| Data Submission Guidelines | ||
| 1. | Fill in the experiment description spread sheet 
| |
| 2. | Based on the molecule data type you are submitting, fill in the appropriate spreadsheet(s) Protein spread sheet Mass spectromtery based protein spread sheet Lipid spread sheet mRNA spread sheet miRNA spread sheet Post-translational modifications spreadsheet | |
| 3. |
| |
| Information on column headers | |
 Experiment description | |
| The spread sheet includes meta annotations pertaining to the experiments performed. It is critical to know what samples were used and how the extracellular vesicles (EVs) are isolated. These information will allow the users to differentiate between crude and close-to-pure populations of EVs. | |
| Experiment # | The experiment number can be any number (e.g., 21). Please give different experiment numbers if more than 1 sample (e.g., urine and serum) or more than 1 organism (e.g., mouse and human) is used. |
| PubMed ID | PubMed identifier provided for published article. If the article is unpublished,please include unpublished in this section. If the article is not indexed in PubMed, provide 0. |
| Species | Organism name. Please provide based on the taxonomical nomenclature (e.g., Homo sapiens) |
| Experiment Description | Provide the title of the article/study. |
| Sample | Provide the sample source in a broader context (e.g., colorectal cancer cells). In case of working with whole organisms, please provide the organism name in taxonomical nomenclature (e.g., Aedes aegypti). |
| Sample source | Provide two letter codes (ts-tissue, cl-cell lines, fl-fluid, wo-whole organism). |
| Cell line or tissue or fluid name | Provide the name of the cell line/tissue/fluid/organism (e.g., SW480) |
| Identifications | Provide the molecules identified (e.g., Protein, mRNA, miRNA or Lipids). When more than one kind of molecule is found in the study, use | to separate them (e.g., Protein|miRNA|mRNA). |
| Methods used | All the methods used in the study that identified the molecules (e.g., FACS, Western blotting). When more than one method was used in the study, use | to separate them (e.g., Western blotting|FACS). |
| Journal name | Provide the journal name as in PubMed. If unpublished, place “-“. |
| Authors as in PubMed | Author list as listed in the study (PubMed style). |
| Year published | Provide the year the article was published. If unpublished, place “-“. |
| Floatation | If density gradient centrifugation was used (sucrose, OptiPrep), provide the floatation density (e.g., 1.10 – 1.22 g/mL). |
| Isolation method | Provide the isolation method used. When multiple steps are used, separate them by | (e.g., Differential centrifugation|Filtration|Ultracenrifugation|Density gradient centrifugation|Exoquick|Immunoaffinity (EPCAM)|FACS (CD63)). |
| Vesicle type | Provide the vesicle type. It will be appreciated if the nomenclature in naming EVs follow the listed article Vesicle naming |
| Protein spread sheet | |
| The spread sheet includes proteins identified in an EV study. | |
| Entrez Gene ID | Provide the NCBI Entrez Gene ID. Why provide gene id rather than a protein (e.g., UniProt) or a RNA database accession (e.g., NCBI GI) identifier? While some experiments (high-throughput) provide sequence specific information many biochemical experiments that are commonly used in labs do not have sequence specific information (e.g., Western blotting – probing for BRCA1 which has multiple isoforms). For this reason, we obtain gene specific identifiers. Please make sure there is only one unique representation of a protein in the spread sheet. |
| Species | Organism name. Please provide based on the taxonomical nomenclature (e.g., Homo sapiens) |
| Experiment # | The experiment number has to be the exact number that was used in the experiment description spread sheet. |
| Method | Provide the method(s) that were used to identify the protein. As we require unique protein identifications, please place all the methods used to identify a protein separated by | (e.g., Western blotting|Mass spectrometry|Immunoelctron microscopy) |
| Sequence identifier (can be any protein sequence database) | Even though we obtain gene specific information for all the proteins, sequence specific data obtained by some techniques cannot be ignored. For this reason, we require sequence specific data (e.g., UniProt ID for the protein identified - P06238.2). |
| Mass spectromtery based protein spread sheet | |
| The spread sheet includes proteins identified by mass spectrometry in an EV study. | |
| Entrez Gene ID | Provide the NCBI Entrez Gene ID used in protein spread sheet. |
| mz | Provide mz obtained from the experiment. |
| z | Provide the charge. |
| Peptide score/E-value | Provide any peptide based score (e.g., Mascot ion score, SEQUEST Xcorr score) |
| Peptide start | Provide the peptide start in the protein sequence. |
| Peptide end | Provide the peptide end in the protein sequence. |
| E-value | Provide the peptide E-value. |
| Residue before | Provide the residue before the peptide in the protein sequence. |
| Peptide sequence | Provide the peptide sequence identified. |
| Residue after | Provide the residue after the peptide in the protein sequence. |
| Sequence identifier (can be any protein sequence database) | Provide the sequence identifier (e.g., UniProt ID for the protein identified - P06238.2). |
| Lipid spread sheet | |
| The spread sheet includes lipids identified in an EV study. | |
| Lipid name | Provide the name of the lipid identified. Please look at this spread sheet to have a list of lipids added in Vesiclepedia. |
| Species | Organism name. Please provide based on the taxonomical nomenclature (e.g., Homo sapiens) |
| Experiment # | The experiment number has to be the exact number that was used in the experiment description spread sheet. |
| Method | Provide the method(s) that were used to identify the lipid. As we require unique lipid identifications, please place all the methods used to identify a protein separated by | (e.g., Thin layer chromatography|Cytofluorographic analysis) |
| mRNA spread sheet | |
| The spread sheet includes mRNA identified in an EV study. | |
| Entrez Gene ID | Provide the NCBI Entrez Gene ID. Please make sure there is only one unique representation of a mRNA in the spread sheet. |
| Species | Organism name. Please provide based on the taxonomical nomenclature (e.g., Homo sapiens). |
| Experiment # | The experiment number has to be the exact number that was used in the experiment description spread sheet. |
| Method | Provide the method(s) that were used to detect the mRNA. As we require unique mRNA identifications, please place all the methods used to identify the mRNA separated by | (e.g., RT-PCR|Microarray). |
| Sequence identifier (can be any nucleotide sequence database) | Provide sequence specific information (e.g., RefSeq nucleotide accession - NM_6239823.8). |
| miRNA spread sheet | |
| The spread sheet includes miRNA identified in an EV study. | |
| miRNA ID | Provide the miRNA ID (e.g., miR-223). Please make sure there is only one unique representation of a miRNA in the spread sheet. |
| Species | Organism name. Please provide based on the taxonomical nomenclature (e.g., Homo sapiens). |
| Experiment # | The experiment number has to be the exact number that was used in the experiment description spread sheet. |
| Method | Provide the method(s) that were used to detect the miRNA. As we require unique miRNA identifications, please place all the methods used to identify the miRNA separated by | (e.g., RT-PCR|Microarray). |
| Post-translational modifications (PTM) spread sheet | |
| The spread sheet includes PTMs identified in an EV study. | |
| Entrez Gene ID | Provide the NCBI Entrez Gene ID. Why provide gene id rather than a protein (e.g., UniProt) or a RNA database accession (e.g., NCBI GI) identifier? While some experiments (high-throughput) provide sequence specific information many biochemical experiments that are commonly used in labs do not have sequence specific information (e.g., Western blotting – probing for AKT phosphorylation). For this reason, we obtain gene specific identifiers. Please make sure there is only one unique representation of a protein in the spread sheet. |
| Species | Organism name. Please provide based on the taxonomical nomenclature (e.g., Homo sapiens) |
| Experiment # | The experiment number has to be the exact number that was used in the experiment description spread sheet. |
| Method | Provide the method(s) that were used to identify the PTM in the protein. |
| PTM site | Provide the position at which the PTM occurred (the position is accordance to the sequence identifier provided). |
| PTM residue | Provide the amino acid residue that is modified. |
| PTM type | Provide the PTM type. |
| Sequence identifier (can be any protein sequence database) | Provide sequence specific data (e.g., UniProt ID for the protein identified - P06238.2). Please make sure that the PTM site is placed in the context of this sequence identifier. |