Zobrazeno 1 - 10 of 150 pro vyhledávání: '"Jason D Buenrostro"'
1
Akademický článek
Cell of origin epigenetic priming determines susceptibility to Tet2 mutation
Autor: Giulia Schiroli, Vinay Kartha, Fabiana M. Duarte, Trine A. Kristiansen, Christina Mayerhofer, Rojesh Shrestha, Andrew Earl, Yan Hu, Tristan Tay, Catherine Rhee, Jason D. Buenrostro, David T. Scadden
Publikováno v: Nature Communications, Vol 15, Iss 1, Pp 1-20 (2024)
Abstract Hematopoietic stem cell (HSC) mutations can result in clonal hematopoiesis (CH) with heterogeneous clinical outcomes. Here, we investigate how the cell state preceding Tet2 mutation impacts the pre-malignant phenotype. Using an inducible sys
Externí odkaz: https://doaj.org/article/b70a34db47874230850c2107fec82dd9
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2
Akademický článek
Deep learning-based enhancement of epigenomics data with AtacWorks
Autor: Avantika Lal, Zachary D. Chiang, Nikolai Yakovenko, Fabiana M. Duarte, Johnny Israeli, Jason D. Buenrostro
Publikováno v: Nature Communications, Vol 12, Iss 1, Pp 1-11 (2021)
ATAC-seq measures chromatin accessibility as a proxy for the activity of DNA regulatory regions across the genome. Here the authors present AtacWorks, a deep learning tool to denoise and identify accessible chromatin regions from low cell count, low-
Externí odkaz: https://doaj.org/article/f55c2ff4dc79402899937bfbce0e742c
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3
Akademický článek
Inference and effects of barcode multiplets in droplet-based single-cell assays
Autor: Caleb A. Lareau, Sai Ma, Fabiana M. Duarte, Jason D. Buenrostro
Publikováno v: Nature Communications, Vol 11, Iss 1, Pp 1-9 (2020)
It is assumed that single-cell analyses capture one barcode per cell. Here, the authors show that up to 21% of cell barcodes on the 10X Chromium scATAC-seq assay may be derived from barcode multiplets.
Externí odkaz: https://doaj.org/article/8d9d4ceede554e67a58633816a18d4ba
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4
Akademický článek
Protocol for single-cell ATAC sequencing using combinatorial indexing in mouse lung adenocarcinoma
Autor: Isabella Del Priore, Sai Ma, Jonathan Strecker, Tyler Jacks, Lindsay M. LaFave, Jason D. Buenrostro
Publikováno v: STAR Protocols, Vol 2, Iss 2, Pp 100583- (2021)
Summary: Single-cell ATAC sequencing using combinatorial indexing (sciATAC-seq) enables the identification of chromatin accessibility profiles at single-cell resolution with a dual-barcoding approach during transposition and library construction. Unl
Externí odkaz: https://doaj.org/article/a5d77e8692f1447982da45153e7cc119
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5
Akademický článek
Assessment of computational methods for the analysis of single-cell ATAC-seq data
Autor: Huidong Chen, Caleb Lareau, Tommaso Andreani, Michael E. Vinyard, Sara P. Garcia, Kendell Clement, Miguel A. Andrade-Navarro, Jason D. Buenrostro, Luca Pinello
Publikováno v: Genome Biology, Vol 20, Iss 1, Pp 1-25 (2019)
Abstract Background Recent innovations in single-cell Assay for Transposase Accessible Chromatin using sequencing (scATAC-seq) enable profiling of the epigenetic landscape of thousands of individual cells. scATAC-seq data analysis presents unique met
Externí odkaz: https://doaj.org/article/1ae37a2a47f74b2fb58bd9ef5d673685
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6
Akademický článek
Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM
Autor: Huidong Chen, Luca Albergante, Jonathan Y. Hsu, Caleb A. Lareau, Giosuè Lo Bosco, Jihong Guan, Shuigeng Zhou, Alexander N. Gorban, Daniel E. Bauer, Martin J. Aryee, David M. Langenau, Andrei Zinovyev, Jason D. Buenrostro, Guo-Cheng Yuan, Luca Pinello
Publikováno v: Nature Communications, Vol 10, Iss 1, Pp 1-14 (2019)
The increasing accessibility of single cell omics technologies beyond transcriptomics demands parallel advances in analysis. Here, the authors introduce STREAM, a pipeline for reconstruction and visualization of differentiation trajectories from both
Externí odkaz: https://doaj.org/article/a8fc084be2f940a8842ac27783508d69
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8
Akademický článek
Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis
Autor: Leif S. Ludwig, Caleb A. Lareau, Erik L. Bao, Satish K. Nandakumar, Christoph Muus, Jacob C. Ulirsch, Kaitavjeet Chowdhary, Jason D. Buenrostro, Narla Mohandas, Xiuli An, Martin J. Aryee, Aviv Regev, Vijay G. Sankaran
Publikováno v: Cell Reports, Vol 27, Iss 11, Pp 3228-3240.e7 (2019)
Summary: Human erythropoiesis serves as a paradigm of physiologic cellular differentiation. This process is also of considerable interest for better understanding anemias and identifying new therapies. Here, we apply deep transcriptomic and accessibl
Externí odkaz: https://doaj.org/article/6398f2df4d4c4128b606c247249494a4
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