Robust single-cell DNA methylome profiling with snmC-seq2

Autor: Chongyuan Luo, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, Joseph R. Nery, António Pinto-Duarte, Brian Bui, Conor Fitzpatrick, Carolyn O’Connor, Seth Ruga, Marc E. Van Eden, David A. Davis, Deborah C. Mash, M. Margarita Behrens, Joseph R. Ecker

Publikováno v: Nature Communications, Vol 9, Iss 1, Pp 1-6 (2018)

Single-cell DNA methylome profiling allows the study of epigenomic heterogeneity in tissues but has been impeded by library quality. Here the authors demonstrate snmC-seq2 which improves mapping, throughput and library complexity.

Externí odkaz: https://doaj.org/article/b58554dbcada4f7c8aeb1384ced312c3

Iterative single-cell multi-omic integration using online learning

Autor: April R Kriebel, Joshua D. Welch, Chao Gao, Sebastian Preissl, Joseph R. Ecker, Angeline Rivkin, Rosa Castanon, Justin P. Sandoval, Bing Ren, M. Margarita Behrens, Jialin Liu, Joseph R. Nery, Chongyuan Luo

Publikováno v: Nature Biotechnology. 39:1000-1007

Integrating large single-cell gene expression, chromatin accessibility and DNA methylation datasets requires general and scalable computational approaches. Here we describe online integrative non-negative matrix factorization (iNMF), an algorithm for

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::2804762e06021b3116650e1dc71d8790
https://doi.org/10.1038/s41587-021-00867-x

Genome and time-of-day transcriptome of Wolffia australiana link morphological extreme minimization with un-gated plant growth

Autor: Klaus-J. Appenroth, Douglas W. Bryant, Nolan Hartwick, Stefan Ortleb, K. Sowjanya Sree, Justin P. Sandoval, Joerg Fuchs, Florian Jupe, Todd C. Mockler, Erin Baggs, Ljudmylla Borisjuk, Ksenia V. Krasileva, Todd P. Michael, Sarah Gilbert, Philomena Chu, Eric Lam, Evan Ernst, Robert A. Martienssen, Joseph R. Ecker

Wolffia is the fastest growing plant genus on Earth with a recorded doubling time of less than a day. Wolffia has a dramatically reduced body plan, primarily growing through a continuous, budding-type asexual reproduction with no obvious phase transi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c04e2cbd68235cf5ecba88896faca26e

The complex architecture and epigenomic impact of plant T-DNA insertions

Autor: Joseph R. Nery, R. Keith Slotkin, Justin P. Sandoval, Huaming Chen, Florian Jupe, S. Timothy Motley, Mark Zander, Rosa Castanon, Todd P. Michael, Joseph R. Ecker, Angeline Rivkin

Publikováno v: PLoS Genetics, Vol 15, Iss 1, p e1007819 (2019)
PLoS Genetics

The bacterium Agrobacterium tumefaciens has been the workhorse in plant genome engineering. Customized replacement of native tumor-inducing (Ti) plasmid elements enabled insertion of a sequence of interest called Transfer-DNA (T-DNA) into any plant g

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2be47a08d2ce67d6231dd99358d93eab
https://doaj.org/article/95ab8fb90c2041d8ab9f191a2f75b785

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

Autor: Stanley Motley, Joseph R. Ecker, Florian Jupe, Olivier Loudet, Todd P. Michael, Detlef Weigel, Christa Lanz, Justin P. Sandoval, Felix Bemm

Publikováno v: Nature Communications
Nature Communications, Nature Publishing Group, 2018, 9, pp.1-8. ⟨10.1038/s41467-018-03016-2⟩
Nature Communications, Vol 9, Iss 1, Pp 1-8 (2018)
Nature Communications, 2018, 9, pp.1-8. ⟨10.1038/s41467-018-03016-2⟩
Nature Communications (9), 1-8. (2018)

The handheld Oxford Nanopore MinION sequencer generates ultra-long reads with minimal cost and time requirements, which makes sequencing genomes at the bench feasible. Here, we sequence the gold standard Arabidopsis thaliana genome (KBS-Mac-74 access

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7c0c14c198b908841ee1f23637623f43
https://hal.inrae.fr/hal-02626875