Literature DB >> 31028635

Seq-Well: A Sample-Efficient, Portable Picowell Platform for Massively Parallel Single-Cell RNA Sequencing.

Toby P Aicher1,2,3, Shaina Carroll4,5,6, Gianmarco Raddi7,8,9,10, Todd Gierahn11, Marc H Wadsworth4,5,6, Travis K Hughes4,5,6, Chris Love4,6,11,12, Alex K Shalek4,5,6,11.   

Abstract

Seq-Well is a low-cost picowell platform that can be used to simultaneously profile the transcriptomes of thousands of cells from diverse, low input clinical samples. In Seq-Well, uniquely barcoded mRNA capture beads and cells are co-confined in picowells that are sealed using a semipermeable membrane, enabling efficient cell lysis and mRNA capture. The beads are subsequently removed and processed in parallel for sequencing, with each transcript's cell of origin determined via the unique barcodes. Due to its simplicity and portability, Seq-Well can be performed almost anywhere.

Entities:  

Keywords:  Picowells; RNA-Seq; Seq-Well; Single-cell RNA sequencing; Single-cell genomics; Systems biology; Transcriptomics

Mesh：

Substances：

Year:  2019        PMID： 31028635      PMCID： PMC7741456          DOI： 10.1007/978-1-4939-9240-9_8

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  13 in total

1.  Counting absolute numbers of molecules using unique molecular identifiers.

Authors:  Teemu Kivioja; Anna Vähärautio; Kasper Karlsson; Martin Bonke; Martin Enge; Sten Linnarsson; Jussi Taipale
Journal:  Nat Methods       Date:  2011-11-20       Impact factor: 28.547

2.  Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.

Authors:  Evan Z Macosko; Anindita Basu; Rahul Satija; James Nemesh; Karthik Shekhar; Melissa Goldman; Itay Tirosh; Allison R Bialas; Nolan Kamitaki; Emily M Martersteck; John J Trombetta; David A Weitz; Joshua R Sanes; Alex K Shalek; Aviv Regev; Steven A McCarroll
Journal:  Cell       Date:  2015-05-21       Impact factor: 41.582

Review 3.  The technology and biology of single-cell RNA sequencing.

Authors:  Aleksandra A Kolodziejczyk; Jong Kyoung Kim; Valentine Svensson; John C Marioni; Sarah A Teichmann
Journal:  Mol Cell       Date:  2015-05-21       Impact factor: 17.970

4.  Comparative Analysis of Single-Cell RNA Sequencing Methods.

Authors:  Christoph Ziegenhain; Beate Vieth; Swati Parekh; Björn Reinius; Amy Guillaumet-Adkins; Martha Smets; Heinrich Leonhardt; Holger Heyn; Ines Hellmann; Wolfgang Enard
Journal:  Mol Cell       Date:  2017-02-16       Impact factor: 17.970

5.  Exponential scaling of single-cell RNA-seq in the past decade.

Authors:  Valentine Svensson; Roser Vento-Tormo; Sarah A Teichmann
Journal:  Nat Protoc       Date:  2018-03-01       Impact factor: 13.491

6.  mRNA-Seq whole-transcriptome analysis of a single cell.

Authors:  Fuchou Tang; Catalin Barbacioru; Yangzhou Wang; Ellen Nordman; Clarence Lee; Nanlan Xu; Xiaohui Wang; John Bodeau; Brian B Tuch; Asim Siddiqui; Kaiqin Lao; M Azim Surani
Journal:  Nat Methods       Date:  2009-04-06       Impact factor: 28.547

7.  Massively parallel digital transcriptional profiling of single cells.

Authors:  Grace X Y Zheng; Jessica M Terry; Phillip Belgrader; Paul Ryvkin; Zachary W Bent; Ryan Wilson; Solongo B Ziraldo; Tobias D Wheeler; Geoff P McDermott; Junjie Zhu; Mark T Gregory; Joe Shuga; Luz Montesclaros; Jason G Underwood; Donald A Masquelier; Stefanie Y Nishimura; Michael Schnall-Levin; Paul W Wyatt; Christopher M Hindson; Rajiv Bharadwaj; Alexander Wong; Kevin D Ness; Lan W Beppu; H Joachim Deeg; Christopher McFarland; Keith R Loeb; William J Valente; Nolan G Ericson; Emily A Stevens; Jerald P Radich; Tarjei S Mikkelsen; Benjamin J Hindson; Jason H Bielas
Journal:  Nat Commun       Date:  2017-01-16       Impact factor: 14.919

8.  Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells.

Authors:  Alex K Shalek; Rahul Satija; Xian Adiconis; Rona S Gertner; Jellert T Gaublomme; Raktima Raychowdhury; Schraga Schwartz; Nir Yosef; Christine Malboeuf; Diana Lu; John J Trombetta; Dave Gennert; Andreas Gnirke; Alon Goren; Nir Hacohen; Joshua Z Levin; Hongkun Park; Aviv Regev
Journal:  Nature       Date:  2013-05-19       Impact factor: 49.962

9.  Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells.

Authors:  Iain C Macaulay; Valentine Svensson; Charlotte Labalette; Lauren Ferreira; Fiona Hamey; Thierry Voet; Sarah A Teichmann; Ana Cvejic
Journal:  Cell Rep       Date:  2016-01-21       Impact factor: 9.423

10.  Global and targeted approaches to single-cell transcriptome characterization.

Authors:  Aleksandra A Kolodziejczyk; Tapio Lönnberg
Journal:  Brief Funct Genomics       Date:  2018-07-01       Impact factor: 4.241
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  10 in total

1.  Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes.

Authors:  Alex S Genshaft; Carly G K Ziegler; Constantine N Tzouanas; Benjamin E Mead; Alex M Jaeger; Andrew W Navia; Ryan P King; Miyeko D Mana; Siyi Huang; Vanessa Mitsialis; Scott B Snapper; Ömer H Yilmaz; Tyler Jacks; Jeffrey F Van Humbeck; Alex K Shalek
Journal:  Nat Commun       Date:  2021-08-17       Impact factor: 17.694

Review 2.  Single-Cell Sequencing: Ariadne's Thread in the Maze of Acute Myeloid Leukemia.

Authors:  Immacolata Redavid; Maria Rosa Conserva; Luisa Anelli; Antonella Zagaria; Giorgina Specchia; Pellegrino Musto; Francesco Albano
Journal:  Diagnostics (Basel)       Date:  2022-04-15

Review 3.  Single-cell sequencing: a promising approach for uncovering the mechanisms of tumor metastasis.

Authors:  Junpu Wang; Chunlin Ou; Yingying Han; Dan Wang; Lushan Peng; Tao Huang; Xiaoyun He
Journal:  J Hematol Oncol       Date:  2022-05-12       Impact factor: 23.168

Review 4.  Single-cell RNA sequencing in Drosophila: Technologies and applications.

Authors:  Hongjie Li
Journal:  Wiley Interdiscip Rev Dev Biol       Date:  2020-09-16       Impact factor: 5.814

5.  Single-Cell RNA Sequencing Analysis of the Drosophila Larval Ventral Cord.

Authors:  Tho Huu Nguyen; Rosario Vicidomini; Saumitra Dey Choudhury; Steven L Coon; James Iben; Thomas Brody; Mihaela Serpe
Journal:  Curr Protoc       Date:  2021-02

Review 6.  Insights from the Applications of Single-Cell Transcriptomic Analysis in Germ Cell Development and Reproductive Medicine.

Authors:  Hyeonwoo La; Hyunjin Yoo; Eun Joo Lee; Nguyen Xuan Thang; Hee Jin Choi; Jeongheon Oh; Ji Hyun Park; Kwonho Hong
Journal:  Int J Mol Sci       Date:  2021-01-15       Impact factor: 5.923

7.  SCAPTURE: a deep learning-embedded pipeline that captures polyadenylation information from 3' tag-based RNA-seq of single cells.

Authors:  Guo-Wei Li; Fang Nan; Guo-Hua Yuan; Chu-Xiao Liu; Xindong Liu; Ling-Ling Chen; Bin Tian; Li Yang
Journal:  Genome Biol       Date:  2021-08-10       Impact factor: 13.583

Review 8.  Tutorial: Guidelines for Single-Cell RT-qPCR.

Authors:  Daniel Zucha; Mikael Kubista; Lukas Valihrach
Journal:  Cells       Date:  2021-09-30       Impact factor: 6.600

Review 9.  A Primer for Single-Cell Sequencing in Non-Model Organisms.

Authors:  James M Alfieri; Guosong Wang; Michelle M Jonika; Clare A Gill; Heath Blackmon; Giridhar N Athrey
Journal:  Genes (Basel)       Date:  2022-02-19       Impact factor: 4.096

10.  High-fat diet-activated fatty acid oxidation mediates intestinal stemness and tumorigenicity.

Authors:  Miyeko D Mana; Amanda M Hussey; Constantine N Tzouanas; Shinya Imada; Yesenia Barrera Millan; Dorukhan Bahceci; Dominic R Saiz; Anna T Webb; Caroline A Lewis; Peter Carmeliet; Maria M Mihaylova; Alex K Shalek; Ömer H Yilmaz
Journal:  Cell Rep       Date:  2021-06-08       Impact factor: 9.423
  10 in total

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