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CNSA: a data repository for archiving omics data

Xueqin Guo, Fengzhen Chen, Fei Gao, Ling Li, Ke Liu, Lijin You, Cong Hua, Fan Yang, Wanliang Liu, Chunhua Peng, Lina Wang, Xiaoxia Yang (+14 others)
2020 Database: The Journal of Biological Databases and Curation  
Complying with the data standards commonly used in the life sciences, CNSA is committed to building a comprehensive and curated data repository for storing, managing and sharing of omics data.  ...  Here, relying on China National GeneBank (CNGB), we present CNGB Sequence Archive (CNSA) for archiving omics data, including raw sequencing data and its further analyzed results which are organized into  ...  Acknowledgements We gratefully thank other colleagues in the CNGB who helped to create and maintain the CNSA.  ... 
doi:10.1093/database/baaa055 pmid:32705130 fatcat:sgmpgg3fnze2pdyokgsfm2ngau

CNSA: a data repository for archiving omics data [article]

Xueqin Guo, Fengzhen Chen, Fei Gao, Ling Li, Ke Liu, Lijin You, Cong Hua, Fan Yang, Wanliang Liu, Chunhua Peng, Lina Wang, Xiaoxia Yang (+14 others)
2020 bioRxiv   pre-print
Here, relying on China National GeneBank (CNGB), we present CNGB Sequence Archive (CNSA) for archiving omics data, including raw sequencing data and its analytical data and related metadata which are organized  ...  Complying with the data standards commonly used in the life sciences, CNSA is committed to improving the data standards and building a comprehensive and curated data repository for the storage, management  ...  Acknowledgements We gratefully thank other colleagues in the CNGB who helped to create and maintain the CNSA.  ... 
doi:10.1101/2020.04.07.030833 fatcat:vmy7cw2qpzabdbdzak66etlfwq

Development of next-generation sequencing-based sterility test [article]

Jianhui Yue, Chao Chen, Xiaohuan Jing, Qiwang Ma, Bo Li, Xi Zhang
2020 bioRxiv   pre-print
Overall, the NGSST can serve as a promising alternative for sterility testing of biological products.  ...  An alternative method that can significantly shorten the detection time and improve the accuracy is in urgent need to meet the sterility testing requirements of regenerative medicine products with a short  ...  CNSA: a data repository for archiving omics data. Database (Oxford) 2020. 387 30 Chen FZ, You LJ, Yang F, et al.  ... 
doi:10.1101/2020.12.27.424516 fatcat:myddcudqdnbyrivgq3ijwrmthe

Microbiome definition re-visited: old concepts and new challenges

Gabriele Berg, Daria Rybakova, Doreen Fischer, Tomislav Cernava, Marie-Christine Champomier Vergès, Trevor Charles, Xiaoyulong Chen, Luca Cocolin, Kellye Eversole, Gema Herrero Corral, Maria Kazou, Linda Kinkel (+22 others)
2020 Microbiome  
of data resulting in a more rapid transfer of knowledge from basic science into practice.  ...  Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might  ...  Lalles (Paris) for their critical reading and helpful comments on the manuscript.  ... 
doi:10.1186/s40168-020-00875-0 pmid:32605663 pmcid:PMC7329523 fatcat:n22hpicp4bdxboxwnijtllee3q

ChromInst: A single cell sequencing technique to accomplish pre-implantation comprehensive chromosomal screening overnight

Fang-Fang Gao, Li Chen, Shi-Ping Bo, Ya-Xin Yao, Zhong-Li Xu, Qing-Yu Ding, Peng Zhang, Si-Jia Lu, Jun Ren
2021 PLoS ONE  
We then validated the feasibility of ChromInst for overnight PCCS assay by examining 14 voluntary donated embryo biopsy samples in a single sequencing run of Miseq with merely 13M reads production.  ...  The good compatibility of ChromInst with the restriction of Illumina sequencing technique along with the good library yield uniformity resulted superior data usage efficiency and reads distribution evenness  ...  The R Project for Statistical Computing. Available from: http://www.r-project.org/. 44. Guo X, Chen F, Gao F, Li L, Liu K, You L, et al. CNSA: a data repository for archiving omics data.  ... 
doi:10.1371/journal.pone.0251971 pmid:34015059 pmcid:PMC8136696 fatcat:evqbqmmnefdqpo4ntwz6lc4hiy

An ATAC-seq atlas of chromatin accessibility in mouse tissues [article]

Chuanyu Liu, Mingyue Wang, Xiaoyu Wei, Liang Wu, Jiangshan Xu, Xi Dai, Jun Xia, Mengnan Cheng, Yue Yuan, Pengfan Zhang, Jiguang Li, Taiqing Feng (+7 others)
2019 bioRxiv   pre-print
A comprehensive reference of ATAC-seq datasets for mammalian tissues is important for the understanding of regulatory specificity and developmental abnormality caused by genetic or environmental alterations  ...  AbstractThe Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a fundamental epigenomics approach and has been widely used in profiling the chromatin accessibility dynamics in multiple  ...  All raw data have been 148 submitted to the CNGB Nucleotide Sequence Archive 40 . The raw data have also been 149 submitted to the NCBI Sequence Read Archive 41 .  ... 
doi:10.1101/582171 fatcat:uztyabygcrawxi6bczwdepibbe

Characteristics and Clinical Significance of T-Cell Receptor Repertoire in Hepatocellular Carcinoma

Zifei Wang, Yu Zhong, Zefan Zhang, Kaiqian Zhou, Zhihao Huang, Hao Yu, Longqi Liu, Shiping Liu, Huanming Yang, Jian Zhou, Jia Fan, Liang Wu (+1 others)
2022 Frontiers in Immunology  
Our study describes the characteristics of tissue infiltration and circulating T-cell bank in patients with HCC and shows the potential of using circulating TCR sequence as a biomarker for the non-invasive  ...  Moreover, we reveal that HCC patients have a unique profile of TCR repertoire in peripheral blood in contrast to healthy individuals.  ...  All authors listed have made a substantial, direct, and intellectual contribution to the work and approved it for publication.  ... 
doi:10.3389/fimmu.2022.847263 pmid:35371059 pmcid:PMC8965762 fatcat:nhhjsokwxbeq7l6cn6m67wfxju

Distinct gut metagenomics and metaproteomics signatures in prediabetics and treatment-naïve type 2 diabetics [article]

Huanzi Zhong, Huahui Ren, Yan Lu, Chao Fang, Guixue Hou, Ziyi Yang, Bing Chen, Fangming Yang, Yue Zhao, Zhun Shi, Baojing Zhao, Jiegen Wu (+18 others)
2019 biorxiv/medrxiv   pre-print
Method: We used a combination of in-depth metagenomics and metaproteomics analyses of faecal samples from treatment-naïve type 2 diabetic (TN-T2D, n=77), pre-diabetic (Pre-DM, n=80), and normal glucose  ...  Interpretation: Our findings suggest a complex, disease stage-dependent interplay between the gut microbiota and the host and emphasize the value of metaproteomics to gain further insight into interplays  ...  We gratefully acknowledge colleagues at BGI for DNA extraction, library preparation and shotgun sequencing experiments, and helpful discussions. Appendix A.  ... 
doi:10.1101/666263 fatcat:b67plpbhsbccxpmic74clx5i3e

Distinct gut metagenomics and metaproteomics signatures in prediabetics and treatment-naïve type 2 diabetics

Huanzi Zhong, Huahui Ren, Yan Lu, Chao Fang, Guixue Hou, Ziyi Yang, Bing Chen, Fangming Yang, Yue Zhao, Zhun Shi, Baojin Zhou, Jiegen Wu (+18 others)
2019 EBioMedicine  
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ...  We used a combination of in-depth metagenomics and metaproteomics analyses of faecal samples from treatment-naïve type 2 diabetic (TN-T2D, n = 77), pre-diabetic (Pre-DM, n = 80), and normal glucose tolerant  ...  We gratefully acknowledge colleagues at BGI for DNA extraction, library preparation and shotgun sequencing experiments, and helpful discussions. Appendix A.  ... 
doi:10.1016/j.ebiom.2019.08.048 pmid:31492563 pmcid:PMC6796533 fatcat:ic2nvljrm5atvk7cg3l5nof7hi

Single-cell transcriptional profiling reveals cellular and molecular divergence in human maternal-fetal interface [article]

Quanlei Wang, Jinlu Li, Shengpeng Wang, Qiuting Deng, Yanru An, Yanan Xing, Xi Dai, Zelong Li, Qiwang Ma, Kuixing Wang, Chuanyu Liu, Yue Yuan (+7 others)
2022 bioRxiv   pre-print
Further, by integrating analysis with the first-trimester placental single cell transcriptome data, we revealed that a subpopulation of trophoblast progenitor-like cells (TPLCs) existed in the full-term  ...  Together, our study offers important resources for better understanding of human placenta, stem cell-based therapy as well as PE, and provides new insights on the study of tissue heterogeneity, the clinical  ...  For instance, Roser Vento-tormo et al. revealed the cellular heterogeneity of the first-trimester placenta, and develop a repository of ligand-receptor complexes that are critical for placentation and  ... 
doi:10.1101/2022.02.15.479798 fatcat:dt4xpbynkjfjlmi6tqglnz7zm4