Experiment description of studies that identified Pdcd6ip in exosomes

1 Experiment ID 26 MISEV standards ✔ EM EV Biophysical techniques ✔ Alix|GAPDH|HSP70|CD9 EV Enriched markers ✘ EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 19109410     Organism Mus musculus Experiment description Proteomic and immunologic analyses of brain tumor exosomes. Authors Graner MW, Alzate O, Dechkovskaia AM, Keene JD, Sampson JH, Mitchell DA, Bigner DD Journal name FASEB Publication year 2008 Sample Brain cancer cells Sample name SMA560vIII Isolation/purification methods Differential centrifugation Sucrose density gradient Flotation density 1.13-1.15 g/mL Molecules identified in the study Protein Methods used in the study Mass spectrometry [MALDI TOF/TOF] Western blotting

2 Experiment ID 914 MISEV standards ✘ EV Biophysical techniques EV Enriched markers ✘ EV Negative markers ✔ NTA EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 33579909     Organism Mus musculus Experiment description Sulfisoxazole does not inhibit the secretion of small extracellular vesicles Authors Fonseka P, Chitti SV, Sanwlani R, Mathivanan S. Journal name Nat Commun Publication year 2021 Sample Breast cancer cells Sample name 4T1 Isolation/purification methods Differential centrifugation Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting

3 Experiment ID 915 MISEV standards ✘ EV Biophysical techniques EV Enriched markers ✘ EV Negative markers ✔ NTA EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 33579909     Organism Mus musculus Experiment description Sulfisoxazole does not inhibit the secretion of small extracellular vesicles Authors Fonseka P, Chitti SV, Sanwlani R, Mathivanan S. Journal name Nat Commun Publication year 2021 Sample Breast cancer cells Sample name 4T1 Isolation/purification methods Differential centrifugation Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting

4 Experiment ID 916 MISEV standards ✘ EV Biophysical techniques EV Enriched markers ✘ EV Negative markers ✔ NTA EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 33579909     Organism Mus musculus Experiment description Sulfisoxazole does not inhibit the secretion of small extracellular vesicles Authors Fonseka P, Chitti SV, Sanwlani R, Mathivanan S. Journal name Nat Commun Publication year 2021 Sample Breast cancer cells Sample name 4T1 Isolation/purification methods Differential centrifugation Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting

5 Experiment ID 917 MISEV standards ✘ EV Biophysical techniques EV Enriched markers ✘ EV Negative markers ✔ NTA EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 33579909     Organism Mus musculus Experiment description Sulfisoxazole does not inhibit the secretion of small extracellular vesicles Authors Fonseka P, Chitti SV, Sanwlani R, Mathivanan S. Journal name Nat Commun Publication year 2021 Sample Breast cancer cells Sample name 4T1 Isolation/purification methods Differential centrifugation Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting

6 Experiment ID 918 MISEV standards ✘ EV Biophysical techniques EV Enriched markers ✘ EV Negative markers ✔ NTA EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 33579909     Organism Mus musculus Experiment description Sulfisoxazole does not inhibit the secretion of small extracellular vesicles Authors Fonseka P, Chitti SV, Sanwlani R, Mathivanan S. Journal name Nat Commun Publication year 2021 Sample Breast cancer cells Sample name 4T1 Isolation/purification methods Differential centrifugation Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting

7 Experiment ID 907 MISEV standards ✔ EM EV Biophysical techniques ✔ Tsg101|Sdcbp|Cd151|Gapdh|Lamp2|Cd81|Cd82|Cd9|Cd63|Cd80|Flot2|Tfrc|Rab35|Rab5a EV Enriched markers ✔ HSPA5 EV Negative markers ✔ NTA EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 37309723     Organism Mus musculus Experiment description Proteomic analysis of the small extracellular vesicles and soluble secretory proteins from cachexia inducing and non-inducing cancer cells Authors Chitti SV, Kang T, Fonseka P, Marzan AL, Stewart S, Shahi S, Bramich K, Ang CS, Pathan M, Gummadi S, Mathivanan S. Journal name Proteomics Publication year 2023 Sample Colon cancer cells Sample name C26 Isolation/purification methods Differential centrifugation Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting Mass spectrometry

8 Experiment ID 907 MISEV standards ✔ EM EV Biophysical techniques ✔ Tsg101|Sdcbp|Cd151|Gapdh|Lamp2|Cd81|Cd82|Cd9|Cd63|Cd80|Flot2|Tfrc|Rab35|Rab5a EV Enriched markers ✔ HSPA5 EV Negative markers ✔ NTA EV Particle analysis Identified molecule Protein Identification method Mass spectrometry PubMed ID 37309723     Organism Mus musculus Experiment description Proteomic analysis of the small extracellular vesicles and soluble secretory proteins from cachexia inducing and non-inducing cancer cells Authors Chitti SV, Kang T, Fonseka P, Marzan AL, Stewart S, Shahi S, Bramich K, Ang CS, Pathan M, Gummadi S, Mathivanan S. Journal name Proteomics Publication year 2023 Sample Colon cancer cells Sample name C26 Isolation/purification methods Differential centrifugation Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting Mass spectrometry

9 Experiment ID 10 MISEV standards ✔ EM EV Biophysical techniques ✔ Alix|CD9|MHCII|MHCI|CD86|LAMP2 EV Enriched markers ✘ EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Mass spectrometry [MALDI TOF] Mass spectrometry [QTOF] Western blotting PubMed ID 11390481     Organism Mus musculus Experiment description Proteomic analysis of dendritic cell-derived exosomes: a secreted subcellular compartment distinct from apoptotic vesicles. Authors Thery C, Boussac M, Veron P, Ricciardi-Castagnoli P, Raposo G, Garin J, Amigorena S. Journal name JIMMU Publication year 2001 Sample Dendritic cells Sample name D1 Isolation/purification methods Differential centrifugation Sucrose density gradient Flotation density 1.15-1.18 g/mL Molecules identified in the study Protein Methods used in the study Mass spectrometry [MALDI TOF] Mass spectrometry [QTOF] Western blotting

10 Experiment ID 73 MISEV standards ✔ EM EV Biophysical techniques ✔ HSP70|HSP90 EV Enriched markers ✘ EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Mass spectrometry Western blotting PubMed ID 18494037     Organism Mus musculus Experiment description Difference gel electrophoresis analysis of Ras-transformed fibroblast cell-derived exosomes. Authors Ji H, Erfani N, Tauro BJ, Kapp EA, Zhu HJ, Moritz RL, Lim JW, Simpson RJ Journal name ELEC Publication year 2008 Sample Embryonic fibroblasts Sample name NIH3T3 Isolation/purification methods Differential centrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Mass spectrometry [LCQ DECA] Western blotting

11 Experiment ID 210 MISEV standards ✔ EM EV Biophysical techniques ✔ CD81|FLOT1 EV Enriched markers ✘ EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Mass spectrometry PubMed ID 23260141     Organism Mus musculus Experiment description Exosomes Mediate Stromal Mobilization of Autocrine Wnt-PCP Signaling in Breast Cancer Cell Migration. Authors Luga V, Zhang L, Viloria-Petit AM, Ogunjimi AA, Inanlou MR, Chiu E, Buchanan M, Hosein AN, Basik M, Wrana JL. Journal name Cell Publication year 2012 Sample Fibroblasts Sample name Normal-Fibroblasts (L cells) Isolation/purification methods Differential centrifugation Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Mass spectrometry

12 Experiment ID 1048 MISEV standards ✔ EM EV Biophysical techniques ✔ Cd63|Tsg101|Cd9 EV Enriched markers ✔ CANX EV Negative markers ✔ NTA EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 30967557     Organism Mus musculus Experiment description KIBRA controls exosome secretion via inhibiting the proteasomal degradation of Rab27a Authors Song L, Tang S, Han X, Jiang Z, Dong L, Liu C, Liang X, Dong J, Qiu C, Wang Y, Du Y. Journal name Nat Commun Publication year 2019 Sample Hippocampal neuronal cells Sample name HT22 Isolation/purification methods Differential centrifugation Filtration Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting

13 Experiment ID 1049 MISEV standards ✔ EM EV Biophysical techniques ✔ Cd63|Tsg101|Cd9 EV Enriched markers ✔ CANX EV Negative markers ✔ NTA EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 30967557     Organism Mus musculus Experiment description KIBRA controls exosome secretion via inhibiting the proteasomal degradation of Rab27a Authors Song L, Tang S, Han X, Jiang Z, Dong L, Liu C, Liang X, Dong J, Qiu C, Wang Y, Du Y. Journal name Nat Commun Publication year 2019 Sample Hippocampal neuronal cells Sample name HT22 Isolation/purification methods Differential centrifugation Filtration Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting

14 Experiment ID 1050 MISEV standards ✘ EV Biophysical techniques ✔ Cd63|Tsg101|Cd9 EV Enriched markers ✔ CANX EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 30967557     Organism Mus musculus Experiment description KIBRA controls exosome secretion via inhibiting the proteasomal degradation of Rab27a Authors Song L, Tang S, Han X, Jiang Z, Dong L, Liu C, Liang X, Dong J, Qiu C, Wang Y, Du Y. Journal name Nat Commun Publication year 2019 Sample Hippocampal neuronal cells Sample name HT22 Isolation/purification methods Differential centrifugation Filtration Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting

15 Experiment ID 1051 MISEV standards ✘ EV Biophysical techniques ✔ Cd63|Tsg101|Cd9 EV Enriched markers ✔ CANX EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 30967557     Organism Mus musculus Experiment description KIBRA controls exosome secretion via inhibiting the proteasomal degradation of Rab27a Authors Song L, Tang S, Han X, Jiang Z, Dong L, Liu C, Liang X, Dong J, Qiu C, Wang Y, Du Y. Journal name Nat Commun Publication year 2019 Sample Hippocampal neuronal cells Sample name HT22 Isolation/purification methods Differential centrifugation Filtration Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting

16 Experiment ID 1065 MISEV standards ✘ EV Biophysical techniques ✔ Tsg101 EV Enriched markers ✘ EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 30967557     Organism Mus musculus Experiment description KIBRA controls exosome secretion via inhibiting the proteasomal degradation of Rab27a Authors Song L, Tang S, Han X, Jiang Z, Dong L, Liu C, Liang X, Dong J, Qiu C, Wang Y, Du Y. Journal name Nat Commun Publication year 2019 Sample Hippocampal neuronal cells Sample name HT22 Isolation/purification methods Differential centrifugation Filtration Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting

17 Experiment ID 1066 MISEV standards ✘ EV Biophysical techniques ✔ Tsg101 EV Enriched markers ✘ EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 30967557     Organism Mus musculus Experiment description KIBRA controls exosome secretion via inhibiting the proteasomal degradation of Rab27a Authors Song L, Tang S, Han X, Jiang Z, Dong L, Liu C, Liang X, Dong J, Qiu C, Wang Y, Du Y. Journal name Nat Commun Publication year 2019 Sample Hippocampal neuronal cells Sample name HT22 Isolation/purification methods Differential centrifugation Filtration Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting

18 Experiment ID 214 MISEV standards ✔ EM EV Biophysical techniques ✘ EV Enriched markers ✘ EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Mass spectrometry PubMed ID 23658846     Organism Mus musculus Experiment description Immunomodulatory impact of leishmania-induced macrophage exosomes: a comparative proteomic and functional analysis. Authors Hassani K, Olivier M. Journal name PLoS Negl Trop Dis Publication year 2013 Sample Macrophages Sample name Leishmania-infected-Macrophage (J774A.1) Isolation/purification methods Differential centrifugation Filtration Ultracentrifugation Filtration Protease inhibitors Sucrose density gradient Filtration Ultracentrifugation Flotation density 1.13-1.19 g/mL Molecules identified in the study Protein Methods used in the study Mass spectrometry

19 Experiment ID 215 MISEV standards ✔ EM EV Biophysical techniques ✘ EV Enriched markers ✘ EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Mass spectrometry PubMed ID 23658846     Organism Mus musculus Experiment description Immunomodulatory impact of leishmania-induced macrophage exosomes: a comparative proteomic and functional analysis. Authors Hassani K, Olivier M. Journal name PLoS Negl Trop Dis Publication year 2013 Sample Macrophages Sample name LPS-treated-Macrophage (J774A.1) Isolation/purification methods Differential centrifugation Filtration Ultracentrifugation Filtration Protease inhibitors Sucrose density gradient Filtration Ultracentrifugation Flotation density 1.13-1.19 g/mL Molecules identified in the study Protein Methods used in the study Mass spectrometry

20 Experiment ID 216 MISEV standards ✔ EM EV Biophysical techniques ✘ EV Enriched markers ✘ EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Mass spectrometry PubMed ID 23658846     Organism Mus musculus Experiment description Immunomodulatory impact of leishmania-induced macrophage exosomes: a comparative proteomic and functional analysis. Authors Hassani K, Olivier M. Journal name PLoS Negl Trop Dis Publication year 2013 Sample Macrophages Sample name Normal-Macrophage (J774A.1) Isolation/purification methods Differential centrifugation Filtration Ultracentrifugation Filtration Protease inhibitors Sucrose density gradient Filtration Ultracentrifugation Flotation density 1.13-1.19 g/mL Molecules identified in the study Protein Methods used in the study Mass spectrometry

21 Experiment ID 15 MISEV standards ✔ EM EV Biophysical techniques ✔ CD63 EV Enriched markers ✘ EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Mass spectrometry PubMed ID 17486113     Organism Mus musculus Homo sapiens Experiment description Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells. Authors Valadi H, Ekstrom K, Bossios A, Sjostrand M, Lee JJ, Lotvall JO Journal name NCB Publication year 2007 Sample Mast cells Sample name MC9 Bone marrow-derived mast cells HMC-1 Isolation/purification methods Filtration Ultracentrifugation Sucrose density gradient Flotation density 1.11-1.21 g/mL Molecules identified in the study Protein mRNA miRNA Methods used in the study Mass spectrometry [MALDI TOF] Western blotting Microarray miRCURY LNA Array

22 Experiment ID 968 MISEV standards ✘ EV Biophysical techniques ✔ Tsg101|Gapdh EV Enriched markers ✘ EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 30089911     Organism Mus musculus Experiment description Exosomal PD-L1 contributes to immunosuppression and is associated with anti-PD-1 response Authors Chen G, Huang AC, Zhang W, Zhang G, Wu M, Xu W, Yu Z, Yang J, Wang B, Sun H, Xia H, Man Q, Zhong W, Antelo LF, Wu B, Xiong X, Liu X, Guan L, Li T, Liu S, Yang R, Lu Y, Dong L, McGettigan S, Somasundaram R, Radhakrishnan R, Mills G, Lu Y, Kim J, Chen YH, Dong H, Zhao Y, Karakousis GC, Mitchell TC, Schuchter LM, Herlyn M, Wherry EJ, Xu X, Guo W. Journal name Nature Publication year 2018 Sample Melanoma cells Sample name B16-F10 Isolation/purification methods Differential centrifugation Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting

23 Experiment ID 1101 MISEV standards ✔ EM EV Biophysical techniques ✔ Cd81|Cd9|Tfrc|Gapdh|Lamp1 EV Enriched markers ✔ GOLGA2|CANX EV Negative markers ✔ NTA EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 34957415     Organism Mus musculus Experiment description Melanoma-derived small extracellular vesicles induce lymphangiogenesis and metastasis through an NGFR-dependent mechanism Authors García-Silva S, Benito-Martín A, Nogués L, Hernández-Barranco A, Mazariegos MS, Santos V, Hergueta-Redondo M, Ximénez-Embún P, Kataru RP, Lopez AA, Merino C, Sánchez-Redondo S, Graña-Castro O, Matei I, Nicolás-Avila JÁ, Torres-Ruiz R, Rodríguez-Perales S, Martínez L, Pérez-Martínez M, Mata G, Szumera-Ciećkiewicz A, Kalinowska I, Saltari A, Martínez-Gómez JM, Hogan SA, Saragovi HU, Ortega S, Garcia-Martin C, Boskovic J, Levesque MP, Rutkowski P, Hidalgo A, Muñoz J, Megías D, Mehrara BJ, Lyden D, Peinado H. Journal name Nat Cancer Publication year 2021 Sample Melanoma cells Sample name B16-F1 Isolation/purification methods Differential centrifugation Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting Mass spectrometry

24 Experiment ID 1102 MISEV standards ✔ EM EV Biophysical techniques ✔ Cd81|Cd9|Tfrc|Gapdh|Lamp1 EV Enriched markers ✔ GOLGA2|CANX EV Negative markers ✔ NTA EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 34957415     Organism Mus musculus Experiment description Melanoma-derived small extracellular vesicles induce lymphangiogenesis and metastasis through an NGFR-dependent mechanism Authors García-Silva S, Benito-Martín A, Nogués L, Hernández-Barranco A, Mazariegos MS, Santos V, Hergueta-Redondo M, Ximénez-Embún P, Kataru RP, Lopez AA, Merino C, Sánchez-Redondo S, Graña-Castro O, Matei I, Nicolás-Avila JÁ, Torres-Ruiz R, Rodríguez-Perales S, Martínez L, Pérez-Martínez M, Mata G, Szumera-Ciećkiewicz A, Kalinowska I, Saltari A, Martínez-Gómez JM, Hogan SA, Saragovi HU, Ortega S, Garcia-Martin C, Boskovic J, Levesque MP, Rutkowski P, Hidalgo A, Muñoz J, Megías D, Mehrara BJ, Lyden D, Peinado H. Journal name Nat Cancer Publication year 2021 Sample Melanoma cells Sample name B16-F10 Isolation/purification methods Differential centrifugation Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting Mass spectrometry Flow cytometry

25 Experiment ID 1103 MISEV standards ✔ EM EV Biophysical techniques ✔ Cd81|Cd9|Tfrc|Gapdh|Lamp1 EV Enriched markers ✔ GOLGA2|CANX EV Negative markers ✔ NTA EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 34957415     Organism Mus musculus Experiment description Melanoma-derived small extracellular vesicles induce lymphangiogenesis and metastasis through an NGFR-dependent mechanism Authors García-Silva S, Benito-Martín A, Nogués L, Hernández-Barranco A, Mazariegos MS, Santos V, Hergueta-Redondo M, Ximénez-Embún P, Kataru RP, Lopez AA, Merino C, Sánchez-Redondo S, Graña-Castro O, Matei I, Nicolás-Avila JÁ, Torres-Ruiz R, Rodríguez-Perales S, Martínez L, Pérez-Martínez M, Mata G, Szumera-Ciećkiewicz A, Kalinowska I, Saltari A, Martínez-Gómez JM, Hogan SA, Saragovi HU, Ortega S, Garcia-Martin C, Boskovic J, Levesque MP, Rutkowski P, Hidalgo A, Muñoz J, Megías D, Mehrara BJ, Lyden D, Peinado H. Journal name Nat Cancer Publication year 2021 Sample Melanoma cells Sample name B16-F1R2 Isolation/purification methods Differential centrifugation Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting Mass spectrometry Flow cytometry

26 Experiment ID 1104 MISEV standards ✘ EV Biophysical techniques ✔ Cd81|Cd9 EV Enriched markers ✘ EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 34957415     Organism Mus musculus Experiment description Melanoma-derived small extracellular vesicles induce lymphangiogenesis and metastasis through an NGFR-dependent mechanism Authors García-Silva S, Benito-Martín A, Nogués L, Hernández-Barranco A, Mazariegos MS, Santos V, Hergueta-Redondo M, Ximénez-Embún P, Kataru RP, Lopez AA, Merino C, Sánchez-Redondo S, Graña-Castro O, Matei I, Nicolás-Avila JÁ, Torres-Ruiz R, Rodríguez-Perales S, Martínez L, Pérez-Martínez M, Mata G, Szumera-Ciećkiewicz A, Kalinowska I, Saltari A, Martínez-Gómez JM, Hogan SA, Saragovi HU, Ortega S, Garcia-Martin C, Boskovic J, Levesque MP, Rutkowski P, Hidalgo A, Muñoz J, Megías D, Mehrara BJ, Lyden D, Peinado H. Journal name Nat Cancer Publication year 2021 Sample Melanoma cells Sample name B16-F10 - Fraction 6 Isolation/purification methods Differential centrifugation OptiPrep density gradient centrifugation Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting

27 Experiment ID 1105 MISEV standards ✘ EV Biophysical techniques ✔ Cd81|Cd9 EV Enriched markers ✘ EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 34957415     Organism Mus musculus Experiment description Melanoma-derived small extracellular vesicles induce lymphangiogenesis and metastasis through an NGFR-dependent mechanism Authors García-Silva S, Benito-Martín A, Nogués L, Hernández-Barranco A, Mazariegos MS, Santos V, Hergueta-Redondo M, Ximénez-Embún P, Kataru RP, Lopez AA, Merino C, Sánchez-Redondo S, Graña-Castro O, Matei I, Nicolás-Avila JÁ, Torres-Ruiz R, Rodríguez-Perales S, Martínez L, Pérez-Martínez M, Mata G, Szumera-Ciećkiewicz A, Kalinowska I, Saltari A, Martínez-Gómez JM, Hogan SA, Saragovi HU, Ortega S, Garcia-Martin C, Boskovic J, Levesque MP, Rutkowski P, Hidalgo A, Muñoz J, Megías D, Mehrara BJ, Lyden D, Peinado H. Journal name Nat Cancer Publication year 2021 Sample Melanoma cells Sample name B16-F1R2 - Fraction 5 Isolation/purification methods Differential centrifugation OptiPrep density gradient centrifugation Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting

28 Experiment ID 1106 MISEV standards ✘ EV Biophysical techniques ✔ Cd81|Cd9 EV Enriched markers ✘ EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 34957415     Organism Mus musculus Experiment description Melanoma-derived small extracellular vesicles induce lymphangiogenesis and metastasis through an NGFR-dependent mechanism Authors García-Silva S, Benito-Martín A, Nogués L, Hernández-Barranco A, Mazariegos MS, Santos V, Hergueta-Redondo M, Ximénez-Embún P, Kataru RP, Lopez AA, Merino C, Sánchez-Redondo S, Graña-Castro O, Matei I, Nicolás-Avila JÁ, Torres-Ruiz R, Rodríguez-Perales S, Martínez L, Pérez-Martínez M, Mata G, Szumera-Ciećkiewicz A, Kalinowska I, Saltari A, Martínez-Gómez JM, Hogan SA, Saragovi HU, Ortega S, Garcia-Martin C, Boskovic J, Levesque MP, Rutkowski P, Hidalgo A, Muñoz J, Megías D, Mehrara BJ, Lyden D, Peinado H. Journal name Nat Cancer Publication year 2021 Sample Melanoma cells Sample name B16-F1R2 - Fraction 6 Isolation/purification methods Differential centrifugation OptiPrep density gradient centrifugation Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting

29 Experiment ID 14 MISEV standards ✔ EM EV Biophysical techniques ✔ RAB7|RAB11|CD9|CD63|LAMP1|LAMP2 EV Enriched markers ✔ DNM EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Mass spectrometry PubMed ID 16081791     Organism Mus musculus Experiment description Proteomic analysis of microglia-derived exosomes: metabolic role of the aminopeptidase CD13 in neuropeptide catabolism. Authors Potolicchio I, Carven GJ, Xu X, Stipp C, Riese RJ, Stern LJ, Santambrogio L Journal name JIMMU Publication year 2005 Sample Microglia Sample name N9 Isolation/purification methods Differential centrifugation Sucrose density gradient Flotation density 1.15 g/mL Molecules identified in the study Protein Methods used in the study Mass spectrometry [LCQ DECA XP] Western blotting

30 Experiment ID 505 MISEV standards ✘ EV Biophysical techniques ✔ Flot2 EV Enriched markers ✔ Tomm20 EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 36214496     Organism Mus musculus Experiment description Contaminating transfection complexes can masquerade as small extracellular vesicles and impair their delivery of RNA Authors McCann J, Sosa-Miranda CD, Guo H, Reshke R, Savard A, Zardini Buzatto A, Taylor JA, Li L, Gibbings DJ. Journal name J Extracell Vesicles Publication year 2022 Sample Motor neuron-like cells Sample name NSC-34 Isolation/purification methods Differential centrifugation Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting

31 Experiment ID 506 MISEV standards ✘ EV Biophysical techniques ✔ Flot2 EV Enriched markers ✔ Tomm20 EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 36214496     Organism Mus musculus Experiment description Contaminating transfection complexes can masquerade as small extracellular vesicles and impair their delivery of RNA Authors McCann J, Sosa-Miranda CD, Guo H, Reshke R, Savard A, Zardini Buzatto A, Taylor JA, Li L, Gibbings DJ. Journal name J Extracell Vesicles Publication year 2022 Sample Motor neuron-like cells Sample name NSC-34 Isolation/purification methods Differential centrifugation Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting

32 Experiment ID 262 MISEV standards ✔ EM EV Biophysical techniques ✔ Alix|TSG101|HSP70|HSP90|CD63|CD9| EV Enriched markers ✘ EV Negative markers ✔ Y EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 25242146     Organism Mus musculus Experiment description Extracellular Vesicles from Neural Stem Cells Transfer IFN-γ via Ifngr1 to Activate Stat1 Signaling in Target Cells Authors Chiara Cossetti, Nunzio Iraci, Tim R. Mercer, Tommaso Leonardi, Emanuele Alpi, Denise Drago, Clara Alfaro-Cervello, Harpreet K. Saini, Matthew P. Davis, Julia Schaeffer, Beatriz Vega, Matilde Stefanini, CongJian Zhao, Werner Muller, Jose Manuel Garcia-Verdugo, Suresh Mathivanan, Angela Bachi, Anton J. Enright, John S. Mattick, Stefano Pluchino Journal name Molecular Cell Publication year 2014 Sample Neural stem cells Sample name NPCs Isolation/purification methods Differential centrifugation Ultracentrifugation Sucrose density gradient Flotation density 1.13-1.20 g/mL Molecules identified in the study Protein Methods used in the study Western blotting Mass spectrometry Microarray

33 Experiment ID 33 MISEV standards ✔ EM|IEM EV Biophysical techniques ✔ Alix|TSG101 EV Enriched markers ✘ EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 21136642     Organism Mus musculus Experiment description Oligodendrocytes secrete exosomes containing major myelin and stress-protective proteins: Trophic support for axons? Authors Kramer-Albers EM, Bretz N, Tenzer S, Winterstein C, Mobius W, Berger H, Nave KA, Schild H, Trotter J Journal name PROTEOMICS_CL Publication year 2007 Sample Oligodendrocytes Sample name Oligodendrocytes Oli-neu Isolation/purification methods Differential centrifugation Sucrose density gradient Flotation density 1.10-1.14 g/mL Molecules identified in the study Protein Methods used in the study Mass spectrometry [QTOF] Western blotting Immunoelectron Microscopy

34 Experiment ID 130 MISEV standards ✔ EM EV Biophysical techniques ✔ Alix|FLOT2 EV Enriched markers ✔ CANX|GOLGA2 EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 18309083     Organism Mus musculus Experiment description Ceramide triggers budding of exosome vesicles into multivesicular endosomes Authors Trajkovic K, Hsu C, Chiantia S, Rajendran L, Wenzel D, Wieland F, Schwille P, Brugger B, Simons M. Journal name SCIENCE Publication year 2008 Sample Oligodendrocytes Sample name Oli-neu cells Isolation/purification methods Differential centrifugation Sucrose density gradient Flotation density - Molecules identified in the study Protein Lipids Methods used in the study Western blotting Mass spectrometry [QTOF]

35 Experiment ID 1052 MISEV standards ✘ EV Biophysical techniques ✔ Cd63|Tsg101|Cd9 EV Enriched markers ✔ CANX EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 30967557     Organism Mus musculus Experiment description KIBRA controls exosome secretion via inhibiting the proteasomal degradation of Rab27a Authors Song L, Tang S, Han X, Jiang Z, Dong L, Liu C, Liang X, Dong J, Qiu C, Wang Y, Du Y. Journal name Nat Commun Publication year 2019 Sample Podocytes Sample name MPC-5 Isolation/purification methods Differential centrifugation Filtration Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting

36 Experiment ID 1053 MISEV standards ✘ EV Biophysical techniques ✔ Cd63|Tsg101|Cd9 EV Enriched markers ✔ CANX EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 30967557     Organism Mus musculus Experiment description KIBRA controls exosome secretion via inhibiting the proteasomal degradation of Rab27a Authors Song L, Tang S, Han X, Jiang Z, Dong L, Liu C, Liang X, Dong J, Qiu C, Wang Y, Du Y. Journal name Nat Commun Publication year 2019 Sample Podocytes Sample name MPC-5 Isolation/purification methods Differential centrifugation Filtration Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting

37 Experiment ID 870 MISEV standards ✔ EM EV Biophysical techniques ✔ Flot1 EV Enriched markers ✘ EV Negative markers ✘ EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 35173168     Organism Mus musculus Experiment description Lin28B-high breast cancer cells promote immune suppression in the lung pre-metastatic niche via exosomes and support cancer progression Authors Qi M, Xia Y, Wu Y, Zhang Z, Wang X, Lu L, Dai C, Song Y, Xu K, Ji W, Zhan L. Journal name Nat Commun Publication year 2022 Sample Serum Sample name BALB/c bearing 4T07 primary tumour Isolation/purification methods Differential centrifugation Filtration Ultracentrifugation Flotation density - Molecules identified in the study Protein mRNA Methods used in the study Western blotting RNA sequencing qRT-PCR

38 Experiment ID 908 MISEV standards ✔ EM EV Biophysical techniques ✔ Tsg101|Sdcbp|Cd151|Gapdh|Lamp2|Cd81|Cd82|Cd9|Cd63|Cd80|Flot2|Tfrc|Rab35|Rab5a EV Enriched markers ✔ HSPA5 EV Negative markers ✔ NTA EV Particle analysis Identified molecule protein Identification method Western blotting PubMed ID 37309723     Organism Mus musculus Experiment description Proteomic analysis of the small extracellular vesicles and soluble secretory proteins from cachexia inducing and non-inducing cancer cells Authors Chitti SV, Kang T, Fonseka P, Marzan AL, Stewart S, Shahi S, Bramich K, Ang CS, Pathan M, Gummadi S, Mathivanan S. Journal name Proteomics Publication year 2023 Sample T-cell lymphoma cells Sample name EL4 Isolation/purification methods Differential centrifugation Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting Mass spectrometry

39 Experiment ID 908 MISEV standards ✔ EM EV Biophysical techniques ✔ Tsg101|Sdcbp|Cd151|Gapdh|Lamp2|Cd81|Cd82|Cd9|Cd63|Cd80|Flot2|Tfrc|Rab35|Rab5a EV Enriched markers ✔ HSPA5 EV Negative markers ✔ NTA EV Particle analysis Identified molecule Protein Identification method Mass spectrometry PubMed ID 37309723     Organism Mus musculus Experiment description Proteomic analysis of the small extracellular vesicles and soluble secretory proteins from cachexia inducing and non-inducing cancer cells Authors Chitti SV, Kang T, Fonseka P, Marzan AL, Stewart S, Shahi S, Bramich K, Ang CS, Pathan M, Gummadi S, Mathivanan S. Journal name Proteomics Publication year 2023 Sample T-cell lymphoma cells Sample name EL4 Isolation/purification methods Differential centrifugation Ultracentrifugation Flotation density - Molecules identified in the study Protein Methods used in the study Western blotting Mass spectrometry

Protein-protein interactions for Pdcd6ip

Protein Interactor ExoCarta ID Identification method PubMed Species No interactions are found.

Pathways in which Pdcd6ip is involved

No pathways found