Výsledky vyhledávání - "Harold, Swerdlow"

Akademický článek

Direct sequencing of small genomes on the Pacific Biosciences RS without library preparation

Autor: Paul Coupland, Tamir Chandra, Mike Quail, Wolf Reik, Harold Swerdlow

Publikováno v: BioTechniques, Vol 53, Iss 6, Pp 365-372 (2012)

We have developed a sequencing method on the Pacific Biosciences RS sequencer (the PacBio) for small DNA molecules that avoids the need for a standard library preparation. To date this approach has been applied toward sequencing single-stranded and d

Externí odkaz: https://doaj.org/article/b215e4d024064e8298a2f38818ba0098

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Single-cell stabilization method identifies gonadotrope transcriptional dynamics and pituitary cell type heterogeneity

Autor: Hanna Pincas, Nadejda M. Tsankova, Yongchao Ge, Stuart C. Sealfon, Peter Smibert, Harold Swerdlow, Jessica Tome-Garcia, Venugopalan D. Nair, Gregory R. Smith, Boris M. Hartmann, Michel Zamojski, Miguel Fribourg, Daniel J. Bernard, Chirine Toufaily, Marlon Stoeckius, Frederique Ruf-Zamojski, William Stephenson, Judith L Turgeon

Publikováno v: Ruf-Zamojski, Frederique; Ge, Yongchao; Nair, Venugopalan; Zamojski, Michel; Pincas, Hanna; Toufaily, Chirine; et al.(2018). Single-cell stabilization method identifies gonadotrope transcriptional dynamics and pituitary cell type heterogeneity.. Nucleic acids research, 46(21), 11370-11380. doi: 10.1093/nar/gky991. UC Davis: Retrieved from: http://www.escholarship.org/uc/item/273146m1
Nucleic Acids Research

Immediate-early response genes (IEGs) are rapidly and transiently induced following an extracellular signal. Elucidating the IEG response patterns in single cells (SCs) requires assaying large numbers of timed samples at high accuracy while minimizin

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cd3fa7c20459fe142498d9fa3e7c3beb
https://doi.org/10.1093/nar/gky991

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Simultaneous epitope and transcriptome measurement in single cells

Autor: Christoph Hafemeister, Brian Houck-Loomis, Marlon Stoeckius, Peter Smibert, Harold Swerdlow, William Stephenson, Rahul Satija, Pratip K. Chattopadhyay

Publikováno v: Nature Methods. 14:865-868

High-throughput single-cell RNA sequencing has transformed our understanding of complex cell populations, but it does not provide phenotypic information such as cell-surface protein levels. Here, we describe cellular indexing of transcriptomes and ep

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::4687e8c07104c37a93708aa80c9ebc48
https://doi.org/10.1038/nmeth.4380

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Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation

Autor: Bernadette Bracken, Cristina Rozo, Andrew Butler, William Stephenson, Ali Rashidfarrokhi, Dana E. Orange, Rahul Satija, Lionel B. Ivashkiv, Vivian P. Bykerk, Laura T. Donlin, Susan M. Goodman, Harold Swerdlow, Robert B. Darnell

Publikováno v: Nature Communications
Nature Communications, Vol 9, Iss 1, Pp 1-10 (2018)

Droplet-based single-cell RNA-seq has emerged as a powerful technique for massively parallel cellular profiling. While this approach offers the exciting promise to deconvolute cellular heterogeneity in diseased tissues, the lack of cost-effective and

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0cbcfe075726225592f1055698c27485
http://europepmc.org/articles/PMC5824814

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Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low cost microfluidic instrumentation

Autor: Dana E. Orange, Lionel B. Ivashkiv, Laura T. Donlin, Robert B. Darnell, Ali Rashidfarrokhi, Andrew Butler, Rahul Satija, William Stephenson, Cristina Rozo, Susan M. Goodman, Harold Swerdlow, Vivian P. Bykerk

Droplet-based single cell RNA-seq has emerged as a powerful technique for massively parallel cellular profiling. While these approaches offer the exciting promise to deconvolute cellular heterogeneity in diseased tissues, the lack of cost-effective,

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0306f4b8f8f08b9b649a432ce156e01e

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Large-scale simultaneous measurement of epitopes and transcriptomes in single cells

Autor: Marlon Stoeckius, Christoph Hafemeister, William Stephenson, Brian Houck-Loomis, Pratip K. Chattopadhyay, Harold Swerdlow, Rahul Satija, Peter Smibert

Recent high-throughput single-cell sequencing approaches have been transformative for understanding complex cell populations, but are unable to provide additional phenotypic information, such as protein levels of well-established cell-surface markers

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4c54935309a4063a9edf97e73ce35a94
https://doi.org/10.1101/113068

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The variant call format and VCFtools

Publikováno v: Bioinformatics

Summary: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::838dedd304e128d267677f60ba564747
https://ora.ox.ac.uk/objects/uuid:065b1c9a-2a19-4ea2-b5e7-5802d0d3496d

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An In-Solution Hybridisation Method for the Isolation of Pathogen DNA from Human DNA-rich Clinical Samples for Analysis by NGS

Autor: Arjen M. Dondorp, Harold Swerdlow, Mallika Imwong, Yong Gu, Magnus Manske, Thomas D. Otto, Gareth Maslen, Taane G. Clark, Miriam Smith, Michael A. Quail, Susana Campino, Dominic P. Kwiatkowski

Publikováno v: The Open Genomics Journal

Studies on DNA from pathogenic organisms, within clinical samples, are often complicated by the presence of large amounts of host, e.g., human DNA. Isolation of pathogen DNA from these samples would improve the efficiency of next-generation sequencin

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::70443139b8e3290aa2f978127de79328
https://doi.org/10.2174/1875693x01205010018

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Timing, rates and spectra of human germline mutation

Publikováno v: Nature genetics

Germline mutations are a driving force behind genome evolution and genetic disease. We investigated genome-wide mutation rates and spectra in multi-sibling families. Mutation rate increased with paternal age in all families, but the number of additio

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fe5ec03837eecd7d80066cf9e1d284ff
https://eprints.gla.ac.uk/114411/1/114411.pdf

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Evaluation and optimisation of preparative semi-automated electrophoresis systems for Illumina library preparation

Autor: Yong Gu, Matthew Mayho, Harold Swerdlow, Michael A. Quail

Publikováno v: ELECTROPHORESIS. 33:3521-3528

Size selection can be a critical step in preparation of next-generation sequencing libraries. Traditional methods employing gel electrophoresis lack reproducibility, are labour intensive, do not scale well and employ hazardous interchelating dyes. In

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::d9e9c10f267649e2e675b6743c8a6d72
https://doi.org/10.1002/elps.201200128

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