Contributors:mickish zhang, Dan-Ya Wu, Hui Zheng, Yao Wang, Qiao-Ran Sun, Xin Liu, Li-Yan Wang, Wen-Jing Xiong, Qiujun Wang, James D. P. Rhodes, Kai Xu, lijia li, zili LIN, Guang Yu, Weikun Xia, Bo Huang, zhenhai du, Yao Yao, Kim A. Nasmyth, Robert J. Klose, Yi-Liang Miao, Wei Xie
Somatic cell nuclear transfer (SCNT) can reprogram a somatic nucleus to a totipotent state. However, the re-organization of three-dimensional chromatin structure in this process remains poorly understood. Using low-input Hi-C, we revealed that during SCNT, the transferred nucleus first enters a mitotic-like state (premature chromatin condensation). Unlike fertilized embryos, SCNT embryos show stronger TADs at the 1-cell stage. TADs become weaker at the 2-cell stage, followed by gradual consolidation. Compartments A/B are markedly weak in 1-cell SCNT embryos and become increasingly strengthened afterward. By the 8-cell stage, somatic chromatin architecture is largely reset to embryonic patterns. Unexpectedly, we found cohesin represses minor zygotic genome activation (ZGA) genes (2-cell specific genes) in pluripotent and differentiated cells, and pre-depleting cohesin in donor cells facilitates minor ZGA and SCNT. These data reveal multi-step reprogramming of 3D chromatin architecture during SCNT and support dual roles of cohesin in TAD formation and minor ZGA repression.
Contributors:Joseph Kanja, Xiangwei Li, Andrew Hunter, Henry Brunskill, Rob Dwyer-Joyce
This data provides the reader with a sample of raw data and processed data which was used for the measurement of surface film thickness using a superimposed standing wave.
The reader is advised to refer to the research article "Non-contact measurement of the thickness of a surface film using a superimposed ultrasonic standing wave" for more information on this data and how to interpret it.
For the full database, please visit: www.projectipad.org
The 2011 accident at Japan’s Fukushima Daiichi Nuclear Power Plant released a considerable inventory of radioactive material into the local and global environments. While the vast majority of this contamination was in the form of gaseous and aerosol species, of which a large component was distributed out over the neighbouring Pacific Ocean (where is was subsequently deposited), a substantial portion of the radioactive release was in particulate form and was deposited across Fukushima Prefecture. To provide an underpinning understanding of the dynamics of this catastrophic accident, alongside assisting in the off-site remediation and eventual reactor decommissioning activities, the ‘International Particle Analysis Database’, or ‘IPAD’, was established to serve as an interactive repository for the continually expanding analysis dataset of the sub-mm ejecta particulate. In addition to a fully interrogatable database of analysis results for registered users (exploiting multiple search methods), the database also comprises an open-access front-end for members of the public to engage with the multi-national analysis activities by exploring a streamlined version of the data.
This dataset consists of raw sequencing data (fasta) and analysed relative abundance data (histograms of the dominant 10 species in respective taxonomic ranks ). This project shows the first bacterial diversity profiling of high-microbial-abundance wild tropical marine sponges of southern South China Sea, which are Aaptos aaptos and Xestospongia muta from Bidong and Redang islands, Malaysia. Marine sponges are acknowledged as a bacterial hotspot and resource of novel natural products or genetic material. However, sponge-associated bacteria are difficult to be cultivated and the production of their desirable metabolites are inadequate in terms of rate and quantity, yet bioinformatics and metagenomics tools are progressing. Therefore, the diversity profiling of bacterial communities in marine sponges reveals the approximate gene pool for the gene mining or isolation of bacteria that are potentially and commercially beneficial in manufacturing industry, medicine, or agriculture. The bacterial community data exploited from this project is useful for critical comparison through additional or integrated bioinformatics processing with other marine sponge-associated bacterial community profile data. The community data of this project also unveils some general physiological function of the sponge-associated bacterial assemblage in its local environment. In the data provided, the sponge-associated bacterial communities in A. aaptos of Pulau Bidong, A. aaptos of Pulau Redang, and X. muta of Pulau Bidong have been denoted by A, B, and M, respectively.
Contributors:Elia-Aguado Fraile, Evangelia Chavdoula, Georgios I. Laliotis, Vollter Anastas, Oksana Serebrennikova, Maria D. Paraskevopoulou, Philip N. Tsichlis
KDM2B is a JmjC domain H3K36me2/H3K36me1 demethylase, which immortalizes cells in culture and contributes to the biology of both embryonic and adult stem and progenitor cells. It also functions as an oncogene that contributes to the self-renewal of breast cancer stem cells by regulating polycomb complexes. Here we show that the silencing of KDM2B results in the downregulation of SNAI2 (SLUG), SNAI1 (SNAIL) and SOX9, which also contribute to the biology of mammary stem and progenitor cells. The downregulation of these molecules is posttranscriptional and in the case of the SNAI2-encoded SLUG, it is due to calpain-dependent proteolytic degradation. Mechanistically, the latter depends on the activation of calpastatin-sensitive classical calpain(s) and on the phosphorylation-dependent inhibition of GSK3 via paracrine mechanisms. GSK3 inhibition sensitizes its target SLUG to classical calpains, which are activated by Ca2+ influx and calpastatin down regulation. The degradation of SLUG, induced by the KDM2B knockdown, promotes the differentiation of breast cancer stem cells in culture and reveals an unexpected mechanism of stem cell regulation by a histone demethylase.
Contributors:Raquel de M. Barbosa, Marcelo A. C. Fernandes
The dataset provides five types of k-mers genome representation characterized as k-mers count 1D, k-mers probability 1D, k-mers count 2D, k-mers probability 2D, and k-mers image. The dataset is composed of 1557 virus instances of SARS-CoV-2. Besides, the dataset also provides a data stream of 11540 viruses from the Virus-Host DB dataset and the other three Riboviria viruses from NCBI (Betacoronavirus RaTG13, bat-SL-CoVZC45, and bat-SL-CoVZXC21).