5 research outputs found
Processing single-cell RNA-seq data for dimension reduction-based analyses using open-source tools
- Publication venue
- 'Elsevier BV'
- Publication date
- 01/06/2021
- Field of study
Summary: Single-cell RNA sequencing data require several processing procedures to arrive at interpretable results. While commercial platforms can serve as âone-stop shopsâ for data analysis, they relinquish the flexibility required for customized analyses and are often inflexible between experimental systems. For instance, there is no universal solution for the discrimination of informative or uninformative encapsulated cellular material; thus, pipeline flexibility takes priority. Here, we demonstrate a full data analysis pipeline, constructed modularly from open-source software, including tools that we have contributed.For complete details on the use and execution of this protocol, please refer to Petukhov et al. (2018), Heiser et al. (2020), and Heiser and Lau (2020)
A contamination focused approach for optimizing the single-cell RNA-seq experiment
- Author
- Publication venue
- 'Elsevier BV'
- Publication date
- 01/07/2023
- Field of study
Summary: Droplet-based single-cell RNA-seq (scRNA-seq) data are plagued by ambient contaminations caused by nucleic acid material released by dead and dying cells. This material is mixed into the buffer and is co-encapsulated with cells, leading to a lower signal-to-noise ratio. Although there exist computational methods to remove ambient contaminations post-hoc, the reliability of algorithms in generating high-quality data from low-quality sources remains uncertain. Here, we assess data quality before data filtering by a set of quantitative, contamination-based metrics that assess data quality more effectively than standard metrics. Through a series of controlled experiments, we report improvements that can minimize ambient contamination outside of tissue dissociation, via cell fixation, improved cell loading, microfluidic dilution, and nuclei versus cell preparation; many of these parameters are inaccessible on commercial platforms. We provide end-users with insights on factors that can guide their decision-making regarding optimizations that minimize ambient contamination, and metrics to assess data quality
Annotated Bibliography
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- Tehon
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- Temkin
- Temkin
- Temple
- Tennent
- Tenney
- Thacher
- Thacher
- Thieret
- Thomas
- Thomas
- Thompson
- Thompson
- Thomson
- Thomson
- Thomson
- Thomson
- Thomson
- Thomson
- Thorndike
- Thornton
- Tiera
- Tin-Wa
- Tisserand
- Tobe
- Torrey
- Tournefort
- Train
- Trease
- Trelease
- Trotter
- Trotter
- Trusler
- Truswell
- Tschirch
- Tsotsoriya
- Tsuda
- Tubaro
- Tucker
- Tucker
- Tuntiwachwuttikul
- Turner
- Turner
- Turner
- Tutin
- Twain
- Tyler
- Tyler
- Tyler
- Tyler
- Tyler
- Tyler
- Tyler
- Tyree
- Tétényi
- Tétényi
- Tétényi
- Tétényi
- Ulubelen
- United States Pharmacopoeial Convention
- Vaillancourt
- Valnet
- van Helmont
- Vander Kloet
- Vander Kloet
- Vaughan
- Vaughan
- Veninga
- Vennesland
- Verpoort
- Verstille
- Vickers
- Vickery
- Vickery
- Visser
- Vitetta
- Vogel
- Vogel
- Vogel
- Vuilleumier
- Vulto
- Vulto
- Wachtel
- Wacker
- Wagner
- Wagner
- Wagner
- Wagner
- Wagner
- Wagner
- Wakeman
- Walker
- Wall
- Waller
- Waller
- Waller
- Waller
- Wallis
- Walshe
- Walters
- Walton
- Ward
- Ware
- Waring
- Waring
- Waring
- Warner
- Warren
- Warren
- Waterman
- Watson
- Watson
- Watt
- Waxdal
- Weibel
- Wells
- Wells
- Wells
- Wells
- Welsh
- Wenzell
- Wesley-Hadzija
- Wheelwright
- Whitaker
- White
- White
- White
- Whitener
- Whitlaw
- Wieand
- Wigginton
- Wigginton
- Wigginton
- Wigginton
- Wigginton
- Wigginton
- Wigginton
- Wilcox
- Wilhelm
- Wilkinson
- Willaman
- Williams
- Williams
- Williamson
- Willich
- Willis
- Wilson
- Wilson
- Wilson
- Wilson
- Winkelman
- Withering
- Wittop Koning
- Witzel
- Wohlfart
- Wolfe
- Wolswinkel
- Wong
- Woo
- Wood
- Wood
- Wood
- Wood
- Wood
- Wood
- Wood
- Wood
- Wood
- Wood
- Woodard
- Woodville
- Woodward
- Worthington-Roberts
- Wren
- Wren
- Wyman
- Wynter
- Xiao
- Yamaguchi
- Yamahara
- Yeo
- Yonge
- Young
- Youngken
- Youngken
- Youngken
- Yuncker
- Zdero
- Zennie
- Zollickoffer
- Publication venue
- 'Duke University Press'
- Publication date
- 01/01/1997
- Field of study
Reproductive modes and strategies in vertebrate evolution
- Author
- Aitken R. J.
- Aitken R. N.C.
- Amoroso E. C.
- Amoroso E. C.
- Amoroso E. C.
- Andrews R. A.
- Andrews R. M.
- Angelini F.
- Angelini F.
- Angelini F.
- Angelini F.
- Angelini F.
- Angelini F.
- Antony R.
- Austin C. R.
- Austin C. R.
- Avery R. A.
- Avery R. A.
- Badir N.
- Baevski U. B.
- Bagenal T. B.
- Baker J. R.
- Ballinger R. E.
- Ballinger R. E.
- Ballinger R. E.
- Baranov F. I.
- Bauchot R.
- Bell G.
- Bellairs A.
- Benazzi M.
- Bertin L.
- Bertin L.
- Bertin L.
- Bertin L.
- Bertin L.
- Beyer H. M.
- Bischoff T. L.W.
- Bishop D. W.
- Blackburn D. G.
- Blaxter K. L.
- Blount R.
- Bobr L. W.
- Bock W. J.
- Bogardt J. P.
- Botte V.
- Botte V.
- Botte V.
- Botte V.
- Bourne A. R.
- Bragdom D. E.
- Brockelmann W. Y.
- Brosset A.
- Budker P.
- Callard I. P.
- Callard I. P.
- Calow P.
- Campanella C.
- Canivenc R.
- Carroll R. L.
- Carscaden J. E.
- Cei G.
- Chapman B. M.
- Church G.
- Clausen H. J.
- Cody M. L.
- Cole L. C.
- Conner J.
- Corben C. J.
- Cowles R. B.
- Crews D.
- Crews D.
- Cuellar H. S.
- Cuellar H. S.
- Cuellar O.
- Cuellar O.
- Cuellar O.
- Cusick E. K.
- Dalcq A. M.
- Daniel J. C.
- Dewsbury D. A.
- Duellman W. E.
- Duellman W. E.
- Edmund A. G.
- Ewing H. E.
- Farner D. S.
- Filosa S.
- Fischer K.
- Fitch H. S.
- Fitch H. S.
- Fitz V. Simons F.M.
- Fitzpatrick L. C.
- Flower S. S.
- Foerster R. E.
- Follett B. K.
- Foster M. S.
- Fox H.
- Fox P. J.
- Fox W.
- Fox W.
- Friess A. E.
- Gadgil M.
- Galgano M.
- Galgano M.
- Galgano M.
- Galgano M.
- Gans C.
- Gardnier B. G.
- Ghiara G.
- Ghiara G.
- Giacomini E.
- Giacomini E.
- Giesberg H.
- Goldberg S. R.
- Golley F. B.
- Goodman D.
- Gorman G. C.
- Greer A. E.
- Grzimek B.
- Guillette L. J.
- Guillette L. J.
- Guillette L. J.
- Guillette L. J.
- Gwinner E.
- Haffer J.
- Halpert A. P.
- Hamner W. M.
- Harrison R. J.
- Hartman C. G.
- Hartman C. G.
- Hecht M. K.
- Heiser J. B.
- Hennig W.
- Herlant M.
- Hester F. J.
- Heyer W. R.
- Heyer W. R.
- Hildebrandt S. F.
- Hirshfield M. F.
- Hirshfield M. F.
- Hoar W. S.
- Hoffman J. C.
- Hoffmann L. H.
- Howarth B.
- Howe G. R.
- Immelmann
- Immelmann
- Immelmann K.
- Inger R. F.
- Jalabert B.
- Janvier P.
- Jarrans P.
- Jarvik E.
- Jennes R.
- Joly J.
- Jones R. E.
- Kehl R.
- Kehl R.
- Kendeigh S. C.
- Kiester A. R.
- King M.
- Kirsch J. A.
- Koheler P. D.
- Kosh R. J.
- Koyanagi F.
- La Pointe J. L.
- Lack D.
- Lamotte M.
- Lamotte M.
- Levey I. L.
- Licht P.
- Licht P.
- Licht P.
- Licht P.
- Licht P.
- Licht P.
- Lisk R. D.
- Lord R. D.
- Love M. R.
- Lovtrup S.
- Low B. S.
- Luckett P. W.
- Ludwing M.
- MacArthur R. H.
- Maiorana V. C.
- Marshall A. J.
- Martin A. A.
- Maslin T. P.
- Mayhew W. W.
- Mayr E.
- McDiarmid R. W.
- McMillan J. P.
- McNab K. B.
- Menaker M.
- Metten H.
- Miller M. R.
- Mittwoch V.
- Moll E. O.
- Morton S. R.
- Mossman H. W.
- Mossman H. W.
- Mossmann H. W.
- Mueller C. F.
- Murphy G. I.
- Murton R. K.
- Needham J.
- Neill W. T.
- Nichols J. D.
- Nilson G.
- Noble G. K.
- O'Malley B. W.
- Odum E. P.
- Olson E. C.
- Olson E. C.
- Orton G. L.
- Packard G. C.
- Packard G. C.
- Parkes A. S.
- Pasteels J.
- Perron F. P.
- Perron F. P.
- Pianka E. R.
- Pianka E. R.
- Pianka E. R.
- Pianka E. R.
- Pianka E. R.
- Pond C. M.
- Pratt H. P.M.
- Price P. W.
- Prim R. C.
- Racey P. A.
- Rahn H.
- Rahn H.
- Ralph C. L.
- Rand A. S.
- Randall L. G.
- Randolph P. A.
- Ranzi S.
- Ranzi S.
- Ranzi S.
- Rastogi R. K.
- Rastogi R. K.
- Raynaud A.
- Rebel T. P.
- Reiter R. J.
- Reiter R. J.
- Renfree M. B.
- Richardson K. C.
- Ricklefs R. E.
- Robertson I. A.D.
- Rodney A. M.
- Roff D.
- Roger J.
- Romanoff A. L.
- Romer A. S.
- Romer A. S.
- Roth J. J.
- Rothchild I.
- Russel F. S.
- Sadleir R. M.S.F.
- Saint-Girons H.
- Saint-Girons H.
- Saint-Girons H.
- Salthe S. N.
- Salthe S. N.
- Sandoz D.
- Schaefer G. C.S.
- Schaffer W. M.
- Schaffer W. M.
- Schlonage D. C.
- Schultz R. J.
- Session S. K.
- Sharman
- Sharman G. B.
- Shine R.
- Skutch A. F.
- Smith C. L.
- Smith M.
- Snell W. T.
- Spellerber J. F.
- Spencer A. W.
- Stearns S. C.
- Stetson M. H.
- Taddei C.
- Taylor E. H.
- Thomson K. S.
- Tingari M. D.
- Tinkle D. W.
- Tinkle D. W.
- Tinkle D. W.
- Tinkle D. W.
- Tinkle D. W.
- Tortonese E.
- Underwood H.
- Vainio J.
- Van Demark N. L.
- Van Dijk D. E.
- Van Ooordt P. G.W.J.
- Vilter V.
- Wake M. H.
- Wake M. H.
- Wake M. H.
- Wake M. H.
- Wallace R.
- Weekes H. C.
- Weekes H. C.
- Weeks H. C.
- Weeks H. C.
- White M. J.D.
- Wilbur H. M.
- Williams E. E.
- Williams G. C.
- Wingfield J. C.
- Woodside B.
- Xavier F.
- Xavier F.
- Yaron Z.
- Yaron Z.
- Publication venue
- 'Informa UK Limited'
- Publication date
- Field of study
The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution
- Author
- Aaron Hata
- Aaron Horning
- Achim
- Adam Resnick
- Adrienne Boire
- Ajit George
- Ajit Johnson Nirmal
- Akimasa Hayashi
- Akshay Balsubramani
- Alan J. Simmons
- Alanna Gould
- Albert H. Kim
- Alex Felmeister
- Alex K. Shalek
- Alex Ooms
- Alex Shalek
- Alexander B. Sibley
- Alexander Borowsky
- Alexander R. Guimaraes
- Allison Frangieh
- Allison L. Creason
- Alyce A. Chen
- Amir Bahmani
- Amodio
- Anastasiya Olson
- Andrew C. Adey
- Angela Waanders
- Angelo
- Angelo De Marzo
- Angelo Fortunato
- Anil Vachani
- Anirban Maitra
- Anna Hupalowska
- Annette Kolodzie
- Anshul Kundaje
- Arastoo Vossough
- Argelaguet
- Arjun Raj
- Artem Sokolov
- Asaf Rotem
- Ashley M. Laughney
- Ashley N. Reeb
- Austin Southard-Smith
- Aviv Regev
- Aviv Regev
- Avrum E. Spira
- Avrum Spira
- Aziz Khan
- Azizi
- Barbara Engelhardt
- Barkas
- Beane
- Benjamin Izar
- Binnewies
- Blue B. Lake
- Bob Chen
- Brendan OâConnell
- Brett E. Johnson
- Bruce E. Johnson
- Bruce Johnson
- Buenrostro
- BĂŒttner
- Carina Leonard
- Carlo Maley
- Casey R. Hansen
- Changya Chen
- Charles M. Rudin
- Chen
- Chen
- Chen
- Chi-yun Wu
- Chia-hui Chen
- Christina Curtis
- Christine A. Iacobuzio-Donahue
- Christine A. Iacobuzio-Donahue
- Christine G. Lian
- Christopher A. Maher
- Christopher Amos
- Clarence Yapp
- Cody Heiser
- Connor A. Jacobson
- Courtney B. Betts
- Cynthia L. Sears
- Cynthia X. Ma
- Dadong Zhang
- Damir Sudar
- Dana Peâer
- Dana Peâer
- Daniel Crichton
- Daniel Cui Zhou
- Daniel Martinez
- Daniel Merrick
- Daniel Persson
- Danielle Galipeau
- Danika Makowski
- David Barrett
- David G. DeNardo
- David Gutman
- David L. Gibbs
- Deborah J. Veis
- Deborah Schrag
- Denis Schapiro
- Denis Schapiro
- Denise Aberle
- Deyali Chatterjee
- Diane E. Bender
- Diego Mallo
- Dinah S. Singer
- Dinh Diep
- Du
- Durruthy-Durruthy
- E. Shelley Hwang
- Ecker
- Ed Boyden
- Edward D. Esplin
- Edward D. Esplin
- Edward Novikov
- Eliezer Van Allen
- Eliot T. McKinley
- Elizabeth H. Williams
- Elizabeth H. Williams
- Elizabeth Moses
- Elizabeth Stover
- Ellen Todres
- Emek Demir
- Emek Demir
- Eran Kotler
- Erik A. Burlingame
- Erika Kim
- Ethan Cerami
- Ethan Cerami
- Fatemeh Alikarami
- Feng Chen
- Foley
- Foluso O. Ademuyiwa
- Frank Hodi
- Gad Getz
- Galon
- Gao
- Garry Nolan
- Gary J. Patti
- Gaublomme
- Genevieve Boland
- George F. Murphy
- George V. Thomas
- Gierahn
- Giesen
- Gilliam Hirst
- Goltsev
- Goodfellow
- Gordon B. Mills
- Graham A. Colditz
- Graham Erwin
- Guillaume Thibault
- Habib
- Hanspeter Pfister
- Hao Wu
- Hassan Chaib
- Hayan Lee
- Heba Ijaz
- Heidi S. Feiler
- Houxiang Zhu
- Humam Kadara
- Hung-Yi Wu
- Huy Lam
- Iacobuzio-Donahue
- Ignas Masilionais
- Ignaty Leshchiner
- Ino de Bruijn
- Itsik Pe'er
- Jacklynn Egger
- Jacob Kagan
- Jaeyoung Chun
- James Brooks
- James J. Hsieh
- James M. Ford
- James M. Ford
- Janet Stein
- Jeff Sheng
- Jeffrey Marks
- Jennifer Beane
- Jennifer E. Rood
- Jennifer Eng
- Jennifer Flournoy
- Jennifer L. Frye
- Jennifer L. Guerriero
- Jennifer Mason
- Jerby-Arnon
- Jeremy Goecks
- Jeremy Goecks
- Jeremy Gresham
- Jeremy L. Muhlich
- Jerry Li
- Jessica L. Riesterer
- Jha
- Jia-Ren Lin
- Jianjiong Gao
- Joan Massagué
- Joe W. Gray
- Joe W. Gray
- John M. Herndon
- John Maris
- Johnson
- Jon C. Aster
- Joseph M. Chan
- Joseph T. Roland
- Joshua Campbell
- Joshua F. McMichael
- Judit Jané-Valbuena
- Judit Jané-Valbuena
- Julia Drewes
- Julia R. Miessner
- Julie Bletz
- Junhyong Kim
- Justin Guinney
- Justin Guinney
- Kai Tan
- Kai Tan
- Kamyar Pourfarhangi
- Kang
- Karla Helvie
- Kate Gowers
- Kathleen A. Harris
- Kathrin Bernt
- Katie Blise
- Kazuhito Sato
- Keith Flaherty
- Ken S. Lau
- Ken S. Lau
- Kevin Contrepois
- Kian-Huat Lim
- Kiara Siex
- Klaus Kaestner
- Koei Chin
- Kooresh I. Shoghi
- Kornelia Polyak
- Korsunsky
- Kostyantyn Krysan
- Kouros Owzar
- Kristen Anton
- Kristina Cole
- Kristopher Bosse
- Krueger
- Kun Zhang
- Laura Dellostritto
- Laura Esserman
- Lea Surrey
- Lee
- Li
- Li Ding
- Li Ding
- Liang-Bo Wang
- Lihua Jiang
- Lin
- Lin
- Linas Mazutis
- Linh Tran
- Lisa M. Coussens
- Lisa Thammavong
- Liu
- Long Gao
- Lopez
- Luecken
- Luis Cisneros
- Lukas Kalinke
- Luke Ternes
- Lynne Berry
- Ma
- Macosko
- Madison Tyler
- Marc D. Ryser
- Marc Lenburg
- Maria Santi-Vicini
- Mario SuvĂ
- Marios Giannakis
- Marisol Ramirez-Solano
- Marissa Mattar
- Martha J. Shrubsole
- Marvin Petty
- Mary Catherine Macedonia
- Mary Reid
- Mateusz Kopytra
- Matthew A. Wyczalkowski
- Matthew Bott
- Matthew Meyerson
- Meredith Mills
- Mianlei Zhang
- Michael C. Wendl
- Michael Dyer
- Michael Offin
- Michael P. Snyder
- Michael P. Snyder
- Michael R. Angelo
- Michal Slyper
- Michel Nederlof
- Miguel Ossandon
- Milan G. Chheda
- Milen Nikolov
- Moffitt
- Moffitt
- Motomi Mori
- Nadezhda V. Terekhanova
- Nancy Zhang
- Natalie Collins
- Netta Makinen
- Nicholas E. Navin
- Nick Markham
- Nikhil Wagle
- Nikolaus Schultz
- Nir Hacohen
- Ojasvi Chaudhary
- Olivier Harismendy
- Orit Rozenblatt-Rosen
- Orit Rozenblatt-Rosen
- Orr Ashenberg
- Orr Ashenberg
- Ozgun Babur
- Patel
- Peng Gao
- Peter K. Sorger
- Peter K. Sorger
- Philipp Oberdoerffer
- Philipp Oberdoerffer
- Phillip Storm
- Pierre Massion
- Qi Liu
- Qi Qiu
- Qin Zhu
- Qiuyin Cai
- Quanhu Sheng
- Rachana Agarwal
- Raphael Bueno
- Rebecca L. Aft
- Regev
- Reid Ness
- Reyka G. Jayasinghe
- Richard Mazurchuk
- Robert A. Anders
- Robert B. West
- Robert J. Coffey
- Robert J. Coffey
- Robert J. Mashl
- Robert Keith
- Robert Krueger
- Robert S. Fulton
- Robert West
- Rochelle Levy
- Rodrigo Chuaqui
- Rosalie C. Sears
- Rosenberg
- Roxanne Chiu
- Rozelle Laquindanum
- Rozenblatt-Rosen
- Ruben A. Aguilar
- Rudnick
- Ruiyang Liu
- Rumana Rashid
- Ryan C. Fields
- Ryan Sullivan
- Samuel I. Achilefu
- Samuel Janes
- Sandro Santagata
- Sandro Santagata
- Sarah A. Mazzilli
- Sarah A. Mazzilli
- Satija
- Scott Rodig
- Sean E. Hanlon
- Sean Hanlon
- Shain
- Shalek
- Shamilene Sivagnanam
- Shannon Hughes
- Shannon K. Hughes
- Sharma
- Sharmistha Ghosh
- Sharmistha Ghosh
- Sharon Diskin
- Sheila M. Reynolds
- Shelley E. Hwang
- Sheng-Kwei Song
- Sherri R. Davies
- Shih-Kai Chu
- Sidharth V. Puram
- Simon P. Goedegebuure
- Simon Vandekar
- Siri H. Strand
- Siting Gan
- Slyper
- Smillie
- Sonia Rosenfield
- Srivastava
- Stephanie Nevins
- Stephen Dubinett
- Stephen Fisher
- Stephen Hunger
- Stephen T. Oh
- Stoeckius
- Stoeckius
- Stuart
- StÄhl
- Subrata Sen
- Sudhir Srivastava
- Sudhir Srivastava
- Sudipta Roy
- Suman B. Mondal
- Swapnil Parmar
- SĂ©bastien Vigneau
- Tal Nawy
- Tal Nawy
- Tanja Davidsen
- Tao Ju
- Tao Peng
- Tasleema Patel
- Teri Longacre
- Teytelman
- Tim Geiger
- Timothy Su
- Tirosh
- Tirosh
- Tracy Lively
- Tracy Lively
- Travis Hollmann
- Triparna Sen
- Trombetta
- Tuhin K. Guha
- Tyler Madison
- Uri Ladabaum
- Vianne R. Gao
- Vickovic
- Viola Allaj
- Vitak
- VĂ©steinn Thorsson
- Wagma Caravan
- Wallrapp
- Wang
- Wang
- Warren Kibbe
- Weinstein
- Welch
- Wenbao Yu
- Wilkinson
- William E. Gillanders
- William Greenleaf
- William J.R. Longabaugh
- Won Jae Huh
- Xengie Doan
- Xiangzhu Zhu
- Xiaolu Yang
- Xiaowei Zhuang
- Yael Mosse
- Yang
- Yantian Zhang
- Yanyan Zhao
- Yasin Uzun
- Yinyin Yuan
- Yiyun Lin
- Yosinski
- Young Hwan Chang
- Yu Shyr
- Yu-An Chen
- Yuankun Zhu
- Yubin Xie
- Yuriko Mori
- Zilu Zhou
- Zoltan Maliga
- Ălvaro Quintanal-Villalonga
- Publication venue
- 'Elsevier BV'
- Publication date
- Field of study