Zobrazeno 1 - 10
of 224
pro vyhledávání: '"Benjamin D. Humphreys"'
Publikováno v:
Scientific Data, Vol 11, Iss 1, Pp 1-12 (2024)
Abstract The three major anatomic regions of the human kidney include the cortex, medulla and papilla, with different functions and vulnerabilities to kidney diseases. Epigenetic mechanisms underlying these anatomic structures are incompletely unders
Externí odkaz:
https://doaj.org/article/fd3b9b06d50b4b74a97f852952e3bb5a
Autor:
Haikuo Li, Benjamin D. Humphreys
Publikováno v:
STAR Protocols, Vol 5, Iss 3, Pp 103049- (2024)
Summary: Simultaneous high-throughput ATAC and RNA expression with sequencing (SHARE-seq) profiles transcriptomics and chromatin accessibility in the same cells at high throughput. Here, we present a protocol for multimodal profiling of human kidneys
Externí odkaz:
https://doaj.org/article/930ab38c3e45410791f5d4a259aed2e9
Autor:
Nicolas Ledru, Parker C. Wilson, Yoshiharu Muto, Yasuhiro Yoshimura, Haojia Wu, Dian Li, Amish Asthana, Stefan G. Tullius, Sushrut S. Waikar, Giuseppe Orlando, Benjamin D. Humphreys
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-19 (2024)
Abstract Renal proximal tubule epithelial cells have considerable intrinsic repair capacity following injury. However, a fraction of injured proximal tubule cells fails to undergo normal repair and assumes a proinflammatory and profibrotic phenotype
Externí odkaz:
https://doaj.org/article/21b437906a8640e29bb0a46408938792
Autor:
Haojia Wu, Eryn E. Dixon, Qiao Xuanyuan, Juanru Guo, Yasuhiro Yoshimura, Chitnis Debashish, Anezka Niesnerova, Hao Xu, Morgane Rouault, Benjamin D. Humphreys
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-16 (2024)
Abstract Emerging spatially resolved transcriptomics technologies allow for the measurement of gene expression in situ at cellular resolution. We apply direct RNA hybridization-based in situ sequencing (dRNA HybISS, Cartana part of 10xGenomics) to co
Externí odkaz:
https://doaj.org/article/227cd3e034c34e63baed1ad49c0fbc42
Autor:
Haikuo Li, Benjamin D. Humphreys
Publikováno v:
Data in Brief, Vol 54, Iss , Pp 110431- (2024)
Cortex, medulla and papilla are three major human kidney anatomic structures and they harbour unique metabolic functions, but the underlying metabolomic profiles are largely unknown at spatial resolution. Here, we generated a spatially resolved metab
Externí odkaz:
https://doaj.org/article/89f29254353542f4b1c7de9c16286a1d
Mosaic loss of Y chromosome is associated with aging and epithelial injury in chronic kidney disease
Autor:
Parker C. Wilson, Amit Verma, Yasuhiro Yoshimura, Yoshiharu Muto, Haikuo Li, Nicole P. Malvin, Eryn E. Dixon, Benjamin D. Humphreys
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-27 (2024)
Abstract Background Mosaic loss of Y chromosome (LOY) is the most common chromosomal alteration in aging men. Here, we use single-cell RNA and ATAC sequencing to show that LOY is present in the kidney and increases with age and chronic kidney disease
Externí odkaz:
https://doaj.org/article/551e6c9819dd473baf7dff771a4e8c17
Autor:
Seong Kyu Han, Michelle T. McNulty, Christopher J. Benway, Pei Wen, Anya Greenberg, Ana C. Onuchic-Whitford, Nephrotic Syndrome Study Network (NEPTUNE), Dongkeun Jang, Jason Flannick, Noël P. Burtt, Parker C. Wilson, Benjamin D. Humphreys, Xiaoquan Wen, Zhe Han, Dongwon Lee, Matthew G. Sampson
Publikováno v:
Nature Communications, Vol 14, Iss 1, Pp 1-16 (2023)
Abstract Expression quantitative trait locus (eQTL) studies illuminate genomic variants that regulate specific genes and contribute to fine-mapped loci discovered via genome-wide association studies (GWAS). Efforts to maximize their accuracy are ongo
Externí odkaz:
https://doaj.org/article/7d29a604d3e4432e9d83b826b3e053bc
Autor:
Yige Wu, Nadezhda V. Terekhanova, Wagma Caravan, Nataly Naser Al Deen, Preet Lal, Siqi Chen, Chia-Kuei Mo, Song Cao, Yize Li, Alla Karpova, Ruiyang Liu, Yanyan Zhao, Andrew Shinkle, Ilya Strunilin, Cody Weimholt, Kazuhito Sato, Lijun Yao, Mamatha Serasanambati, Xiaolu Yang, Matthew Wyczalkowski, Houxiang Zhu, Daniel Cui Zhou, Reyka G. Jayasinghe, Daniel Mendez, Michael C. Wendl, David Clark, Chelsea Newton, Yijun Ruan, Melissa A. Reimers, Russell K. Pachynski, Chris Kinsinger, Scott Jewell, Daniel W. Chan, Hui Zhang, Aadel A. Chaudhuri, Milan G. Chheda, Benjamin D. Humphreys, Mehdi Mesri, Henry Rodriguez, James J. Hsieh, Li Ding, Feng Chen
Publikováno v:
Nature Communications, Vol 14, Iss 1, Pp 1-25 (2023)
Abstract Identifying tumor-cell-specific markers and elucidating their epigenetic regulation and spatial heterogeneity provides mechanistic insights into cancer etiology. Here, we perform snRNA-seq and snATAC-seq in 34 and 28 human clear cell renal c
Externí odkaz:
https://doaj.org/article/f1e225c958cf48d29abdb4ad3857630a
Autor:
Gabriel Khelifi, Theresa Chow, Jennifer Whiteley, Victoire Fort, Benjamin D. Humphreys, Samer M.I. Hussein, Ian M. Rogers
Publikováno v:
Scientific Reports, Vol 12, Iss 1, Pp 1-15 (2022)
Abstract The majority of nucleated somatic cells can be reprogrammed to induced pluripotent stem cells (iPSCs). The process of reprogramming involves epigenetic remodelling to turn on pluripotency-associated genes and turn off lineage-specific genes.
Externí odkaz:
https://doaj.org/article/738933756aa04e2099e7caff6f1ea857
Autor:
Yoshiharu Muto, Eryn E. Dixon, Yasuhiro Yoshimura, Haojia Wu, Kohei Omachi, Nicolas Ledru, Parker C. Wilson, Andrew J. King, N. Eric Olson, Marvin G. Gunawan, Jay J. Kuo, Jennifer H. Cox, Jeffrey H. Miner, Stephen L. Seliger, Owen M. Woodward, Paul A. Welling, Terry J. Watnick, Benjamin D. Humphreys
Publikováno v:
Nature Communications, Vol 13, Iss 1, Pp 1-19 (2022)
Autosomal dominant polycystic kidney disease (ADPKD) is a complicated disease that involves numerous cell types. Here the authors used a multiomics approach consisting of single nucleus transcriptomes and epigenomes to redefine cell states in ADPKD a
Externí odkaz:
https://doaj.org/article/7703e88d9d3a4383b2b0dd9ea8ab76ec