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