cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16834825.v4
title: Metadata on the oxidative stress related RNA-seq samples in the dataset used for the meta-analysis (OS dataset)

description: Information on oxidative stress related RNA-seq samples used for meta-analysis is organized as the dataset called OS dataset. It includes information on pairs of oxidative stress and normal state samples.
DOI: 10.6084/m9.figshare.16834825.v3
title: Metadata on the oxidative stress related RNA-seq samples in the dataset used for the meta-analysis (OS dataset)

description: Information on oxidative stress related RNA-seq samples used for meta-analysis is organized as the dataset called OS dataset. It includes information on pairs of oxidative stress and normal state samples.
DOI: 10.34740/kaggle/dsv/2880437
title: NASA Project; Marine Debris Machine Learning
DOI: 10.6084/m9.figshare.17030138.v4
title: Transaction Records

description: Financial transaction records from 09/2017 to 11/2017
DOI: 10.6084/m9.figshare.17119091
title: Transaction Records

description: Financial transaction records from 09/2017 to 11/2017
DOI: 10.26036/cnp0000527
title: Beachrock microbial communities reconstruction

description: This is a study on microbial communities on beach rock.
DOI: 10.26036/cnp0001391
title: Systematical engineering of synthetic yeast for enhanced production of lycopene

description: Synthetic biology allows the re-engineering of biological systems and promotes the development of bioengineering to a whole new level, showing great potentials in bio-manufacture. Here, in order to make the heterologous pathway compatible with the chassis, we evolved the strain with a unique Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) system which is built in the synthetic chromosome. By inducing SCRaMbLE, we successfully identified a chassis strain that can maintain the high yield while the rearranged chromosome content and introduced heterologous pathway show minimal effect on the yeast cell physiology. Then in the SCRaMbLEd strains we integrated the lycopene biosynthesis pathway into rDNA array to further increase its copy number and optimized the culturing condition, which lead to a 55.7-times increase of lycopene yield in the final yeast strain comparing to its parental strain. Our work potentially shows that by combining the engineering efforts on both natural product biosynthesis pathway and its host strain can further promote the potential of engineered host strain that is also high compatible to its heterologous over-expressed pathway of target product.
DOI: 10.26036/cnp0001465
title: Transcriptome data from Trichosanthes cucumerina L.

description: Transcriptome data were obtained from callus, leaf, and fruit of Trichosanthes cucumerina L.
DOI: 10.26036/cnp0001677
title: Dual reporter gene system with Pgap

description: A dual reporter‑gene system was developed, in which the opmCherry reporter gene driven by the constitutive PlacUV5 promoter for calibration, and the EGFP reporter gene driven by Pgap.
DOI: 10.26036/cnp0001629
title: Mus musculus

description: Polymannuronic acid and Lactobacillus rhamnosus GG probiotic in combination synergically prevented dopaminergic neuronal loss in Parkinson’s disease mice model
DOI: 10.26036/cnp0001649
title: Pinus tabuliformis genome

description: The genome sequence of Chinese pine (Pinus tabuliformis)
DOI: 10.26036/cnp0001300
title: Meta大数据研究-骨质疏松

description: 探究鼠李糖（LGG）、动物双歧（B.animals）、齿双歧（B.dentium）单菌在小鼠模型中对骨保护的研究；本实验为时间维度的研究，时间维度为：基线点（T1）、手术后（OVX）T2和T3、建模结束点（T4）、灌胃单菌或者培养基的时间点（T5-T8）、最终取样点（T8），本实验除了三个实验组（鼠李糖（LGG）、动物双歧（B.animals）、齿双歧（B.dentium）），还包括阴性对照和阳性对照组。
DOI: 10.26036/cnp0001862
title: 人类结直肠癌肠道菌群

description: 本研究基于法国、奥地利、中国、美国、加拿大、德国、日本、意大利已公开发表的结直肠癌（CRC）粪便样品宏基因组数据，运用生物信息学和统计学分析方法，搭建宏基因组代表基因组组装筛选和菌群单核苷酸突变（Single Nucleotide Polymorphisms，SNP）calling流程，获得东西方人群中与CRC有关的基因组集以及共有和特有的菌群SNPs信息，获得健康人群与CRC患者在肠道菌群亚基因组水平的变异数据库。
DOI: 10.26036/cnp0001878
title: genome assemblies of 20 wild S. pombe isolates

description: We collect 20 wild S. pombe isolates and assemble the genome sequence with two independent softwares respectively, canu and wtdbg. After the evaluation of the assemblies, only the superior assembly for each strain is kept.
DOI: 10.26036/cnp0001903
title: The genome of Conticribra weissflogii

description: This project provide a draft assembly and annotation of a centric diatom Conticribra weissflogii
DOI: 10.26036/cnp0002037
title: Black cutworm antioxidant enzyme

description: Identification and characterization of antioxidant enzyme genes from the black cutworm Agrotis ipsilon
DOI: 10.26036/cnp0002057
title: The remediation effects of microbial organic fertilizer on soil microorganisms fumigated by chloropicrin

description: The remediation effects of microbial organic fertilizer on soil microorganisms fumigated by chloropicrin
DOI: 10.26036/cnp0002068
title: Spatiotemporal reconstruction of axolotl brain development and regeneration at single-nuclei resolution

description: Brain regeneration upon injury requires a precise coordination of complex cellular and molecular responses in a time- and region-specific manner. Identifying key types of cells directing specific brain regeneration processes and underlying mechanisms hold great promise for the advance of regenerative medicine. However, progress in the field has been hampered largely due to lack of injury recovery capacity of mammal brain models and appropriate tools to comprehensively dissect the regeneration process at molecular level. Here, using the brain injury model of axolotl that can almost fully regenerate the injured tissue, and the high-resolution Stereo-seq (Spatio-Temporal Enhanced REsolution Omics-sequencing), we present the first in situ transcriptomic atlas at single-nuclei resolution that enables spatial characterization of cells combined with global gene expression information throughout brain development and regeneration. Excitingly, we discovered a marked heterogeneity of radial glial cell (RGC) types with distinct behaviors. Particularly, one subtype of RGCs is immediately activated at early stages of telencephalon regeneration and start to proliferate while other RGCs remain dormant. Such RGC subtype appears to be the major cell type gradually covering the injured area before potentially transformed into the lost neurons of exactly the same cellular identity. Altogether, our study provides a systematic dissection of the molecular events underlying neural cell plasticity in the amphibian brain, laying the foundation for further mechanistic studies in this and other species.
DOI: 10.26036/cnp0002092
title: 虱蝇科线粒体基因组

description: 虱蝇科线粒体基因组数据
DOI: 10.26036/cnp0002157
title: Ophiocordyceps sinensis comparative genomic analysis

description: Ophiocordyceps sinensis genome sequencing and comparative genomic analysis
DOI: 10.26036/cnp0002170
title: Unrevealing the transcriptome complexity of octoploid strawberry through ONT long read sequencing

description: Despite the advances in the finding of genome-wide alternatively spliced genes in strawberry, it remains unexplored how AS responds to developmental cues and what relevance of these outcomes have been linked to the gene function. In this study, we have systematically investigated the transcriptome complexity using long-read Oxford Nanopore Technologies along the four successive developmental stages. The full-length cDNA sequencing results unraveled thousands of previously unexplored AS isoforms. Alternative transcription start site (aTSS) and alternative transcription termination site (aTTS) were the two AS types that were more abundant than intron retention. Differentially expressed transcripts unrevealed the key transitional role of the white fruit stage. Isoform switches of transcripts from 757 genes with protein-coding potential change and domain gain or loss as the main consequences were observed. These genes with switched isoforms take part in key processes of maturation processes in the late maturation stages.
DOI: 10.26036/cnp0002180
title: 扩增子平台比较数据

description: 比较不同平台的扩增子数据
DOI: 10.26036/cnp0002196
title: Long-term positioning networked agricultural experiment

description: The database of soil metagenomics which have been monitored and collected continuously under natural conditions in Huanghuaihai Region of China.
DOI: 10.26036/cnp0002327
title: Whole-genome sequencing of Tarim red deer (Cervus elaphus yarkandensis)

description: Tarim Red Deer (Cervus elaphus yarkandensis, TRD) have adapted to the harsh environmental conditions in this basin, including high solar radiation and temperature, aridity, and poor nutritional conditions. The genomic sequencing data for TRD could be valuable and useful for both conservation of wild populations and utilization of domestic ones as a resource for further study, providing baseline sequence and annotation data for the species.
DOI: 10.26036/cnp0002270
title: LIANTI

description: The coverage in single cell methylation sequencing was poor, and the need arose to improve the coverage, accuracy and the read length of single cell. In our method, we found the most popular method only have 10% coverage in the 2x sequencing depth. Even if the most methods focused on the single strand library construction, and they ignored the base unblanced problem in the amplification. We found the DNA polymerase have amplification bias on the ATGC, so we used T7 transcription amplification to avoid the base unbalance in the amplifcaiton. The transposon insert the T7 adaptor in the genome without using random primer could increase the accuracy and tagmentation effiency. Then the gentle and high convertion efficiency kit is used by protect the methylation site by TET2 and convert the unmethylatate sites to the uracil by the APOBEC3A. Finally, we achieve the superior 70% coverage efficiency with only 2x sequencing depth on the single cell sequencing, which is the highest reported single cell methylation coverage until now.
DOI: 10.26036/cnp0002212
title: transcriptome of endophytic fungus Shiraia sp. Slf14

description: transcriptome of endophytic fungus Shiraia sp. Slf14
DOI: 10.26036/cnp0002250
title: Genome-wide association analysis of tolerant traits in terrestrial cotton seedling stage

description: Genome-wide association analysis of tolerant traits in terrestrial cotton seedling stage
DOI: 10.26036/cnp0002363
title: Grampus griseus genome sequencing

description: 10X sequencing raw reads for Grampus griseus
DOI: 10.26036/cnp0002359
title: Serum Metabolic Signatures of High-fat-induced Bone Loss in Mice

description: Accumulating evidence indicates that high-fat diet (HFD) is a controllable risk factor for osteoporosis, but the underlying mechanism remains to be elucidated. As a primary biological barrier for nutrient entry into the human body, the composition and function of gut microbiota (GM) can be altered rapidly by HFD, which may trigger abnormal bone metabolism. In the current study, we analyzed the signatures of GM and serum metabolomics in HFD-induced bone loss and explored the potential correlations of GM and serum metabolites on HFD-related bone loss.
DOI: 10.26036/cnp0002338
title: Transcriptome assembly of Larix olgensis

description: Transcriptome data assembly files from various tissues of Larix olgensis
DOI: 10.26036/cnp0002272
title: chickpea 3k SNP variations

description: SNPs by whole genome sequencing of 3,171 cultivated spcies accessions and 195 accessions from seven wild species.
DOI: 10.26036/cnp0002251
title: Denoise the contaminant species in metagenomics data

description: Denoise the contaminant species in metagenomics data to get precise source specie
DOI: 10.26036/cnp0002267
title: Raw sequencing data of Spelaeogriphacea

description: BGISEQ500 Raw sequencing data of Spelaeogriphacea
DOI: 10.26036/cnp0002183
title: Mitochondrial genome of Elymus sibiricus

description: Mitochondrial genome of Elymus sibiricus
DOI: 10.26036/cnp0002259
title: 暗纹东方鲀受低氧和副溶血弧菌胁迫的代谢组学

description: 我们对暴露于低氧胁迫或者副溶血弧菌感染下的暗纹东方鲀的全肝进行了非靶向代谢组学分析。
DOI: 10.26036/cnp0002018
title: The chromosome-scale genomes of Dipterocarpaceae provide insights into fragrant oleoresin biosynthesis and hard wood formation

description: Dipterocarpaceae are typical tropical plants (dipterocarp forests) and famous for its high economic value because of their production of fragrant oleoresins, top-quality timber and usage in traditional Chinese medicine. To better understand the genetic basis of the fragrant oleoresin biosynthesis and obtain evolutionary insights into high-quality wood formation in Dipterocarpaceae, we generated chromosome-level genome assemblies for two representative Dipterocarpaceae species viz. Dipterocarpus turbinatus Gaertn. f. and Hopea hainanensis Merr. et Chun.
DOI: 10.26036/cnp0002284
title: Genome assembly and annotation of Taxus chinensis var. mairei

description: Genome assembly and annotation of Taxus chinensis var. mairei
DOI: 10.26036/cnp0002285
title: Genome sequences of two types of Prototheca wickerhamii

description: Genome sequences of two types of Prototheca wickerhamii
DOI: 10.26036/cnp0002290
title: Chromosome-level genome assembly of Pogostemon cablin

description: Chromosome-level genome assembly of Pogostemon cablin provides insights into patchoulol biosynthesis and regulation
DOI: 10.26036/cnp0002321
title: A full-length transcriptome of Populus alba x Populus tremula var. glandulosa clone 84K

description: The male hybrid poplar P. alba × P. tremula var. glandulosa, or 84K poplar, is an important model plant due to its excellent properties and ease of transformation. Because of its two subgenomes, alleles in 84K poplar have different transcription bias and expression patterns, making it more complex than traditional model plants. To investigate a more realistic transcriptional profile of its genes, full-length transcriptome was sequenced.
DOI: 10.26036/cnp0002337
title: Rice SNPs for convergent evolution

description: Rice SNPs for convergent evolution.
DOI: 10.26036/cnp0002414
title: Microbiota of Gymnocypris przewalskii

description: The microbial dynamic of aquatic animal is crucial for the health of host. Gymnocypris przewalskii, Qinghai Lake naked carp, a short-distance anadromous fish, is the predominant species in Qinghai Lake. In Qinghai Lake, G. przewalskii needs more than 7 years to reach sexual maturity, and then its breeding group seasonally migrates to inflowing rivers to spawn over sandy gravel beds when the river water temperature rises to 6~17.5°C from April to July. Along with migration, there is a crucial dynamic on symbiotic microorganism. Moreover, the colonization of symbiotic microorganism in post-spawn eggs, post-hatch larvae and post-feed juveniles is important for artificial culture. Here, we used 16S rRNA gene amplicon sequencing to get the structure dynamic of the symbiotic microbial community in several development stages of G. przewalskii from eggs to adults.
DOI: 10.26036/cnp0002382
title: lncRNA-Seq of axillary bud

description: 本项目对烟草不同部位腋芽以及打顶后不同时间腋芽进行lncRNA测序，分析鉴定打顶响应相关的lncRNA
DOI: 10.26036/cnp0002411
title: Gut microbial community of wild fishes in Yangtze River

description: In aquatic animals, gut microbial communities shift with host development and living environment. Understanding the mechanism how environment impacts the gut microbial communities of aquatic animals is crucial for assessing and managing aquatic ecosystem health. Here, we proposed a simplified framework for the colonization and dynamic of gut microbial communities. Then, to quantify the colonization of environmental microbes in wild fish gut, the current study used 16S rRNA gene amplicon sequencing to get the structure of the water environmental microbial community and the gut microbial community in several wild fish populations from Yangtze River, and the relationship of these microbial communities were analyzed.
DOI: 10.26036/cnp0002407
title: Genomic analysis for Biosynthesis and Metabolic Pathway of Elsinochrome Toxin produced by Elsinoe arachidis

description: Analysis of genomic information of E. arachidis lays a solid molecular data foundation for further exploration of pathogenic mechanisms and toxin biosynthesis pathways. Provide a valuable foundation in the biosynthesis of elsinochrome and essential information for further comprehend its virulence mechanism
DOI: 10.26036/cnp0002410
title: eDNA sequences in Middle Yangtze River

description: For supporting the aquatic biodiversity conservation and the fishing ban in Yangtze River Basin, it is essential to monitor and estimate the high resolution spatial-temporal distribution of fishes and related microbiota in the middle reach of Yangtze River. Monitoring fishes and related microbiota using environmental DNA (eDNA) would be an efficient method for getting the high resolution spatial-temporal distribution of fishes in the middle reach of Yangtze River. In this project, we focused on the fishes and related microbiota monitoring using eDNA in the middle reach of Yangtze River during the breeding season, growing season and wintering season of fishes. This project will test the usage of eDNA in monitoring the fishes and related microbiota spatial-temporal distribution in the middle reach of Yangtze River.
DOI: 10.26036/cnp0002401
title: Rabbit GGTA1 gene edition

description: Rabbit GGTA1 gene edition via Crispr/Cas 9 technique
DOI: 10.26036/cnp0002271
title: The chromosome-level genome of Pistia stratiotes

description: Pistia stratiotes (Araceae) is one of the most notorious weeds that can cause serious damage to economy and natural ecosystems of infested areas. Herein, we assembled a chromosome-level for P. stratiotes with a genome size of 311.87 Mb based on PacBio, Illumina, and Hi-C data. In total, assembling the Pistia stratiotes genome provides new insights into its evolution and rapid invasive adaptation and the genome evolution of the Araceae family.
DOI: 10.25912/rdf_1638497851797
title: Bee colony strength and temperature data
DOI: 10.6084/m9.figshare.15302229.v1
title: Chiridota genome sequences, cds sequence, protein sequences.

description: We sequenced a C. heheva captured under 1400 meters deep in the Haima cold spring in the South China Sea. After assemblying the genome, the genome was annotated by ab initio and homolog annotation, including braker and genomethreader.
DOI: 10.5517/ccdc.csd.cc28tcfx
title: CCDC 2109749: Experimental Crystal Structure Determination

description: Related Article: John T. Brown, Olivia Grounds, Matthias Zeller, Neil R. Dilley, Sergiy V. Rosokha|2021|Cryst.Growth Des.|21|7257|doi:10.1021/acs.cgd.1c01116
DOI: 10.5517/ccdc.csd.cc28tcgy
title: CCDC 2109750: Experimental Crystal Structure Determination

description: Related Article: John T. Brown, Olivia Grounds, Matthias Zeller, Neil R. Dilley, Sergiy V. Rosokha|2021|Cryst.Growth Des.|21|7257|doi:10.1021/acs.cgd.1c01116
DOI: 10.5517/ccdc.csd.cc28yzw3
title: CCDC 2114196: Experimental Crystal Structure Determination

description: Related Article: Ruyan Zhao, Randy P. Sabatini, Tong Zhu, Sasa Wang, Amin Morteza Najjarian, Andrew Johnston, Alan J. Lough, Sjoerd Hoogland, Edward H. Sargent, Dwight S. Seferos|2021|J.Am.Chem.Soc.|143|19901|doi:10.1021/jacs.1c09515
DOI: 10.5281/zenodo.5750960
title: Training and test dataset for Receiver functions for quality classification and inversion

description: traindata_inv.dat file contains the 60,000 1D crust layered-model and synthetic receiver functions, as well as surface wave dispersion. First row: the name of synthetic models, Second row: Receiver functions with 300 sample points (-5~25 s) Third row: Surface wave dispersion data with 16 sample points (4~32 s with 2 s interval) Fourth row: Shear wave velocities of 60-layer-model, and the thickness from the first layer to the last layer are <pre>0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0</pre>
description: {"references": ["Lu Gan et al, Quality classification and inversion of receiver function using convolutional neural network"]}
DOI: 10.5281/zenodo.5731551
title: Training and test dataset for Receiver functions for quality classification and inversion

description: traindata_inv.dat file contains the 60,000 1D crust layered-model and synthetic receiver functions, as well as surface wave dispersion. First row: the name of synthetic models, Second row: Receiver functions with 300 sample points (-5~25 s) Third row: Surface wave dispersion data with 16 sample points (4~32 s with 2 s interval) Fourth row: Shear wave velocities of 60-layer-model, and the thickness from the first layer to the last layer are <pre>0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0</pre>
description: {"references": ["Lu Gan et al, Quality classification and inversion of receiver function using convolutional neural network"]}
DOI: 10.5281/zenodo.5731552
title: Training and test dataset for Receiver functions for quality classification and inversion

description: traindata_pick.dat file contains the receiver function data form North China, as well as manually labels. traindata_inv.dat file contains the 60,000 1D crust layered-model and synthetic receiver functions, as well as surface wave dispersion. traindata_pick.dat: First row is the label of quality of receiver function, 1 for good, and 0 for bad. Other rows are the data of receiver function with 419 sample points (-2~42 s) traindata_inv.dat: First row: the name of synthetic models, Second row: Receiver functions with 300 sample points (-5~25 s) Third row: Surface wave dispersion data with 16 sample points (4~32 s with 2 s interval) Fourth row: Shear wave velocities of 60-layer-model, and the thickness from the first layer to the last layer are <pre>0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0</pre>
description: {"references": ["Lu Gan et al, Quality classification and inversion of receiver function using convolutional neural network"]}
DOI: 10.5281/zenodo.5242991
title: Simulation results for "Modeling the joint effects of vegetation characteristics and soil properties on ecosystem dynamics in a Panama tropical forest"

description: This dataset is the ELM-FATES simulation outputs for the paper entitled "Modeling the joint effects of vegetation characteristics and soil properties on ecosystem dynamics in a Panama tropical forest".
DOI: 10.5281/zenodo.5242990
title: Simulation results for "Modeling the joint effects of vegetation characteristics and soil properties on ecosystem dynamics in a Panama tropical forest"

description: This dataset is the ELM-FATES simulation outputs for the paper entitled "Modeling the joint effects of vegetation characteristics and soil properties on ecosystem dynamics in a Panama tropical forest".
DOI: 10.5281/zenodo.5750954
title: BioVAE: a pre-trained latent variable language model for biomedical text mining

description: We release BioVAE, the first large-scale pre-trained latent variable language model for the biomedical domain, which uses the OPTIMUS framework to train on large volumes of biomedical text. This version contains the pre-trained models for text mining tasks such as named entity recognition or relation extraction, and text generation task. Explanation of each file: (lt32: latent_size = 32, beta05: beta=0.5) pm-full-lt32-beta00 pm-full-lt32-beta05 pm-full-lt768-beta00 pm-full-lt768-beta05 pm-full-generation