FixNCut: single-cell genomics through reversible tissue fixation and dissociation

被引：0
作者：
Laura Jiménez-Gracia
Domenica Marchese
Juan C. Nieto
Ginevra Caratù
Elisa Melón-Ardanaz
Victoria Gudiño
Sara Roth
Kellie Wise
Natalie K. Ryan
Kirk B. Jensen
Xavier Hernando-Momblona
Joana P. Bernardes
Florian Tran
Laura Katharina Sievers
Stefan Schreiber
Maarten van den Berge
Tessa Kole
Petra L. van der Velde
Martijn C. Nawijn
Philip Rosenstiel
Eduard Batlle
Lisa M. Butler
Ian A. Parish
Jasmine Plummer
Ivo Gut
Azucena Salas
Holger Heyn
Luciano G. Martelotto
机构：
[1] Centro Nacional de Análisis Genómico (CNAG),Inflammatory Bowel Disease Group
[2] Universitat de Barcelona (UB),Cancer Immunology Program
[3] Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS),Sir Peter MacCallum Department of Oncology
[4] Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD),Monash University Department of Surgery
[5] Peter MacCallum Cancer Centre,Adelaide Centre for Epigenetics (ACE)
[6] The University of Melbourne,South Australian immunoGENomics Cancer Institute (SAiGENCI)
[7] Alfred Hospital,Freemasons Foundation Centre for Men’s Health
[8] University of Adelaide,Institute of Clinical Molecular Biology
[9] University of Adelaide,Department of Internal Medicine I
[10] Australian Genomics Research Facility,Department of Pulmonary Diseases
[11] University of Adelaide,Department of Pathology & Medical Biology
[12] South Australian Health and Medical Research Institute,undefined
[13] Institute for Research in Biomedicine (IRB Barcelona),undefined
[14] The Barcelona Institute of Science and Technology,undefined
[15] Centro de Investigación Biomédica en Red de Cáncer (CIBERONC),undefined
[16] Kiel University,undefined
[17] University Hospital Schleswig-Holstein (UKSH),undefined
[18] University of Groningen,undefined
[19] University Medical Center Groningen,undefined
[20] Groningen Research Institute for Asthma and COPD,undefined
[21] University of Groningen,undefined
[22] University Medical Center Groningen,undefined
[23] University of Groningen,undefined
[24] University Medical Center Groningen,undefined
[25] ICREA,undefined
[26] St Jude Children’s Research Hospital,undefined
[27] Omniscope,undefined
来源：
Genome Biology | / 25卷
关键词：
Single-cell genomics; RNA sequencing; Sample fixation; Tissue dissociation; Cellular stress;
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摘要：
The use of single-cell technologies for clinical applications requires disconnecting sampling from downstream processing steps. Early sample preservation can further increase robustness and reproducibility by avoiding artifacts introduced during specimen handling. We present FixNCut, a methodology for the reversible fixation of tissue followed by dissociation that overcomes current limitations. We applied FixNCut to human and mouse tissues to demonstrate the preservation of RNA integrity, sequencing library complexity, and cellular composition, while diminishing stress-related artifacts. Besides single-cell RNA sequencing, FixNCut is compatible with multiple single-cell and spatial technologies, making it a versatile tool for robust and flexible study designs.
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[1]  
Ziegenhain C(2018)Quantitative single-cell transcriptomics Brief Funct Genomics. 17 220-232
[2]  
Vieth B(2019)Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses Genome Biol. 20 210-316
[3]  
Parekh S(2020)Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows Genome Biol. 21 130-245
[4]  
Hellmann I(2020)Sampling time-dependent artifacts in single-cell genomics studies Genome Biol. 21 112-22
[5]  
Enard W(2022)Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain Nat Neurosci. 25 306-547
[6]  
O’Flanagan CH(1980)Cryopreservation of human granulocytes: study of granulocyte function and ultrastructure Blood. 56 237-885.e19
[7]  
Campbell KR(2012)Myeloid-derived suppressor cell measurements in fresh and cryopreserved blood samples J Immunol Methods. 381 14-897
[8]  
Zhang AW(2018)A field-applicable method for flow cytometric analysis of granulocyte activation: cryopreservation of fixed granulocytes Cytom Part J Int Soc Anal Cytol. 93 540-1135.e7
[9]  
Kabeer F(2021)The effect of methanol fixation on single-cell RNA sequencing data BMC Genomics. 22 420-353
[10]  
Lim JLP(2021)ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics Genome Biol. 22 89-928
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