Reagent or resource	Source	Identifier
Antibodies
Monoclonal anti‐CD9	Merck	Cat. #SAB470
Purified Mouse anti‐human CD63	BD Biosciences	Cat. #556019; RRID: AB_396297
CD81	BD Biosciences	Cat. #555675; RRID: AB_396028
TSPAN4	ThermoFisher	PA5‐69344; RRID: AB_2688603
TSPAN8	ThermoFisher	MA5‐24179; RRID: AB_2609273
Purified mouse IgG1, k isotype control	BD Biosciences	Cat. #555746; RRID: AB_396088
Rabbit bridging anti‐mouse antibody	DAKO	Cat. #Z0259
Bacterial and virus strains
CD63 NanoLuciferase plasmid	Generated as described in bioRxihttps://doi.org/10.1101/2023.02.23.529257v1	N/A
Biological samples
RNA samples patients	Jeroen Bosch ziekenhuis and UMC Utrecht	N/A
Plasma samples patients	Jeroen Bosch ziekenhuis and UMC Utrecht	N/A
Chemicals, peptides and recombinant proteins
DMEM/F12	ThermoFisher	Cat. #31330038
Pen/Strep	Gibco	Cat. #15140122
FCS	Serana	Cat. #s‐FBS‐SA‐025
Culture‐Inserts 3 Well self‐insertion	Ibidi	Cat. #80369
Lipofectamine 2000	ThermoFisher	Cat. #11668027
Cross‐linked Sepharose 2B beads	GE Healthcare	Cat. #GE17‐0140‐01
BSA	Sigma–Aldrich	Cat. #A4503‐50G; CAS9048‐46‐8
PBS	Gibco	Cat. #18912‐014
Glycine	Merck	Cat. #K27662101
Colloidal gold particles	Utrecht University	N/A
Uranyl acetate	EMS	Cat. #22400
QIAzol Lysis Reagent	QIAgen	Cat. #79306
Centricon Plus‐70 ultrafiltration units	Milipore	Cat. #UFC710008
qEVoriginal/70 nm gen2	Izon Science Limited	Cat. #ICO‐70
Amicon Ultra‐2 Centrifugal Filter Unit	Milipore	Cat. #UFC201024
LDS sample buffer	ThermoFisher	Cat. #NP0007
DTT	Sigma–Aldrich	Cat. #d9163
IAA	Merck	Cat. #1149
Urea	Sigma–Aldrich	Cat. #51456
Tris‐buffer	Merck	Cat. #1.08382.0500
Eppendorf concentrator plus	Eppendorf	Cat. #EP5305000509
Nanosep 30k Omega centrifugal devices	Pall Life Sciences	Cat #DO010C34 / Cat #OD010C33
Oasis columns (10 mg)	Waters	Cat. #186000383
ReproSil C18 aqua	Dr. Maisch	Cat. #R119 aq
Trypsin	Promega	Cat. #V5111
Fused silica emitter	New objective	N/A
Critical commercial assays
Nano‐Glo(R) Luciferase Assay	Promega	N1110
miRNeasy serum/plasma kit	QIAgen	Cat. #217184
TaqManMicroRNA Reverse Transcription kit	ThermoFisher	Cat. #4366596
SMARTer Stranded Total RNA‐Seq Kit v3 – Pico Input Mammalian	Takara Bio USA	Cat. #634488
NucleoMag NGS Clean‐up and Size Select	Takara Bio USA	Cat. #744970.50
Deposited data
mRNA and miRNA seq data	GEO Accession viewer (nih.gov)	GEO: GSE280385
Proteomics data	ProteomeXchange	Data are available via ProteomeXchange with identifier PXD057149
Experimental models: Cell lines
HuTu 80	ATCC	CVCL_1301
CaR‐1	ATCC	CVCL_1116
HT55	ATCC	CVCL_1294
MDST8	ATCC	CVCL_2588
SW1116	ATCC	CVCL_0544
RCM‐1	ATCC	CVCL_1648
Software and algorithms
CMS classifier	Guinney et al. (Guinney et al. 2015)	GitHub—Sage‐Bionetworks/CMSclassifier
R2 bioinformatics platform	AMC	R2: Genomics Analysis and Visualization Platform (amc.nl)
ImageJ	Schneider et al. (Schneider et al. 2012)	https://imagej.nih.gov/ij/
Prism 9.5.1	Graphpad	www.graphpad.com
R 4.3.2	The R project for Statistical Computing	https://www.r‐project.org/
MaxQuant 1.6.10.43	N/A	https://www.maxquant.org/
Other
Plate spectrophotometer	BioTek Instruments	Biotek HT
Transmission electron microscope	ThermoFisher	FEI Technai T12
PowerPlex 16 system	Promega	Cat. #DC6531
U3000 RSLC high pressure nanoLC	Dionex	N/A
Q Exactive mass spectrometer	ThermoFisher	N/A
EVOS FL Cell Imaging System	ThermoFisher	N/A