References which are useful for FACS Measurements and FACS Data Analysis:

Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition). Cossarizza A et al., Eur. J. Immunol. 2019, 49: 1457–1973. DOI: 10.1002/eji.201970107
The second edition of "Flow Cytometry Guidelines" provides key aspects to consider when performing flow cytometry experiments and data analysis.

Guidelines for the use of flow cytometry and cell sorting in immunological studies (third edition). Cossarizza A. et al., Eur. J. Immunol. 2021. 51: 2708–3145. DOI: 10.1002/eji.202170126
The third edition is focusing on biological applications and provides a lot of tips to avoid pitfalls e.g. in sample preparation.

MIFlowCyt: the minimum information about a Flow Cytometry Experiment. Lee JA et al., Cytometry A. 2008 Oct;73(10):926-30. doi: 10.1002/cyto.a.20623.
This publication provides a very useful guide about which information to include when you prepare your own paper containing flow cytometry experiments.

A new "Logicle" display method avoids deceptive effects of logarithmic scaling for low signals and compensated data. Parks DR, Roederer M, Moore AW. Cytometry Part A. 2006, 69(6):541-51. DOI: 10.1002/cyto.a.20258

Interpreting flow cytometry data: a guide for the perplexed. Herzenberg LA et al., Nat Immunol 2006; 7(7):681-685. DOI: 10.1038/ni0706-681.

Compensation in Flow Cytometry. Roederer M, Current Protocols in Cytometry 2002, 1.14.1-1.14.20 DOI: 10.1002/0471142956.cy0114s22

Spectral Compensation for Flow Cytometry: Visualization Artifacts, Limitations, and Caveats. Roederer M, Cytometry 2001, 45:194–205. DOI: 10.1002/1097-0320(20011101)45:3<194::aid-cyto1163>3.0.co;2-c

A gain and dynamic range independent index to quantify spillover spread to aid panel design in flow cytometry. Bhowmick D, van Diepen F, Pfauth A, Tissier R, Ratliff ML, Scientific Reports 2021, 11:20553. DOI: 10.1038/s41598-021-99831-7

Reproducibility of Flow Cytometry Through Standardization: Opportunities and Challenges. Kalina T, Cytometry Part A 2020, 97A: 137–147. DOI: 10.1002/cyto.a.23901

Practical Flow Cytometry. Shapiro HM, 2003 John Wiley & Sons, ISBN:9780471411253, DOI:10.1002/0471722731

Flow Cytometry: An Overview. McKinnon KM, Curr Protoc Immunol. 2018; 120: 5.1.1–5.1.11. DOI:10.1002/cpim.40.

Relevance of Antibody Validation for Flow Cytometry. Kalina T, Lundsten K, Engel P, Cytometry A 2020 Feb;97(2):126-136. DOI: 10.1002/cyto.a.23895.

A Guide to Choosing Fluorescent Protein Combinations for Flow Cytometric Analysis Based on Spectral Overlap. Kleeman B et al, Cytometry A 2018 May;93(5):556-562. DOI: 10.1002/cyto.a.23360

Cell Sorting by Flow Cytometry. Davies D. in: Flow Cytometry Nov 2007 pp.257-276. DOI:10.1007/978-1-59745-451-3_11

Best Practices for Preparing a Single Cell Suspension from Solid Tissues for Flow Cytometry. Reichard A, Asosingh K, Cytometry Part A 2019, 95A: 219–226. DOI: 10.1002/cyto.a.23690

Do more with Less: Improving High Parameter Cytometry Through Overnight Staining. Whyte CE, Tumes DJ, Liston A, Burton OT, Curr Protoc. 2022 Nov;2(11):e589.