cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5bz6185z
title: MassIVE Reanalysis RMSV000000354.3275 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ZNF219 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.5281/zenodo.5890230
title: Experimental Investigation of the Heat Transfer between Finned Tubes and a Bubbling Fluidized Bed with Horizontal Sand Mass Flow

description: Data repository for the paper: Thanheiser, S.; Haider, M.; Schwarzmayr, P. Experimental Investigation of the Heat Transfer between Finned Tubes and a Bubbling Fluidized Bed with Horizontal Sand Mass Flow. Energies 2022, 15, 1316. https://doi.org/10.3390/en15041316
DOI: 10.5281/zenodo.5474019
title: Experimental Investigation of the Heat Transfer between Finned Tubes and a Bubbling Fluidized Bed with Horizontal Sand Mass Flow

description: Data repository for the paper: Thanheiser, S.; Haider, M.; Schwarzmayr, P. Experimental Investigation of the Heat Transfer between Finned Tubes and a Bubbling Fluidized Bed with Horizontal Sand Mass Flow. Energies 2022, 15, 1316. https://doi.org/10.3390/en15041316
DOI: 10.5281/zenodo.6199839
title: Dataset related to article "Early de-tethering: analysis of urological and clinical consequences in a series of 40 children"

description: clinical dataset of raw data related to article at title
DOI: 10.5281/zenodo.6199838
title: Dataset related to article "Early de-tethering: analysis of urological and clinical consequences in a series of 40 children"

description: clinical dataset of raw data related to article at title
DOI: 10.26036/cnp0001062
title: 德尔卑沙门菌和肠道菌群互作

description: 德尔卑沙门菌感染对小鼠肠道菌群的影响
DOI: 10.25345/c57659g2m
title: MassIVE Reanalysis RMSV000000354.3277 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ELMO1 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.26036/cnp0000555
title: 东北黑土细菌群落与土壤水分的关系

description: 东北黑土细菌群落与土壤水分的关系
DOI: 10.26036/cnp0000472
title: pathogens isolated from wild animals

description: Mycobacterium and Serratia marcescens were detected in wild animals
DOI: 10.26036/cnp0000902
title: Transcriptome analysis of roots of Arabidopsis thaliana in response to allelopathic effects

description: Transcriptome analysis of roots of Arabidopsis thaliana in response to allelopathic effects of invasive horseweed (Conyza canadensis)
DOI: 10.26036/cnp0001468
title: RNA-Seq analysis of rosa petal

description: RNA-seq result s of the red rose variety and the white rose variety
DOI: 10.25345/c53f4kn8v
title: MassIVE Reanalysis RMSV000000354.3131 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, DPEP3 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.6084/m9.figshare.19207398
title: HPLP raw file

description: raw files of HPLP study
DOI: 10.6084/m9.figshare.19207404
title: P. notatum genome

description: High-quality chromosome-scale de novo assembly of the Paspalum notatum ‘Flugge’ genome
DOI: 10.6084/m9.figshare.19207404.v1
title: P. notatum genome

description: High-quality chromosome-scale de novo assembly of the Paspalum notatum ‘Flugge’ genome
DOI: 10.6084/m9.figshare.19207398.v1
title: HPLP raw file

description: raw files of HPLP study
DOI: 10.26036/cnp0001469
title: Cell transcriptomic atlas of the non-human primate Macaca fasciculari

description: Studying tissue composition and function in non-human primates (NHP) is crucial to understand the nature of our own species. Here, we present a large-scale cell transcriptomic atlas encompassing over one million cells from 45 tissues of the adult NHP Macaca fascicularis. This dataset provides a vast annotated resource to study a species phylogenetically close to humans. To demonstrate its utility, we have reconstructed the cell-cell interaction networks driving Wnt signalling across the body, mapped the distribution of receptors and co-receptors for viruses causing human infectious diseases, and intersected our data with human genetic disease orthologues to establish potential clinical associations. Our Macaca fascicularis cell atlas constitutes an essential reference for future studies in human and NHP.
DOI: 10.26036/cnp0001612
title: genome of Rhodococcus ruber ZM07

description: The whole genome sequence of Rhodococcus ruber ZM07
DOI: 10.25345/c5zp3w12d
title: MassIVE Reanalysis RMSV000000354.3276 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PTGER3 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.17179/excli2021-4622_supplementary_data_xlsx
title: Hypoxia-inducible factor (HIF)-3α2 serves as an endothelial cell fate executor during chronic hypoxia

description: The adaptive response to hypoxia involves the transcriptional induction of three transcription factors called hypoxia inducible factor alpha 1, 2 and 3 (HIF-1α, HIF-2α, and HIF-3α) which dimerize with constitutively expressed beta chains that together form the HIF-1, -2 and -3 transcription factors. During normoxic conditions, the alpha chain is expressed at low levels since its stability is regulated by prolyl-hydroxylation that promotes subsequent ubiquitination and degradation. During hypoxic conditions, however, the prolyl hydroxylases are less active, and the alpha chain accumulates through elevated protein stability and the elevated induction of expression. Two of the three HIFs isoforms present in mammals, HIF-1 and HIF-2, are well characterized and have overlapping functions that promote cell survival, whereas HIF-3’s role remains less clear. The HIF-3 response is complicated because the HIF3A gene can utilize different promotors and alternate splicing sites that result in a number of different HIF-3α isoforms. Here, using human umbilical vein endothelial cells (HUVECs), we demonstrate that one of the isoforms of HIF-3α, isoform 2 (HIF-3α2) accumulates at a late stage of hypoxia and induces the expression of DNA damage inducible transcript 3 (DDIT4), a gene known to promote apoptosis. We also demonstrate that caspase 3/7 activity is elevated, supporting that the role of the HIF-3α2 isoform is to promote apoptosis. Furthermore, we provide evidence that HIF-3α2 is also expressed in seven other primary endothelial cell types, suggesting that this may be a common feature of HIF-3α2 in endothelial cells.
description: EXCLI Journal; 21:Doc454; ISSN 1611-2156
DOI: 10.26036/cnp0001620
title: microbial community structure of H-1

description: The microbial community structure of H-1 with or witout exogenous thiamine in the 1st and 40th tranfers .
DOI: 10.26036/cnp0002648
title: SURRO-seq:massively targeted evaluation of CRISPR off-targets in cells_2

description: Sensitive and high-throughput methods for evaluating CRISPR RNA-guided nucleases (RGNs) off-targets (OTs) in cells are essential for advancing RGN-based gene therapies. Here we report a method for simultaneously evaluating thousands of potential RGN off-target sites in cells, called SURRO-seq, which relies on capturing RGN-induced indels in potential SURROgate off-target sites in cells by a pool of lentiviral vectors and targeted deep sequencing. We first evaluate 170 previously investigated OTs from 11 RGNs with SURRO-seq in HEK293T cells. SURRO-seq sensitively captures nearly 100% OTs found by T7E1, most (70%) GUIDEseq-identified OTs, and about half (51%) OTs found by CIRCLE-seq. We next apply SURRO-seq to evaluate 7160 potential OTs from 111 therapeutic RGNs and identify 754 potential OTs with significantly detectable indels, which are further validated in 23 endogenous genome loci in five human cells. Analyses of pOTs with significantly high indel frequencies reveal that thermodynamically stable wobble base pair (rG•dT) strongly increases RGN OT effect. Benchmark analysis of SURRO-seq identified OTs with latest RGN prediction tools further confirms that thermodynamic energy-based predictors provide the most accurate RGN OT prediction. SURRO-seq thus offers a scalable, high-throughput, sensitive and complementary for evaluating RGN OTs and advancing RGN-based gene therapy applications.
DOI: 10.26036/cnp0001635
title: genome of Rhizobium daejeonense ZM10

description: The whole genome sequence of Rhizobium daejeonense ZM10
DOI: 10.26036/cnp0001634
title: genome of Stenotrophomonas acidaminiphila ZM09

description: The whole genome sequence of Stenotrophomonas acidaminiphila ZM09
DOI: 10.26036/cnp0001630
title: 甘蓝型油菜全基因组重测序

description: 甘蓝型油菜双亲本以及后代混池重测序，分离群体200个单株基因组重测序
DOI: 10.26036/cnp0000703
title: Changes of Cell-free Echinococcus spp. DNA

description: Changes of Cell-free Echinococcus spp. DNA after chemotherapy.
DOI: 10.26036/cnp0001024
title: Litchi chinensis Genome

description: Lychee (Litchi chinensis Sonn.), which belongs to the flowering plant family Sapindaceae, is the second most important tropical fruit tree species worldwide and the most valuable fruit for which the edible portion is an aril. It is one of the most important woody fruit tree species that is cultivated in tropical regions for global commerce. We sequenced the genome of the cultivar ‘Feizixiao’ and assembled a ~470 megabase reference genome of 15 pseudo-chromosomes. The extremely high heterozygosity of ‘Feizixiao’ (2.27%) enabled us to obtain two distinct haplotypes.
DOI: 10.26036/cnp0001253
title: Genome survey and reference gene construction of the bloom-forming toxic dinoflagellate Dinophysis acuminata

description: In this project, we performed transcriptome-sequencing for the cultures of Dinophysis acuminata. We also performed genome-sequencing for DNA extracted from Dinophysis acuminata.
DOI: 10.26036/cnp0002664
title: 髓核单细胞测序矩阵

description: 我们对5例椎间盘病人和1例正常对照的髓核组织进行了单细胞测序，公开相关表达矩阵用于学术交流。
DOI: 10.26036/cnp0002674
title: Chlamydomonas Mutant hpm91 Lacking PGR5 is a Scalable and Valuable Strain for Algal Hydrogen (H2) Production

description: Renewable hydrogen (H2) photoproduction by Chlamydomonas reinhardtii offers an attractive approach virtually driven by solar energy. However, it is currently not scalable due to lacking ideal strains that hindered mainly by insufficient knowledge of the molecular regulation mechanism. Previously, we have reported a Chlamydomonas PGR5-deficient mutant named hpm91 capable of prolonged H2 production for 25 days with more than 30-fold yield increase relative to its wild type in 100 ml set-ups. Here, we report that hpm91 is largely scalable and valuable in terms of key issues in algal-H2 production. Up to 100-fold extention of H2-photobioreacter (HPBR; 10 L) was established, leading to an average of H2 output 7287 ml/10L-HPBR during 26 days of sulfur deprivation. We found that hpm91 was robust and remained metabolically active over a long period of sulfur deprivation, most likely due to decreased intracellular ROS relative to wild type. To understand the molecular mechanism of H2 metabolism underlying in hpm91, we performed iTRAQ quantitative proteomics and compared proteomic change profiles of wild type and hpm91 that undergo H2 production process. Major proteome changes of hpm91, based on identified differentially expressed proteins with known function, include modifications in photosynthetic antanna, primary metabolic pathways and anti-ROS responses. Together with successful isolation of new strain(s) with enhanced H2-producing capability relative to hpm91, we highlight that the strain (hpm91) is not only up-scalable but also valuable in both basic and applied research aiming at elucidation of the molecular regulation mechanisms of H2 photoproduction and development of advanced algal-H2 photoproduction biotechnology.
DOI: 10.26249/fk2/ujwlj2/ux09cw
title: goal_processing_pipeline.zip

description: Archive with data, documentation, and code.
DOI: 10.26249/fk2/ujwlj2
title: Students' Educational Goals in Natural Language

description: We built this dataset is on 2.262 student goals in natural language, collected at the Universities of Bremen, Hannover, and Osnabrück in 2019. Six independent raters assigned tags from a set of 28 to those goals. The dataset includes the complete data processing pipeline, from raw data to results and figures generated by a data analysis script written in Python. The README.md file describes folders, files, and processing.
DOI: 10.26036/cnp0002656
title: RNA-Seq of cotton fiber development

description: RNA-Seq data of ovule or fiber at ten time points during fiber development in three cotton cultivars, G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124 and acc. 3-79.
DOI: 10.26036/cnp0002668
title: Mus musculus strain:BALB/c Raw sequence reads

description: Angiostrongylus cantonensis (A. cantonensis) infection can result in increased risk of eosinophilic meningitis. Accumulation of eosinophils and inflammation can result in the A. cantonensis infection playing an important role in brain tissue injury during this pathological process. However, underlying mechanisms regarding the transcriptomic responses during brain tissue injury caused by A. cantonensis infection are yet to be elucidated. This study is aimed at identifying and transcriptomic factors influencing the accumulation of eosinophils and inflammation in the mouse brain infected with larval A. cantonensis (0d, 2d, 7d, 14d and 21d).
DOI: 10.26036/cnp0002672
title: Euglena gracilis promotes Lactobacillus growth and antioxidants accumulation as a potential next generation prebiotic

description: Euglena gracilis promotes Lactobacillus growth and antioxidants accumulation as a potential next generation prebiotic
DOI: 10.26249/fk2/yyidke/5rsbiy
title: siddata_study_assistant_donated_userdata_p2.csv

description: :unav
DOI: 10.26036/cnp0000939
title: The genome assembly and annotation of Zea mays cultivar inbred line RP125

description: Using Nanopore long reads, Illumina short reads, and Hi-C data to assemble the genome of maize inbred line, RP125. Using RNAseq data to annotate the assembly.
DOI: 10.26249/fk2/yyidke
title: Siddata Study Assistant Dataset from Prototpye 2.0

description: We collected these data from user interaction with version 2.0 of the SIDDATA study assistant software. Students from three German universities used the software, and the dataset contains data from all three universities, only from those students who explicitly agreed to donate their data. Data aggregation occurred over the course of 11 months, from December 2020 to November 2021. The dataset consists of one .csv file with 41.520 rows representing one activity. The semantics and the context of data acquisition are described in detail in the related publication.
DOI: 10.26036/cnp0002679
title: DNBSEQ-T7_WGS_PE150_PCR-free_NA12878

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。 PCR-free文库，读长PE150，ECR3.1， AD153接头。
DOI: 10.25345/c5tx3567j
title: MassIVE Reanalysis RMSV000000354.3279 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ARL4C [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.5281/zenodo.6011689
title: PEATCLSM_Trop: Integrating peat-specific land surface hydrology of natural and drained tropical peatlands in the GEOS CLSM framework

description: The datasets archived here include simulation results shown in the peer-reviewed article “Tropical peatland hydrology simulated with a global land surface model“, published in the open access AGU Journal of Advances in Modeling Earth Systems (JAMES; Apers et al., 2022). The output was produced using the Catchment land surface model (CLSM), the land model component of the NASA Goddard Earth Observing System (GEOS) modeling framework, and various versions of peatland-specific adaptations of CLSM, i.e. PEATCLSM. Here, we provide netCDF files (*.nc or *.nc4c) for CLSM, the natural (PEATCLSM<sub>Trop,Nat</sub>), and drained (PEATCLSM<sub>Trop,Drain</sub>) tropical versions of PEATCLSM. The simulations are at a 9-km spatial resolution (EASEv2 grid) for the three major tropical peatland regions in Central and South America, the Congo Basin, and Southeast Asia, using a peat grid cell distribution that is a combination of the PEATMAP distribution from Xu et al. (2018) and the peat distribution from De Lannoy et al. (2014). Simulations with the northern version of PEATCLSM (PEATCLSM<sub>North,Nat</sub>) are not included in the archived dataset but can be obtained upon request. We provide three types of netCDF files:<br> • daily_images_*.nc4c: daily land states and fluxes for variables discussed in Apers et al., (2022; Table 1), provided as netCDF image-chunked image stack;<br> • daily_mean_*.nc: 20-year mean of the land states and fluxes (Table 1), provided as a single netCDF image;<br> • daily_std_*.nc: 20-year standard deviation of the land states and fluxes (Table 1), provided as a single netCDF image. The file content is described in the file PEATCLSM_Trop-Simulations.pdf. Please contact Sebastian Apers (sebastian.apers@kuleuven.be) or Michel Bechtold (michel.bechtold@kuleuven.be) for any questions.<br> <br> References:<br> Apers, S., De Lannoy, G. J. M., Baird, A. J., Cobb, A. R., Dargie, G. C., del Aguila Pasquel, J., … others (2022). Tropical peatland hydrology simulated with a global land surface model. <em>Journal of Advances in Modeling Earth Systems</em>. https://doi.org/10.1029/2021MS002784<br> Bechtold, M., De Lannoy, G. J. M., Koster, R. D., Reichle, R. H., Mahanama, S. P., Bleuten, W., ... others (2019). PEAT-CLSM: A specific treatment of peatland hydrology in the NASA Catchment Land Surface Model. <em>Journal of Advances in Modeling Earth Systems, 11</em>(7), 2130–2162. https://doi.org/10.1029/2018MS001574<br> De Lannoy, G. J. M., Koster, R. D., Reichle, R. H., Mahanama, S. P. P., & Liu, Q. (2014). An updated treatment of soil texture and associated hydraulic properties in a global land modeling system. <em>Journal of Advances in Modeling Earth Systems, 6</em>(4), 957– 979. https://doi.org/10.1002/2014MS000330<br> Xu, J., Morris, P. J., Liu, J., & Holden, J. (2018). PEATMAP: Refining estimates of global peatland distribution based on a meta-analysis. <em>Catena, 160</em>, 134–140. https://doi.org/10.1016/j.catena.2017.09.010
DOI: 10.5281/zenodo.6011688
title: PEATCLSM_Trop: Integrating peat-specific land surface hydrology of natural and drained tropical peatlands in the GEOS CLSM framework

description: The datasets archived here include simulation results shown in the peer-reviewed article “Tropical peatland hydrology simulated with a global land surface model“, published in the open access AGU Journal of Advances in Modeling Earth Systems (JAMES; Apers et al., 2022). The output was produced using the Catchment land surface model (CLSM), the land model component of the NASA Goddard Earth Observing System (GEOS) modeling framework, and various versions of peatland-specific adaptations of CLSM, i.e. PEATCLSM. Here, we provide netCDF files (*.nc or *.nc4c) for CLSM, the natural (PEATCLSM<sub>Trop,Nat</sub>), and drained (PEATCLSM<sub>Trop,Drain</sub>) tropical versions of PEATCLSM. The simulations are at a 9-km spatial resolution (EASEv2 grid) for the three major tropical peatland regions in Central and South America, the Congo Basin, and Southeast Asia, using a peat grid cell distribution that is a combination of the PEATMAP distribution from Xu et al. (2018) and the peat distribution from De Lannoy et al. (2014). Simulations with the northern version of PEATCLSM (PEATCLSM<sub>North,Nat</sub>) are not included in the archived dataset but can be obtained upon request. We provide three types of netCDF files:<br> • daily_images_*.nc4c: daily land states and fluxes for variables discussed in Apers et al., (2022; Table 1), provided as netCDF image-chunked image stack;<br> • daily_mean_*.nc: 20-year mean of the land states and fluxes (Table 1), provided as a single netCDF image;<br> • daily_std_*.nc: 20-year standard deviation of the land states and fluxes (Table 1), provided as a single netCDF image. The file content is described in the file PEATCLSM_Trop-Simulations.pdf. Please contact Sebastian Apers (sebastian.apers@kuleuven.be) or Michel Bechtold (michel.bechtold@kuleuven.be) for any questions.<br> <br> References:<br> Apers, S., De Lannoy, G. J. M., Baird, A. J., Cobb, A. R., Dargie, G. C., del Aguila Pasquel, J., … others (2022). Tropical peatland hydrology simulated with a global land surface model. <em>Journal of Advances in Modeling Earth Systems</em>. https://doi.org/10.1029/2021MS002784<br> Bechtold, M., De Lannoy, G. J. M., Koster, R. D., Reichle, R. H., Mahanama, S. P., Bleuten, W., ... others (2019). PEAT-CLSM: A specific treatment of peatland hydrology in the NASA Catchment Land Surface Model. <em>Journal of Advances in Modeling Earth Systems, 11</em>(7), 2130–2162. https://doi.org/10.1029/2018MS001574<br> De Lannoy, G. J. M., Koster, R. D., Reichle, R. H., Mahanama, S. P. P., & Liu, Q. (2014). An updated treatment of soil texture and associated hydraulic properties in a global land modeling system. <em>Journal of Advances in Modeling Earth Systems, 6</em>(4), 957– 979. https://doi.org/10.1002/2014MS000330<br> Xu, J., Morris, P. J., Liu, J., & Holden, J. (2018). PEATMAP: Refining estimates of global peatland distribution based on a meta-analysis. <em>Catena, 160</em>, 134–140. https://doi.org/10.1016/j.catena.2017.09.010