Collection and preprocessing of fine needle aspirate patient samples for single cell profiling and data analysis

Aizhan Tastanova; Egle Ramelyte; Zsolt Balázs; Ulrike Menzel; Christian Beisel; Michael Krauthammer; Reinhard Dummer; Mitchell Paul Levesque

doi:10.1016/j.xpro.2021.100581

Collection and preprocessing of fine needle aspirate patient samples for single cell profiling and data analysis

STAR Protoc. 2021 Jun 5;2(2):100581. doi: 10.1016/j.xpro.2021.100581. eCollection 2021 Jun 18.

Authors

Aizhan Tastanova¹, Egle Ramelyte¹, Zsolt Balázs^{2

3}, Ulrike Menzel⁴, Christian Beisel⁴, Michael Krauthammer^{2

3}, Reinhard Dummer¹, Mitchell Paul Levesque¹

Affiliations

¹ Dermatology Department, University Hospital Zurich and Medical Faculty, University of Zurich, 8091 Zurich, Switzerland.
² Department of Quantitative Biomedicine, University of Zurich, 8057 Zurich, Switzerland.
³ Biomedical Informatics, University Hospital of Zurich, 8057 Zurich, Switzerland.
⁴ Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.

Abstract

High cell viability and recovered cell concentration are typical quality control requirements for single-cell processing and quality data. This protocol describes procedures for sampling, live-cell biobanking, preprocessing for single-cell RNA sequencing, and analysis of fine-needle aspiration (FNA) samples of the skin. The minimally invasive nature of FNA collection is more accepted by patients and allows for frequent longitudinal sampling, resulting in high-quality single-cell sequencing data that capture cellular heterogeneity in clinical samples.

Keywords: Bioinformatics; Cell isolation; Clinical Protocol; RNAseq; Single Cell.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Biopsy, Fine-Needle / methods*
Data Analysis*
Humans
Sequence Analysis, RNA / methods
Single-Cell Analysis / methods*
Specimen Handling / methods*