Correlative light and soft X-ray tomography of in situ mesoscale heterochromatin structure in intact cells

Autor: Rajshikhar Gupta, Yagyik Goswami, Luezhen Yuan, Bibhas Roy, Eva Pereiro, GV Shivashankar

Publikováno v: Scientific Reports, Vol 14, Iss 1, Pp 1-14 (2024)

Abstract Heterochromatin organization is critical to many genome-related programs including transcriptional silencing and DNA repair. While super-resolution imaging, electron microscopy, and multiomics methods have provided indirect insights into the

Externí odkaz: https://doaj.org/article/fcb2c40d7d3f476189e7093443b7d1f4

Supplementary Table.1 from TGFβ Promotes Genomic Instability after Loss of RUNX3

Autor: Yoshiaki Ito, Jean-Paul Thiery, GV Shivashankar, Dominic C. Voon, Linda Shyue Huey Chuang, Amudha Ganesan, Doorgesh S. Jokhun, Haresh Sankar, Lavina Sierra Tay, Muhammad Bakhait Bin Rahmat, Madhura Kulkarni, Tuan Zea Tan, Yu Lin Chong, Vaidehi Krishnan

Supplementary Table 1 shows the differential expression analysis of RNA sequencing data. A list of genes that are differentially expressed upon TGF-beta treatment as well as upon RUNX3-Knockdown are shown.

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4f104ab82d80ece1dcb38d10e8859721
https://doi.org/10.1158/0008-5472.22417421.v1

Supplementary Information from TGFβ Promotes Genomic Instability after Loss of RUNX3

Autor: Yoshiaki Ito, Jean-Paul Thiery, GV Shivashankar, Dominic C. Voon, Linda Shyue Huey Chuang, Amudha Ganesan, Doorgesh S. Jokhun, Haresh Sankar, Lavina Sierra Tay, Muhammad Bakhait Bin Rahmat, Madhura Kulkarni, Tuan Zea Tan, Yu Lin Chong, Vaidehi Krishnan

Supplementary Methods, Legends for Supplementary Figures,Legend for Table 1 and References

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::339f1e99c26b9a276c5c647d2e7d63ee
https://doi.org/10.1158/0008-5472.22417424.v1

How enzymatic activity is involved in chromatin organization

Autor: Rakesh Das, Takahiro Sakaue, GV Shivashankar, Jacques Prost, Tetsuya Hiraiwa

Publikováno v: eLife, 11

Spatial organization of chromatin plays a critical role in genome regulation. Previously, various types of affinity mediators and enzymes have been attributed to regulate spatial organization of chromatin from a thermodynamics perspective. However, a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::aaced88f63be7aa9dea9a77a69eb7e5d

Unsupervised representation learning of chromatin images identifies changes in cell state and tissue organization in DCIS.

Autor: Zhang X; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, USA.; Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, USA., Venkatachalapathy S; Department of Health Sciences and Technology, ETH Zurich, Switzerland.; Laboratory of Nanoscale Biology, Paul Scherrer Institute, Villigen, Switzerland., Paysan D; Department of Health Sciences and Technology, ETH Zurich, Switzerland.; Laboratory of Nanoscale Biology, Paul Scherrer Institute, Villigen, Switzerland., Schaerer P; Department of Health Sciences and Technology, ETH Zurich, Switzerland.; Laboratory of Nanoscale Biology, Paul Scherrer Institute, Villigen, Switzerland., Tripodo C; Tumor Immunology Unit, University of Palermo, Palermo, Italy.; IFOM, FIRC Institute of Molecular Oncology, Milan, Italy., Uhler C; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, USA. cuhler@mit.edu.; Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, USA. cuhler@mit.edu., Shivashankar GV; Department of Health Sciences and Technology, ETH Zurich, Switzerland. gshivasha@ethz.ch.; Laboratory of Nanoscale Biology, Paul Scherrer Institute, Villigen, Switzerland. gshivasha@ethz.ch.

Publikováno v: Nature communications [Nat Commun] 2024 Jul 20; Vol. 15 (1), pp. 6112. Date of Electronic Publication: 2024 Jul 20.