Zobrazeno 1 - 10
of 13
pro vyhledávání: '"Ryan M Mulqueen"'
Autor:
Hao Zhang, Ryan M. Mulqueen, Natalie Iannuzo, Dominique O. Farrera, Francesca Polverino, James J. Galligan, Julie G. Ledford, Andrew C. Adey, Darren A. Cusanovich
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-41 (2024)
Abstract We develop a large-scale single-cell ATAC-seq method by combining Tn5-based pre-indexing with 10× Genomics barcoding, enabling the indexing of up to 200,000 nuclei across multiple samples in a single reaction. We profile 449,953 nuclei acro
Externí odkaz:
https://doaj.org/article/45dac0a06c854b82a3eca3eae9b2d359
Autor:
Ruth V. Nichols, Brendan L. O’Connell, Ryan M. Mulqueen, Jerushah Thomas, Ashley R. Woodfin, Sonia Acharya, Gail Mandel, Dmitry Pokholok, Frank J. Steemers, Andrew C. Adey
Publikováno v:
Nature Communications, Vol 13, Iss 1, Pp 1-10 (2022)
Despite the importance of DNA methylation, accessible and high-throughput methods to profile methylation at the single-cell level are lacking. Here, the authors present sciMETv2, a high-throughput workflow that provides high-quality single-cell methy
Externí odkaz:
https://doaj.org/article/819c0be9d5a24f45850610d10e5f6cef
Autor:
Casey A. Thornton, Ryan M. Mulqueen, Kristof A. Torkenczy, Andrew Nishida, Eve G. Lowenstein, Andrew J. Fields, Frank J. Steemers, Wenri Zhang, Heather L. McConnell, Randy L. Woltjer, Anusha Mishra, Kevin M. Wright, Andrew C. Adey
Publikováno v:
Nature Communications, Vol 12, Iss 1, Pp 1-16 (2021)
Spatial orientation of cells in an interconnected network is lost in high-throughput single-cell epigenomic assays. Here the authors present sciMAP-ATAC to produce spatially resolved single-cell ATAC-seq data.
Externí odkaz:
https://doaj.org/article/1ad12e0e2a2a4ba0b41d734d7e7f4e32
Autor:
Aysegul Ors, Alex Daniel Chitsazan, Aaron Reid Doe, Ryan M Mulqueen, Cigdem Ak, Yahong Wen, Syber Haverlack, Mithila Handu, Spandana Naldiga, Joshua C Saldivar, Hisham Mohammed
Publikováno v:
Nucleic Acids Research. 50:11492-11508
Breast cancers are known to be driven by the transcription factor estrogen receptor and its ligand estrogen. While the receptor's cis-binding elements are known to vary between tumors, heterogeneity of hormone signaling at a single-cell level is unkn
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::94c80d95c4fc8fe7696044752c46ea05
https://doi.org/10.1093/nar/gkac908
https://doi.org/10.1093/nar/gkac908
Autor:
Hao Zhang, Ryan M. Mulqueen, Natalie Iannuzo, Dominique O. Farrera, Francesca Polverino, James J. Galligan, Julie G. Ledford, Andrew C. Adey, Darren A. Cusanovich
Measuring chromatin accessibility is a powerful method to identify cell types and states. Performed at single-cell resolution, this assay has generated catalogs of genome-wide DNA regulatory sites, whole-organism cell atlases, and dynamic chromatin r
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::442eda35c864de17b24ddb9f94d423b4
https://doi.org/10.1101/2023.05.11.540245
https://doi.org/10.1101/2023.05.11.540245
Autor:
Brendan O'Connell, Rosalie C. Sears, Frank J. Steemers, Brian J. O'Roak, Andrew Adey, Ryan M. Mulqueen, Casey A. Thornton, Galip Gürkan Yardımcı, Dmitry K. Pokholok, Jason Link, Fan Zhang
Publikováno v:
Nature biotechnology
Single-cell genomics assays have emerged as a dominant platform for interrogating complex biological systems. Methods to capture various properties at the single-cell level typically suffer a tradeoff between cell count and information content, which
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::45b0e12b8aa035bd5e0242804c99517d
https://doi.org/10.1038/s41587-021-00962-z
https://doi.org/10.1038/s41587-021-00962-z
Autor:
Heather L. McConnell, Andrew Adey, Randy Woltjer, Casey A. Thornton, Anusha Mishra, Frank J. Steemers, Kristof A. Torkenczy, Ryan M. Mulqueen, Eve G. Lowenstein, Kevin M. Wright, Andrew Nishida, Andrew J. Fields, Wenri Zhang
Publikováno v:
Nature Communications, Vol 12, Iss 1, Pp 1-16 (2021)
Nature Communications
Nature Communications
High-throughput single-cell epigenomic assays can resolve cell type heterogeneity in complex tissues, however, spatial orientation is lost. Here, we present single-cell combinatorial indexing on Microbiopsies Assigned to Positions for the Assay for T
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e251c5a8208482da7af5a4672eddbb47
https://doaj.org/article/1ad12e0e2a2a4ba0b41d734d7e7f4e32
https://doaj.org/article/1ad12e0e2a2a4ba0b41d734d7e7f4e32
Generation of Tn5 transposome, protein purification and loading for the sci- family of protocols. Protein purification of pTXB1.Tn5 transformed into T7 Express LysY (NEB C3031) cells; reference is PTXB1-Tn5 Addgene #60240 from Picelli et al. Genome R
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::b893b388e36458007ea224876e59b771
https://doi.org/10.17504/protocols.io.6kthcwn
https://doi.org/10.17504/protocols.io.6kthcwn
Autor:
Frank J. Steemers, Andrew Adey, Xiaolin Nan, Brooke A. DeRosa, Brian J. O'Roak, Ramesh Ramji, Ryan M. Mulqueen, Zeynep Sayar, Casey A. Thornton, Kevin M. Wright, Andrew J. Fields, Kristof A. Torkenczy
Development is a complex process that requires the precise modulation of regulatory gene networks controlled through dynamic changes in the epigenome. Single-cell-omic technologies provide an avenue for understanding the mechanisms of these processes
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e370110de18172692e3a4206f0c38f90
https://doi.org/10.1101/637256
https://doi.org/10.1101/637256
Autor:
Andrew Adey, Michael W. Linhoff, Frank J. Steemers, Cole Trapnell, Hannah A. Pliner, Ryan M. Mulqueen, John R. Sinnamon, Gail Mandel, Sarah A. Vitak, Kristof A. Torkenczy
Publikováno v:
Genome research. 29(5)
Here we present a comprehensive map of the accessible chromatin landscape of the mouse hippocampus at single-cell resolution. Substantial advances of this work include the optimization of a single-cell combinatorial indexing assay for transposase acc
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2eb3be05f45cb75b1a8856fb228db753
https://pubmed.ncbi.nlm.nih.gov/30936163
https://pubmed.ncbi.nlm.nih.gov/30936163