TABLE 2.

Samples used for benchmarking the deconvolution methods.

Cells/Organisms	EV1 a source	EV isolation b	RNA library kit	Alignment method	EV validation c	GEO/Data source	Reference
CRC	CCM	UF/dUC	NEBNext	Salmon	EM d WB d	GSE121964	Hinger et al. (2018)
DU145 LNCaP PC3	CCM	dUC	SMARTer	Salmon	NTA EM WB	GSE183070	Almeida et al. (2022)
Adipocytes macrophages	CCM	dUC	SMART‐Seq v4	Salmon	WB	GSE94155	Yang et al. (2017)
Human	Plasma	exoRNeasy	SMARTer	HISAT2 e	EM nanoFCM WB	exorbase.org	Li et al. (2019), Yu et al. (2020)
Human	Urine	exoRNeasy	SMARTer	HISAT2 e	–	exorbase.org	Lai et al. (2021)
Human	Urine	dUC	SMART‐Seq	STAR e	NTA EM WB	Supplement Table S9 of the paper.	Dwivedi et al. (2023)

^a CCM: cell‐conditioned medium.

^b UF: ultrafiltration; dUC: differential ultracentrifugation, exoRNeasy: a kit that isolates EVs by their affinity to a proprietary membrane.

^c EM: electron microscopy; NTA: nanotracking analysis; nanoFCM: nano‐flow cytometry; WB: western blot.

^d Validated in Higginbotham et al. (2011) and Beckler et al. (2013).

^e Alignment to the human genome was done in the original studies.