cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnp0000813
title: Characterizing coverage and accuracy of clinical WGS as a diagnostic test for genetic disorders

description: Purpose: To evaluate the coverage and accuracy of clinical whole genome sequencing as a diagnostic test for monogenic disorders. Methods: All the samples underwent WGS using MGISEQ-2000. The performance of NA12878, NA24631, NA24694 and NA24695 and YH cell line were measured for sensitivity, PPV (analytical positive predictive value), coverage of depth and breadth of coverage. The false-negative rates (FNRs) were estimated using the segregation pattern in the Chinese trios. Results: With a mean depth of 40X, the sensitivity of homozygous and heterozygous SNPs of NA12878 was &gt;99.25% and &gt;99.50% respectively, and PPVs were 99.97% and 98.96%. Homozygous and heterozygous indels showed lower sensitivity and PPV. However, even with a mean depth of ~150X, the sensitivity and PPV is still not 100%. We observed a substantial variation in the detection rate of CNVs across different tools. With a mean depth of ~40X, NA12878-2 showed the highest CNV detection rate of more than 89.66% in our new CNV call set using BreakDancer. In general, the breadth of coverage for disease-associated genes and CNV syndromes increased with mean depth. For the American College of Medical Genetics and Genomics 59 genes, 100% of genes covered at 10X required a mean depth of more than 90X for NA12878. Among the Chinese trios, FNRs in the offspring were 0.52% and 3.64% for SNP and indel detection at well-covered variants. Conclusion: The current standard of a mean depth of 40X may be sufficient for SNV/indel detection and the identification of most CNVs. Clinical scientists should know the range of sensitivity and PPV for different classes of variants for a particular WGS pipeline, which would be useful when interpreting and delivering clinical reports.
DOI: 10.26036/cnp0000780
title: Luffa genome

description: Luffa genome research using Long-read sequencing technology.
DOI: 10.26036/cnp0000944
title: COVID-19-Project-Guangzhou Eighth People's Hospital

description: Genome assembly of SARS-CoV-2.
DOI: 10.26036/cnp0000740
title: An atlas of transcriptomic and chromatin accessibility profiles in Monomorium pharaonis brains

description: The emergence of eusociality is one of the major events in evolution. Although several previous studies have investigated the mechanism underlying caste differentiation and social behavior of eusocial insects including ants and honeybees, the molecular circuits governing the sociality of these insects remain obscure. In this study, we profiled the brain transcriptome and chromatin accessibility of all categories of adult castes: queens, males, gynes and workers in Monomorium pharaonis which is a typical caste-dependent eusocial insect. We created a comprehensive dataset in which 16 RNA-seq and 16 ATAC-seq samples from 4 biological replicates being processed and sequenced. We also demonstrated strong reproducibility of the datasets and identified specific genes and open regions in genome that may be associated with caste differentiation. Overall, our data will be a valuable resource for further study of the mechanisms underlying eusocial insects behaviour, particularly the role of brain in the control of eusociality.
DOI: 10.26036/cnp0000980
title: Novel Target Capture DNA Library Preparation Method Using CircLigase-Mediated Hook Ligation

description: Target capture DNA library preparation methods primarily use the biotin-streptavidin interaction to enrich target DNA, and these methods require complex operations and a time-consuming workflow, such as a series of wash steps at regulated temperatures. Here we present a new method that we call hook ligation for target DNA library preparation using circLigase to capture target DNA. We validated this concept by library preparation, sequencing, and acquiring the target DNA fragment information through bioinformatic analysis. We also provide an efficient reference point for single-strand DNA ligation to a hook sequence using circLigase, and we show that the efficiency can be influenced by the length and the position of the complementary area on the target DNA.
DOI: 10.26036/cnp0000837
title: Sputum microbiome sequencing for COPD

description: Full-length 16S rRNA gene sequencing, and metagenomic sequencing data for sputum samples in COPD and healthy controls
DOI: 10.26036/cnp0001097
title: chloroplast genome of Saccharina latissima

description: Saccharina latissima, a species that distribute in Europe and North America, is of utmost ecological and increasingly economic in coastal areas. to our knowledge, the chloroplast genome has never been reported for S. latissima. In fact, so far only one cpDNA was uncovered in Saccharina genus. We here report the assembly of the complete cpDNA of S. latissima to supplement data resources for researches of evolutionary and genetic conservation.
DOI: 10.26036/cnp0001196
title: Comaprison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC

description: we compared hybrid assemblies for 6 bacterial isolates, including the reference strains Escherichia coli using next generation sequencing (NGS) short reads sequencing, single tube long fragment reads (stLFR) sequencing and Oxford Nanopore Technologies (ONT) sequencing platforms. We obtained the complete genomes assembled by the hybrid assembler Unicycler using ONT and NGS reads, and the other complete genomes de novo assembled by using stLFR and ONT reads. Meanwhile, the long-read-only assembly genomes by Canu with NGS reads base correction, the chromosome-level assembly genomes by Athena with stLFR reads and the draft assembly genomes by SPAdes with NGS data were obtained for the 3 different sequencing strategies comparison.
DOI: 10.26036/cnp0000863
title: The Genome of melon

description: The genome sequencing of HS melon
DOI: 10.26036/cnp0001120
title: genome sequencing of bacterial strain YD01

description: This project aimed to sequenc the genome of a bacterial strain with high xylanase activiey, YD01
DOI: 10.26036/cnp0000736
title: YCSR

description: 阳春砂仁叶绿体双向测序数据
DOI: 10.26036/cnp0000696
title: Cell-free Echinococcus spp. DNA

description: Cell-free Echinococcus spp. DNA sequencing data from echinococcosis patients' plasma
DOI: 10.26036/cnp0000857
title: Control data of cell-free Echinococcus spp. DNA

description: Control data of cell-free Echinococcus spp. DNA, which include cell lines data and simulated data
DOI: 10.26036/cnp0000955
title: Multiple approaches for massively parallel sequencing of HCoV-19 samples

description: COVID-19 has caused a major epidemic worldwide, however, much is yet to be known about the epidemiology and evolution of the virus. One reason is that the challenges underneath sequencing HCoV-19 directly from clinical samples have not been completely tackled. Here we expound the application of amplicon and hybrid capture (capture)-based sequencing, as well as ultra-high-throughput metatranscriptomic (meta) sequencing in retrieving complete genomes, inter-individual and intra-individual variations of HCoV-19.
DOI: 10.26036/cnp0001193
title: T7测序试剂盒开发

description: 在DNBSEQ-T7(MGISEQ-T7)测序仪上，对NA12878进行PE150测序，用于研究T7测序试剂盒是否适用于WGS的测序。
DOI: 10.26036/cnp0001186
title: Macrobrachium nipponense genome

description: Genome-Wide Sequencing for Macrobrachium nipponense.
DOI: 10.26036/cnp0001039
title: The study of cell line infected with HSV1

description: The study is about human cell line infected with HSV1 virus using RNA-seq.
DOI: 10.26036/cnp0001012
title: The genome of the African pike

description: we generated 141X stLFR co-barcode reads and 13X Oxford Nanopore MinION reads and 77X Hi-C reads and obtained a 863Mb African pike genome
DOI: 10.26036/cnp0001099
title: Sequencing of samples from COVID-19 patients re-positive for SARS-CoV-2

description: Serial samples from 18 re-positive individuals from Guangzhou Eighth People's Hospital, Guangdong, China were sequenced to detect SARS-CoV-2 genomes and subgenomic mRNAs. The 10^-4 and 10^-5 dilutions of a cultured SARS-CoV-2 strain were included as the positive control. Forty-five non-re-positive samples were also sequenced to reveal the genetic diversity of SAR-CoV-2 detected in the hospital. Our analysis found that the re-positive viruses, which were more often detected in the anal swabs, may evolve from the previous infection rather than from a novel second infection, and that the virus might be potentially infectious.
DOI: 10.26036/cnp0000619
title: Mice Metagenomes for gene catalog construction

description: Metagenomes of 88 mice stool samples were sequenced and assembled. Those metagenomes were used to expand the previous gut gene catalog of mice published in 2015 which no longer meet the need of recent metagenomic analysis.
DOI: 10.26036/cnp0000817
title: Genome Project of Verasper variegatus

description: This Project is the first genome assembly and annotation of Verasper variegatus. As a Pleuronectidae fish, Verasper variegatus was the first to captured the chromosome level genome. The chromosomal genome assembly constructed in this work will not only be valuable for conservation and aquaculture studies of the Verasper variegatus but will also be of general interest in the phylogenetic and taxonomic studies of Pleuronectiformes.
DOI: 10.26036/cnp0000455
title: Duke-Bgi Environmental Isolates

description: The library of environmental isolates was collected across the Duke University campus as part of an undergraduate program – the Resistome Project (Bass connections project), and analysis for temporal encoding of bacterial identity and traits in growth dynamics.
DOI: 10.26036/cnp0001102
title: Distinct immune response landscapes of COVID-19 and influenza patients revealed by single-cell sequencing

description: The single-cell transcriptional landscape of longitudinally collected PBMCs in both COVID-19 and influenza A virus (IAV)-infected patients
DOI: 10.26036/cnp0001074
title: 补充益生菌产品内测项目

description: 从内蒙古发酵酸奶中分离到两株片球菌，经过菌株鉴定，分别命名为乳酸片球菌JQII-5和戊糖片球菌JQI-7
DOI: 10.26036/cnp0001104
title: Study on the response of Pepper Root to bacterial Wilt

description: Purpose: To determine genes differentially expressed under pepper plants challenged by RSI Methods:transcriptome was comparatively assayed in roots of CK and RSI plants challenged with RSHT, as R. solanacearum invades pepper plants exclusively through the roots. The seedlings with their roots mechanically damaged were dipped to the same solution of R. solanacearum cells (OD600 = 0.6).
DOI: 10.26036/cnp0001133
title: Targeting myeloid-derived suppressor cells is a novel strategy for anti-psoriasis therapy

description: Psoriasis is a common immune-mediated, chronic inflammatory genetic-related disease that affects patients’ quality of life. Myeloid-derived suppressor cells (MDSCs) are a heterogeneous population of progenitor and immature myeloid cells which are expanded in psoriatic skin lesions and peripheral blood. However, the role of MDSCs in the pathogenesis of psoriasis remains unclear. Here, we confirmed that the accumulation of human MDSCs is remarkably increased in skin lesions of psoriasis patients by flow cytometry. Depleting MDSCs by Gemcitabine significantly suppresses IMQ-induced psoriatic inflammation and epidermal thickening as well as Th17 and Treg cells accumulation. Moreover, through the RNA-Seq technique, we validated some differentially expressed genes on CD4+ T cells of IMQ-induced-MDSCs-depleted mice such as IL-21 and Timd2, which are involved in Th17-cell differentiation or T-cell activation. Interestingly, neutralizing IL-21R by antibody reduces IMQ-induced epidermal thickening through down-regulating the infiltration of MDSCs and Th17 cells. Our data suggest that targeting myeloid-derived suppressor cells is a novel strategy for anti-psoriasis therapy. IL-21 may be a potential therapeutic target in psoriasis.
DOI: 10.26036/cnp0000888
title: gilts_faeces_16S rRNA_no_barcode_raw_data

description: Changes of the Gut Microbiota Along with the Stages of a Heat Cycle and Identification of Gut Bacterial Taxa Related to Failure to Observe Oestrus in Gilts
DOI: 10.26036/cnp0001132
title: The Transcriptome of Somatic Hybrids (Potato + Eggplant)

description: In order to identify differentially expressed genes in bacterial wilt resistant and susceptible somatic hybrids (potato + eggplant), we preformed a transcriptomic analysis. Resistant and susceptible pool inoculated with Ralstonia solanacearum and sterile water (control) were sampled and subjected to RNA-seq analysis.
DOI: 10.26036/cnp0001124
title: Amphicarpaea edgeworthii Benth Genome sequencing and assembly

description: Genome sequencing and de novo assembly of Amphicarpaea edgeworthii Benth
DOI: 10.26036/cnp0001177
title: Brain remodeling during queen maturation by a gene-regulation network that was co-opted by ants with reproductive workers

description: Caste differentiation in ants is decided early in development to produce gynes as future colony germ-lines and workers as present colony soma. However, gynes need to be inseminated to become functional queens, a transition triggered by stored sperm that initiates reproductive role differentiation relative to gynes that remain unmated. Here we analyze the anatomy and transcriptomes of brains during this differentiation process within the reproductive caste of Monomorium pharaonis. Insemination terminated brain growth whereas unmated control gynes continued to increase their brain volume. Transcriptomes revealed that a specific gene regulatory network (GRN) mediates both brain anatomy changes and concomitant behavioral modifications. This reproductive role differentiation GRN hardly overlapped with the gyne-worker caste differentiation GRN, but it appears to have been coopted by distantly related ants where workers became germ-line individuals after the queen caste was secondarily lost, entirely or partially. The genes corazonin and neuroparsin-A in the anterior neurosecretory cells were overexpressed in individuals with less or non-reproductive roles across all four ant species investigated.
DOI: 10.26036/cnp0000830
title: 安徽霍山石斛产业化开发协同创新项目

description: 围绕霍山石斛产业开发与品质提升进行研究。研究不同栽培模式、加工方式对霍山石斛品质影响，挖掘霍山石斛品质形成关键基因，解析霍山石斛基因组学，转录组学为其品质形成及其评价提供科学依据，同时为霍山石斛道地性本质属性奠定基础，为霍山石斛生态种植，产品加工及新产品研发提供指导。
DOI: 10.26036/cnp0000567
title: The 14 mangrove plants chloroplast genomes

description: chloroplast genomes of 14 mangrove species were assembled and compared.
DOI: 10.26036/cnp0001199
title: HAST assemblies

description: Haplotype-resolved assemblies by HAST
DOI: 10.26036/cnp0001154
title: Effect of jasmonic acid on gene transcription of early inflorescence buds of Jatropha

description: Jasmonic acid treatment affects gene transcription of JA synthesis and signaling pathway，and even floral organ determination in Jatropha, but not affects phenotype of flower
DOI: 10.26036/cnp0001170
title: s288c_wss1

description: Suppressor mutations were identified by NGS. Genome re-sequencing library was prepared based on the Tn5 transposase mediated tagmentation. Enrichment PCR was performed using the KAPA HiFi HotStart PCR Kit (Kapa Biosystems) and the cycling parameters were as follows: 3 min at 72 °C, 30 s at 95 °C, and then 15 cycles of 10 s at 95 °C, 30 s at 55 °C, and 30 s at 72 °C. The size range of 400–700 bp fragments were selected using the AMPure XP beads (Beckman Coulter). Paired-end sequencing was performed using Illumina HiSeq X Ten sequencers.
DOI: 10.26036/cnp0001203
title: 通过双gRNA进行可预测的高效基因编辑

description: CRISPR基因编辑是通过使用内源DNA修复机制修复Cas9引入的双链断裂（DSB）来完成的。尽管对于给定的CRISPR指导RNA（gRNA），DSB修复的结果是可预测的，但在不同的靶位点之间它是不同的。在这里，我们报道了由Cas9和一对gRNA引入的缺失连接是可预测的发现。我们研究了在三个人类细胞系中靶向四基因（TTR，CREB1，STAT2和IRF9）的8对gRNA的修复连接。使用Sanger和二代测序和ICE分析，我们发现缺失连接主要由非同源平末端连接（NHBEJ）修复。我们进一步评估了24个CRISPR缺失接头的插入缺失谱，以证实这一观察结果，并进一步证明了CRISPR对之间的PAM方向和距离对NHBEJ结果有轻微影响。基于这些观察结果，我们应用NHBEJ策略引入了高度精确且可预测的基因敲除和DMD外显子51的框内缺失，为杜兴氏肌营养不良症和许多其他人类疾病的CRISPR基因治疗提供了一种新颖的替代治疗策略。
DOI: 10.26036/cnp0001174
title: High-variable region sequencing of 16S rDNA

description: The Illumina sequencing strategy for the V6 region of the 16S rDNA
DOI: 10.26036/cnp0001252
title: 金鱼的起源，演化和家驯化历史

description: 本研究组装了一个高质量的金鱼基因组，并重测序了201份金鱼样本，揭示了金鱼的起源，演化和家驯化历史，并通过GWAS鉴定到了与透明鳞、背鳍等性状关联的基因
DOI: 10.26036/cnp0001224
title: Collection of culturable bacterial genomes

description: A genome collection established by culture-based isolation of bacterial isolates from fecal samples of healthy individuals.
DOI: 10.26036/cnp0001207
title: the transcriptomic profiles of female and male P. chinensis flower buds

description: In this work, Illumina paired-end RNAsequencing assay was conducted to unravel the transcriptomic profiles of female and male P. chinensisflower buds.
DOI: 10.26036/cnp0001202
title: project of mj20161212005

description: analysis of high-temperature Daqu with distinct colors
DOI: 10.26036/cnp0001261
title: Viral metagenomic from mosquitoes

description: Metagenomic sequencing reveals viral abundance and diversity from mosquitoes in Shaanxi-Gansu-Ningxia region, China
DOI: 10.26036/cnp0001227
title: 莲藕重测序

description: 莲藕重测序项目数据
DOI: 10.26036/cnp0001271
title: transcriptome of PI437654, WM82, ZH13 and HF47 response to SCN at 8dpi

description: transcriptome of the root samples from a SCN resistant soybean PI437654 and three susceptible soybean WM82, ZH13 and HF47 infected with SCN and their controls
DOI: 10.26036/cnp0001270
title: Chromosome-level assembly of mangrove plant Aegiceras corniculatum genome using PacBio long reads sequencing and Hi-C analysis

description: Aegiceras corniculatum (L.) Blanco, a pioneer species of mangrove plant, is a small tree or shrub, belonging to the genus Aegiceras in the family Peachiaceae. It is salt secreting mangrove species. Current research on the A. corniculatum has focused on community characterization, genetic diversity, and cultivation breeding. Moreover, questions about deeper adaptive mechanisms, genetic evolution are limited due to the lack of genomic data. In this study, we present a chromosome-level genome assembly, which is the first genome of the family Peachiaceae. The results not only lay a solid foundation for further phylogenetical and protective studies of A. corniculatum, but also benefits to the further exploration to its response mechanisms in adaptation to the harsh intertidal coastal environment.
DOI: 10.26036/cnp0001274
title: 旱柳耐盐转录组测序

description: 耐盐性存在差异的两个旱柳材料在清水和150mM盐处理下根系的二代转录组测序
DOI: 10.26036/cnp0001254
title: Extensive Porcine Germline Genome Engineering

description: Porcine xenotransplantation, the use of pig organs for human transplantation, has long been investigated as an alternative for patients suffering from organ failure. However, clinical application has been impeded by two main hurdles: 1) Molecular incompatibilities between donor pigs and humans and 2) Risk of transmission of porcine endogenous retroviruses (PERVs). We previously demonstrated the successful production of genome-modified pigs with PERV inactivated. In this study, we increased the scale of germline editing from targeting a single repetitive locus to engineering 13 different genes using multiple genome engineering methods. We engineered the pig genome at 42 alleles using a combination of CRISPR-Cas9 and transposon technology, producing pigs that carry PERV inactivation, the knock-out of 3 xeno-antigens, and the addition of 9 human transgenes. The engineered pigs exhibit normal physiology, fertility, and germline transmission of the edited alleles. In vitro assays have shown that, as with allogenic transplantation, cells from engineered pigs gain significant resistance to human humoral rejection, cell-mediated damage, and coagulation dysregulations. This represents a significant step towards safe and effective porcine xenotransplantation.
DOI: 10.6084/m9.figshare.14559533
title: Correlation between collum angle and lower lip position in different Class II malocclusions - A retrospective cephalometric study

description: <b>Purpose</b>: Significance of analysing collum angle in class II malocclusions with respect to lip position may lend greater credibility to variable torque brackets (mainly in the anteriors) that are fast gaining traction. Determine the magnitude of collum angle of maxillary central incisors in Class II division 1, division 2 malocclusions and changes in measurement brought about by variations in lower lip position and incisal contact. <b>Materials and methods</b>: 154 lateral cephalograms were divided into three groups- 55(Angle’s class I), 52 (Angle’s class II division 1) and 47 (Angle’s class II division 2). The collum angle was measured along with lower lip line (in Class II division 2) and lower lip contact (in Class II division 1) malocclusions. <b>Results</b>: The mean collum angles were 2.12 ± 1.43°, −0.84 ± 0.87° and 4.67 ± 2.23° in Groups 1, 2, and 3, respectively. Mean collum angle is significantly increased when the lower lip was found to contact the middle-third of the central incisor(in Group 3)and significantly decreased when the anterior one-third of the lower lip was in contact with the incisal edge of the central incisor (in Group 2). ANOVA followed by Tukey HSD test was carried out to determine statistically significant differences (p <b>Conclusion</b>: Collum angle is significantly decreased in Class II division 1 malocclusions necessitating variable torque prescriptions and segmental mechanics of maxillary anteriors. Appropriate alveolar bone support must be assessed prior to en-masse retraction and intrusion respecting the cortical boundaries. <b>KEY MESSAGES</b>: Variable torque brackets are rapidly gaining credence for their ability to provide sufficient alveolar bone support in different clinical scenarios. In this study, we have emphasized upon utilizing similar mechanics to treat class II malocclusions by utilizing the lower lip position as a reference guide.
DOI: 10.26036/cnp0000824
title: Reference gene catalog and metagenome-assembled genomes of pig gut microbiome

description: Reference genomes and gene catalog of gut microbiome are essential resources for understanding the functional role of specific taxa in the microbiome and for quantifying their abundance in metagenomes. Here we constructed a reference gene catalog and metagenome-assembled genomes of pig gut microbiome, and analyzing the evolution of gut microbiome from Wild boars to highly selected pigs, which provide important and powerful resources for generating insights into the pig gut microbiome and future metagenomic sequencing-based studies.
DOI: 10.26036/cnp0000941
title: Genome assembly of three species of the camel family

description: We have assembled the genomes of three species of the camel family：Lama_guanicoe，Vicugna_vicugna and Lama_glama.
DOI: 10.26036/cnp0001265
title: transcriptome of Helicteres Angustifolia

description: transcriptome of Helicteres Angustifolia
DOI: 10.26036/cnp0001069
title: Qianhe raw data

description: The composition of the intestinal microbiome of the pig is highly heritable and directly affected by a common deletion in the ABO glycosyltransferase gene
DOI: 10.26036/cnp0001273
title: 兔瘟病毒2型与经典兔瘟病毒病原特性差异分析

description: 兔瘟，又称兔病毒性出血症（rabbit hemorrhagic disease，RHD），是由嵌杯病毒科（Caliciviridae）兔病毒属（Lagovirus）兔出血症病毒（rabbit hemorrhagic disease virus，RHDV）引起家兔的一种急性、高度致死性传染病。1984年我国首次报道RHD后，世界很多国家相继报道RHD的发生和流行[1]。 2020年4月，我国四川省某养兔场发生疑似RHD疫情，兔死亡率约为73.3%，经红细胞凝集试验、RT-PCR及测序分析等，确定该病原为兔出血症病毒2型（RHDV2），这是在我国首次发现的RHDV2型毒株[2]。RHDV2的感染病例由法国于2010年4月首次报道，导致家养和野生兔群的大面积感染死亡[3]。该病毒在不到一年的时间内传播到南欧。其次是北欧国家（即葡萄牙、意大利和西班牙等）和一些岛屿如亚速尔群岛（葡萄牙）。2015年，在澳大利亚、非洲与其他欧洲国家被发现，次年RHDV2在加拿大被发现，并继续在欧洲传播。在欧洲首次发现该病毒仅6年后，RHDV2在美洲和大洋洲出现（图1）[4]。至2018年11月，全球共报道133例RHDV2疫情。RHDV2严重影响各国养兔业发展，造成巨大的经济损失，同时还导致全球野兔种群数量的急剧减少，破坏生态平衡，给人类社会、民众健康带来严重的负面影响。
DOI: 10.26036/cnp0001251
title: 恒河猴血液甲基化组

description: 两个年龄组别（青年5-7岁；老年15-18岁）的恒河猴，血液全基因组甲基化测序（WGBS）
DOI: 10.26036/cnp0001294
title: flax miRNA-seq

description: Identification and characterization of differentially expressed microRNAs and target gene related to flax stem development