf1 uses the T-rich PAMs 5’-YYN-3’ for target DNA recognition. Moreover, after slightly changing the experimental protocol and analysis threshold, we observed that dCas9, a DNA binding protein lacking endonuclease activity, preferably binds to the previously reported PAMs 5’-NGG-3’. In summary, our studies demonstrate that DocMF is the first tool with the capacity to exhaustively assay both the binding and the cutting site preferences of different DNA-binding proteins.
DOI: 10.26036/cnp0000886
title: The complete plastid chloroplast genome of a drought-tolerant moss, Anomodon attenuatus (Hedw.) Hüb.

description: Anomodon attenuatus (Hedw.) Hüb. is a widespread moss species distributed over Northern Hemisphere, ranging from North America to Europe and central Asia. Here, we assembled the complete plastid genome of A.attenuatus using the NGS technology.
DOI: 10.26036/cnp0000811
title: Ivermectin resistance

description: Ivermectin is a broad spectrum drug to control the helminthic parasites in human and animals. Resistance against ivermectin is now emerging in parasites. This project was aimed to discover the ivermectin resistant genes in parasitic nematode Haemonchus contortus by whole genome re-sequencing .
DOI: 10.26036/cnp0000095
title: Dissecting the spatial heterogeneity of single circulating tumor cells in hepatocellular carcinoma

description: The dismal outcome of hepatocellular carcinoma (HCC) is closely associated with intra- and extrahepatic metastases, which has been proposed to be initiated by circulating tumor cells (CTCs). However, the plasticity of gene expression and immune evasion mechanisms of CTCs during systemic circulation are not well defined. Here, we determined intra- and inter-vascular transcriptional heterogeneity within the circulatory system using single-cell RNA-sequencing of 113 CTCs isolated from four key vascular sites along their dissemination route in ten HCC patients.
DOI: 10.26036/cnp0001008
title: Cellulomonas

description: Separated from livestock or the surrounding environment, strain 40-2 contains a variety of polysaccharide hydrolyzing enzymes and proteases, which have a good hydrolysis effect on cellulose, dextran, xylan, pectin, chitin, casein, etc. It is used as flocculant producing bacterium to produce microbial flocculant. It has good treatment effect on sewage and manure wastewater.This work was supported by financial assistance from project Research, Jilin University Animal Medicine of College and Panjin Center for inspection and testing/Panjin CDC.for the collaborative study conducted together .The research was funded by the National Science and Technology Major Project of China ,reference 2018YFD0500504. This research was also supported by a grant from Panjin CDC allocated to Shasha ZHANG.
DOI: 10.26036/cnp0000925
title: Transcriptome and genome sequencing of the cryptophyte Teleaulax amphioxeia and the ciliate Mesodinium rubrum

description: In this project, we performed transcriptome-sequencing for the cultures of free-swimming T. amphioxeia, M. rubrum well-fed with T. amphioxeia, and starved M. rubrum. Biological triplicates were collected for each condition. We also performed genome-sequencing for DNA extracted from free-swimming T. amphioxeia and starved M. rubrum, respectively.
DOI: 10.26036/cnp0000642
title: Lophius litulon genome

description: Provide a high-quality chromosomal-level assebmly of the yellow goosefish (Lophius litulon).
DOI: 10.26036/cnp0000647
title: 烟草274份RIL家系群体

description: 利用274个RIL家系群体构建烟草高密度遗传图谱。
DOI: 10.26036/cnp0000848
title: light harvesting protein

description: Light harvesting genes and proteins from green tide algal Ulva prolifera
DOI: 10.26036/cnp0000990
title: Whole-genome sequencing of Klebsiella pneumonia isolates from burn-wound infection

description: Klebsiella pneumoniae genomes isolated from two hospitals in 2014-2018.The main purpose of this project is to study the resistance and virulence factors of Klebsiella pneumoniae.
DOI: 10.26036/cnp0000637
title: RPAD treated circular RNA sequencing

description: Using High-purity circular RNA isolation method (RPAD) to identify sperm circular RNAs.
DOI: 10.26036/cnp0000640
title: 植物益生菌挥发性物质可通过影响lncRNA调控关键功能基因表达

description: 测量对照和植物益生菌解淀粉芽孢杆菌GB03处理的拟南芥根部全转录组。
DOI: 10.26036/cnp0001014
title: The Cerusus serrulata genome

description: Cerasus serrulata is germplasm resource of flowering cherry for ornamental purpose. In this work, we present a de novo chromosome-scale genome assembly of C. serrulata using Nanopore and Hi-C sequencing technologies. The assembled C. serrulata genome is 265.40 Mb by 304 contigs and 67 scaffolds, with a contig N50 of 1.56 Mb and a scaffold N50 of 31.12 Mb, respectively. It contains 29,094 coding genes, 27,611 genes (94.90%) are annotated in at least one functional database.
DOI: 10.26036/cnp0000516
title: Microbial taxonomy and functionality in mangrove ecosystem and its potential capability to produce bioactive compounds

description: The research about microbial taxonomy and functionality in mangrove ecosystem and its potential capability to produce bioactive compounds
DOI: 10.26036/cnp0000705
title: Draft Genome of Hariotina reticulata (Sphaeropleales, Chlorophyta) provides the insight into the evolution of Scenedesmaceae

description: Hariotina reticulata P. A. Dangeard 1889 (Scenedesmaceae, Sphaeropleales) is a common member of the summer phytoplankton of meso- to highly eutrophic water bodies with a worldwide distribution. Here, we report the draft whole-genome shotgun sequencing of H. reticulata strain SAG 8.81. The final assembly comprises 107,596,510 bp with over 15,219 scaffolds (&gt;100 bp).
DOI: 10.26036/cnp0000842
title: Exploiting evolutionary trade-offs to combat antibiotic resistance

description: Antibiotic resistance frequently evolves through fitness trade-offs in which the genetic alterations that confer resistance to a drug can also cause growth defects in resistant cells. Here, we use tavaborole-resistant E. coli to demonstrate that antibiotic-resistant cells can be efficiently inhibited by increasing the fitness costs associated with drug-resistance evolution. This finding may lead to a new approach for combating therapeutic resistance, prolonging the effectiveness of drugs and enabling the use of drugs that are no longer effective due to the rapid evolution of resistance.