scQUEST: Quantifying tumor ecosystem heterogeneity from mass or flow cytometry data.
Bioinformatics
Cancer
Flow Cytometry/Mass Cytometry
Single Cell
Journal
STAR protocols
ISSN: 2666-1667
Titre abrégé: STAR Protoc
Pays: United States
ID NLM: 101769501
Informations de publication
Date de publication:
16 09 2022
16 09 2022
Historique:
entrez:
26
7
2022
pubmed:
27
7
2022
medline:
28
7
2022
Statut:
epublish
Résumé
With mass and flow cytometry, millions of single-cell profiles with dozens of parameters can be measured to comprehensively characterize complex tumor ecosystems. Here, we present scQUEST, an open-source Python library for cell type identification and quantification of tumor ecosystem heterogeneity in patient cohorts. We provide a step-by-step protocol on the application of scQUEST on our previously generated human breast cancer single-cell atlas using mass cytometry and discuss how it can be adapted and extended for other datasets and analyses. For complete details on the use and execution of this protocol, please refer to Wagner et al. (2019).
Identifiants
pubmed: 35880127
doi: 10.1016/j.xpro.2022.101578
pii: S2666-1667(22)00458-0
pmc: PMC9307583
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
101578Informations de copyright
© 2022 The Author(s).
Déclaration de conflit d'intérêts
The authors declare no competing interests.
Références
Nat Protoc. 2015 Feb;10(2):316-33
pubmed: 25612231
Oncogene. 2015 Jul;34(28):3617-26
pubmed: 25263438
Cytometry A. 2015 Jul;87(7):636-45
pubmed: 25573116
Curr Protoc Cytom. 2010 Jul;Chapter 10:Unit10.17
pubmed: 20578106
Eur J Immunol. 2016 Nov;46(11):2496-2506
pubmed: 27682842
Nat Methods. 2006 May;3(5):361-8
pubmed: 16628206
Nat Rev Genet. 2010 Oct;11(10):733-9
pubmed: 20838408
Bioinformatics. 2022 Apr 29;:
pubmed: 35485743
Cell. 2015 Jul 2;162(1):184-97
pubmed: 26095251
Science. 2006 Jul 28;313(5786):504-7
pubmed: 16873662
Nat Biotechnol. 2018 Jun;36(5):421-427
pubmed: 29608177
Cytometry A. 2013 May;83(5):483-94
pubmed: 23512433
Cell. 2019 May 16;177(5):1330-1345.e18
pubmed: 30982598
CA Cancer J Clin. 2017 Mar;67(2):93-99
pubmed: 28094848
Cell Syst. 2021 Dec 15;12(12):1173-1186.e5
pubmed: 34536381
Trends Biotechnol. 2022 Jun;40(6):647-676
pubmed: 34972597
Cell Syst. 2018 May 23;6(5):612-620.e5
pubmed: 29605184