DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci.

Autor: Liu Y; Department of Genome Sciences, University of Washington, Seattle, WA, USA.; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.; These authors contributed equally: Yuzhen Liu, Christopher D. McGann., McGann CD; Department of Genome Sciences, University of Washington, Seattle, WA, USA.; These authors contributed equally: Yuzhen Liu, Christopher D. McGann., Krebs M; Department of Genome Sciences, University of Washington, Seattle, WA, USA.; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA., Perkins TA Jr; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Fields R; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Camplisson CK; Department of Genome Sciences, University of Washington, Seattle, WA, USA.; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA., Nwizugbo DZ; Department of Genome Sciences, University of Washington, Seattle, WA, USA.; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA., Hsu C; Department of Genome Sciences, University of Washington, Seattle, WA, USA.; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA., Avanessian SC; Department of Genome Sciences, University of Washington, Seattle, WA, USA.; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA., Tsue AF; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.; Department of Pharmacology, University of Washington, Seattle, WA, USA.; Institute of Stem Cell and Regenerative Medicine, University of Washington, USA., Kania EE; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.; Department of Pharmacology, University of Washington, Seattle, WA, USA.; Institute of Stem Cell and Regenerative Medicine, University of Washington, USA., Shechner DM; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.; Department of Pharmacology, University of Washington, Seattle, WA, USA.; Institute of Stem Cell and Regenerative Medicine, University of Washington, USA., Beliveau BJ; Department of Genome Sciences, University of Washington, Seattle, WA, USA.; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.; Institute of Stem Cell and Regenerative Medicine, University of Washington, USA., Schweppe DK; Department of Genome Sciences, University of Washington, Seattle, WA, USA.; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.; Institute of Stem Cell and Regenerative Medicine, University of Washington, USA.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Jul 29. Date of Electronic Publication: 2024 Jul 29.

Designing Oligonucleotide-Based FISH Probe Sets with PaintSHOP.

Autor: Perez MW; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Camplisson CK; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Beliveau BJ; Department of Genome Sciences, University of Washington, Seattle, WA, USA. beliveau@uw.edu.; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA. beliveau@uw.edu.; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA. beliveau@uw.edu.

Publikováno v: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2024; Vol. 2784, pp. 177-189.

Author Correction: PaintSHOP enables the interactive design of transcriptome- and genome-scale oligonucleotide FISH experiments.

Autor: Hershberg EA; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Camplisson CK; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Close JL; Allen Institute for Brain Science, Seattle, WA, USA., Attar S; Department of Genome Sciences, University of Washington, Seattle, WA, USA.; Department of Pathology, University of Washington, Seattle, WA, USA., Chern R; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Liu Y; Department of Genome Sciences, University of Washington, Seattle, WA, USA.; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA., Akilesh S; Department of Pathology, University of Washington, Seattle, WA, USA., Nicovich PR; Allen Institute for Brain Science, Seattle, WA, USA.; Cajal Neuroscience Incorporated, Seattle, WA, USA., Beliveau BJ; Department of Genome Sciences, University of Washington, Seattle, WA, USA. beliveau@uw.edu.; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA. beliveau@uw.edu.

Publikováno v: Nature methods [Nat Methods] 2021 Oct; Vol. 18 (10), pp. 1265.

Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses.

Autor: Liu S; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA., Punthambaker S; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA., Iyer EPR; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA., Ferrante T; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA., Goodwin D; McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA., Fürth D; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA., Pawlowski AC; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA., Jindal K; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA., Tam JM; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA., Mifflin L; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA., Alon S; McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA., Sinha A; McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA., Wassie AT; McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA., Chen F; Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Broad Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA., Cheng A; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA., Willocq V; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA., Meyer K; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA., Ling KH; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.; Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia., Camplisson CK; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA., Kohman RE; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA., Aach J; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA., Lee JH; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA., Yankner BA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA., Boyden ES; McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USAHoward Hughes Medical Institute, Chevy Chase, MD 20815, USA., Church GM; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2021 Jun 04; Vol. 49 (10), pp. e58.