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This page provides an example of the ISA-TAB-Nano Investigation File leveraging data from an Nanotechnology Characterization Laboratory (NCL) Investigation ( NCL200612A ). For the complete file, refer the NCL Investigation File Example.
The ISA-TAB-Nano Investigation File consists of the following sections:
- ONTOLOGY SOURCE REFERENCE
- INVESTIGATION
- INVESTIGATION PUBLICATIONS
- INVESTIGATION CONTACTS
- MATERIAL
- STUDY
- STUDY DESIGN DESCRIPTORS
- STUDY PUBLICATIONS
- STUDY FACTORS
- STUDY ASSAYS
- STUDY PROTOCOLS
- STUDY CONTACTS
The following sections provide an example of each Investigation File section.
Ontology Source Reference
Example Investigation File Ontology Source Reference Section
| A | B | C | D | E | F | G | ||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Term Source Name | MO | NPO | UO | ChEBI | PATO | NCIt | ||||||||||||||||||||||||||||||||||||||||
| Term Source File | http://purl.bioontology.org/ontology/MO
| http://purl.bioontology.org/ontology/npo
| http://purl.bioontology.org/ontology/UO
| http://purl.bioontology.org/ontology/CHEBI
| http://purl.bioontology.org/ontology/PATO
| http://ncit.nci.nih.gov/ | ||||||||||||||||||||||||||||||||||||||||
| Term Source Version | v.1.3.1.1 | v.2011-02-12 | v.80 | v.11.11d | ||||||||||||||||||||||||||||||||||||||||||
| Term Source Description | MGED Ontology | NanoParticle Ontology | Unit Ontology | Chemical Entities of Biological Interest | Phenotype Ontology | NCI Thesaurus |
Investigation
Example Investigation File Investigation Section
| A | B |
|---|---|
| Investigation Identifier | NCL200612A |
| Investigation Title | Dendrimer-Based MRI Contrast Agents |
| Investigation Description |
Section | Field | Field Status (if applicable) |
|---|---|---|
INVESTIGATION | Investigation disease | Required |
INVESTIGATION | Investigation disease term accession number | Required |
INVESTIGATION | Investigation disease term source REF | Required |
INVESTIGATION | Investigation outcome | Optional |
STUDY | Study disease | Required |
STUDY | Study disease term accession number | Required |
STUDY | Study disease term source REF | Required |
STUDY | Study outcome | Optional |
STUDY ASSAYS | Study assay measurement name | Required |
STUDY ASSAYS | Study assay measurement name term accession number | Required |
STUDY ASSAYS | Study assay measurement name term source REF | Required |
STUDY ASSAYS | Study assay measurement unit | Required |
STUDY ASSAYS | Study assay measurement unit term accession number | Required |
STUDY ASSAYS | Study assay measurement unit term source REF | Required |
STUDY ASSAYS | Study assay measurement statistic | Required |
STUDY ASSAYS | Study assay measurement statistic term accession number | Required |
STUDY ASSAYS | Study assay measurement statistic term source REF | Required |
STUDY FACTORS | Study factor unit | Required |
STUDY FACTORS | Study factor unit term accession number | Required |
STUDY FACTORS | Study factor unit term source REF. | Required |
STUDY PROTOCOLS | Study protocol parameter unit | Required |
STUDY PROTOCOLS | Study protocol parameter unit term accession number | Required |
STUDY PROTOCOLS | Study protocol parameter unit term source REF | Required |
This page is used to describe an Investigation file.
Investigation
An example of the INVESTIGATION section is in the TABLE 1 below along with example data. The INVESTIGATION section uses 9 concepts. These concepts are described below:
Investigation identifier--- A locally unique identifier or an accession number provided by a repository. This concept is taken from ISA-TAB.
Investigation title---A concise phrase used as a title for the investigation. This concept is adapted from ISA-TAB.
Investigation description---A textual description of the investigation. This concept is taken from ISA-TAB.
Investigation disease---Disease(s) that are the subject of an investigation, if applicable. This concept is introduced in nano-TAB to identify the disease(s) related to the subject of the investigation
Investigation disease term accession number---Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for investigation disease. This concept is introduced in nano-TAB.
Investigation disease term source REF--- The name which identifies the source from where the term for investigation disease is selected. This name should match one of the names entered in the term source name field. This concept is introduced in nano-TAB.
Investigation outcome---A textual description of the outcome(s) of an investigation. This concept is introduced in nano-TAB to provide a brief summary or conclusion of an investigation
Investigation submission date---The date on which the investigation was reported to a repository (format: YYYY-MM-DD). This concept is taken from ISA-TAB.
Investigation public release date---The date on which the investigation is publicly released or published (format: YYYY-MM-DD). This concept is taken from ISA-TAB.
TABLE 1: Example Investigation Section
A
B
INVESTIGATION
Investigation Identifier
NCL200612A
Investigation Title
Dendrimer-Based MRI Contrast Agents
| The goal of this investigation is to characterize a PAMAM dendrimer with an associated gadolinium chelate MRI contrast agent. |
Investigation Disease
Investigation Disease Term Accession Number
| Investigation |
| Submission Date | 2002-11-30 |
| Investigation Public Release Date | 2002-11-30 |
| Investigation |
...
The INVESTIGATION CONTACTS section allows for the identification of the point(s) of contact for an investigation. An example of the INVESTIGATION CONTACTS section of the spreadsheet is in TABLE 2 along with example data.
There are 11 concepts used as field names in the INVESTIGATION CONTACTS section. These concepts are taken from ISA-TAB and are described below:
Investigation person last name---The last name of a person who is the point of contact for the investigation.
Investigation person first name---The first name of a person who is the point of contact for the investigation.
Investigation person middle initials---The middle initial(s) of a person who is the point of contact for the investigation.
Investigation person email---The email address of a person who is the point of contact for the investigation.
Investigation person phone---The telephone number of a person who is the point of contact for the investigation.
Investigation person fax---The fax number of a person who is the point of contact for the investigation.
Investigation person address---The mailing address of a person who is the point of contact for the investigation.
Investigation person affiliation--- The name of the organization to which the point of contact belongs.
Investigation person role--- The term which classifies the role(s) performed by person who is the point of contact for the investigation.
Investigation person role term accession number--- Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for investigation person role.
Investigation person role term source REF--- Name of the ontology or controlled vocabulary from which a term is selected and entered as a value for investigation person role.
| Disease | |
| Investigation Disease Term Accession Number | |
| Investigation Disease Term Source REF | |
| Investigation Outcome |
Investigation Publications
Example Investigation Publication Section
| A | B |
|---|---|
| Investigation PubMed ID | 18095846 |
| Investigation Publication DOI | 10.2217/17435889.2.6.789 |
| Investigation Publication Author List | Hall JB; Dobrovolskaia MA; Patri AK; McNeil SE |
| Investigation Publication Title | Characterization of nanoparticles for therapeutics |
| Investigation Publication Status | published |
| Investigation Publication Status Term Accession Number | |
| Investigation Publication Status Term Source REF |
Investigation Contacts
Example Investigation File TABLE 2. Example Investigation Contacts Section
| A | B |
|---|
INVESTIGATION CONTACTS
| Investigation Person Last Name |
| Doe |
| Investigation Person First Name |
| John |
| Investigation Person |
| Mid Initials | E |
| Investigation Person Email |
| doej@mail.nih.gov |
| Investigation Person Phone |
| 1231231234 | |
| Investigation Person Fax | |
| Investigation Person Address |
| Laboratory Street, |
| City, State 111111 |
| Investigation Person Affiliation |
| Doe Laboratories |
| Investigation Person |
| Roles | investigator |
| Investigation Person |
| Roles Term Accession Number | |
| Investigation Person |
| Roles Term Source REF | MO |
Investigation Publications
The INVESTIGATION PUBLICATIONS section allows for the identification of articles (published) associated with the investigation. TABLE 3 shows an example of the INVESTIGATION PUBLICATIONS section along with example data.
There are 7 concepts used in the INVESTIGATION PUBLICATIONS section. These concepts are taken from ISA-TAB and are described below:
Investigation pubmed ID---PubMed identifier of the publication associated with the investigation.
Investigation publication DOI---A Digital Object Identifier (DOI) of the publication associated with the investigation.
Investigation publication author list---A semicolon-delimited (";") list of authors of a publication associated with the investigation.
Investigation publication title---A concise phrase used as a title for the publication associated with the investigation.
Investigation publication status---A term describing the status of a publication (i.e., submitted, in preparation, published).
Investigation publication status term accession number---The identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for investigation publication status.
Investigation publication status term source REF---The name which identifies the source from where the term for investigation publication status is selected. This name should match one of the names entered in the term source name field.
TABLE 3. Example Investigation Publications Section
Material
Example Investigation File Material Section
| A | B |
|---|---|
| Material File Name | m_NCL-21.xls |
| Material Source Name | NCL-21 |
Study
Example Investigation File Study Section
| A | B |
|---|---|
| Study Identifier | NCL200612A-CytoxicityLLC-PK1 |
| Study Title | Cytotoxicity characterization in LLC-PK1 cells |
| Study Description | Nanoparticle biocompatibility was evaluated in the porcine renal proximal tubule cell line, LLC-PK1. Cytotoxicity was determined as described in the NCL protocol for LLC-PK1 Kidney Cytotoxicity Assay(GTA-1). Briefly, test materials were diluted to the desired assay concentrations in cell culture media. Cells were preincubated for 24 h prior to adding test material, reaching an approximate confluence of 80%. Cells were exposed to test material for 6, 24 and 48 h, and cytotoxicity was determined using the MTT cell viability and LDH membrane integrity assays. |
| Study Submission Date | 2002-11-30 |
| Study Public Release Date | 2002-11-30 |
| Study Disease | |
| Study Disease Term Accession Number | |
| Study Disease Term Source REF | |
| Study Outcome | NCL22, NCL23 and NCL24 were found to be minimally cytotoxic, under the testing conditions utilized. |
| Study File Name | s_cytotoxicity-LLC-PK1.xls |
Study Design Descriptors
Example Investigation File Study Design Descriptors Section
| A | B |
|---|---|
| Study Design Type | comparison |
| Study Design Type Term Accession Number | |
| Study Design Type Term Source REF |
Study Publications
Example Investigation File Study Publications Section
| A | B |
|---|---|
| Study PubMed ID | 18095846 |
| Study Publication DOI | 10.2217/17435889.2.6.789 |
| Study Publication Author list | Hall JB; Dobrovolskaia MA; Patri AK; McNeil SE |
| Study Publication Title | Characterization of nanoparticles for therapeutics |
| Study Publication Status | published |
| Study Publication Status Term Accession Number | |
| Study Publication Status Term Source REF |
Study Factors
Example Investigation File Study Factors Section for Study Involving Biospecimens (such as in vitro, in vivo characterization). The study factor name and type must be of nanoparticle sample if the assay is applying a nanoparticle sample to a biological system.
| A | B | C | D |
|---|---|---|---|
| Study Factor Name | nanoparticle sample | dose | time of exposure |
| Study Factor Type | nanoparticle sample | particle concentration | time of exposure |
| Study Factor Type Term Accession Number | NPO_1404 | NPO_1830 | NPO_1819 |
| Study Factor Type Term Source REF | NPO | NPO | NPO |
Example Investigation File Study Factors Section for Physico-Chemical Characterization Study. There should be no study factors of study factor type nanoparticle sample
| A | B | C |
|---|---|---|
| Study Factor Name | temperature | solvent |
| Study Factor Type | temperature | solvent medium |
| Study Factor Type Term Accession Number | PATO_0000146 | NPO_1855 |
| Study Factor Type Term Source REF | PATO | NPO |
Study Assays
Example Investigation File Study Assays Section
| A | B | C |
|---|---|---|
| Study Assay Measurement Type | MTT Assay | LDH Release Assay |
| Study Assay Measurement Type Term Accession Number | NPO_1709 | |
| Study Assay Measurement Type Term Source REF | NPO | |
| Study Assay Technology Type | ||
| Study Assay Technology Type Term Accession Number | ||
| Study Assay Technology Type Term Source REF | ||
| Study Assay Technology Platform | ||
| Study Assay Measurement Name | cell viability | LDH release |
| Study Assay Measurement Name Term Accession Number | NPO_1343 | |
| Study Assay Measurement Name Term Source REF | NPO | |
| Study Assay File Name | a_MTT-LLCPK1.xls | a_LDH-LLCPK1.xls |
Study Protocols
Example Investigation File Study Protocols Section
| A | B | C | D | E | F | G | H | I | J |
|---|---|---|---|---|---|---|---|---|---|
| Study Protocol Name | Time-6-24-48 plate MTT assay | Test plate LDH assay | Time zero plate MTT assay | cell preparation in four 96-well plates | APAP positive control preparation | Triton-X100 positive control preparation | MTT assay reagent preparation | Test sample and positive control addition | LDH assay reagent preparation |
| Study Protocol Type | cell preparation | control preparation | control preparation | reagent preparation | reagent preparation | ||||
| Study Protocol Type Term Accession Number | |||||||||
| Study Protocol Type Term Source REF | |||||||||
| Study Protocol Description | Test Plates: 6, 24 and 48 hour exposures (MTT Assay) 5.4.1 Remove appropriate test plate from incubator and replace media from Triton-X positive control wells (see plate format in Appendix) with 200 mL 1% Triton-X (made in Step 4.1.2). Let the plate set for 10 minutes at room temperature. Spin plate at 700 x g for 3 minutes. 5.4.2 Remove 100 mL of media from each well and transfer it to another plate, maintaining plate format. Use this plate immediately for the LDH assay (see Section 5.5). 5.4.3 Remove remaining media from original plate and discard. 5.4.4 Add 200 mL of fresh media to all wells. 5.4.5 Add 50 mL of MTT to all wells. 5.4.6 Cover in aluminum foil and incubate for 37°C for 4 hours. 5.4.7 Remove plate from incubator and spin at 700 x g for 3 minutes. 5.4.8 Remove media and MTT. 5.4.9 Add 200 mL of DMSO to each well. 5.4.10 Add 25 mL of glycine buffer to each well. Place on shaker to mix. 5.4.11 Read absorbance at 570 nm on plate reader using a reference wavelength of 680 nm. | Test Plates: 0, 6, 24 and 48 hour exposures (LDH Assay) Adapted from Biovision LDH Cytotoxicity Assay Kit, K311-400) 5.5.1 Add 100 mL of the Reaction Mixture (step 4.3.2) to each well of transfer plate. Shake plate on an orbital shaker briefly to mix samples. 5.5.2 Incubate at room temperature for up to 20 minutes in the dark. 5.5.3 Read the plate on plate reader at 490 nm using a reference wavelength of 680 nm. | 5.2.1 Remove time zero plate from incubator and replace media from Triton-X positive control wells (see plate format in Appendix) with 200 mL 1% Triton-X (made in Step 4.1.2). Add 100 mL of media to the remaining wells. Let the plate set for 10 minutes at room temperature. Spin plate at 700 x g for 3 minutes. 5.2.2 Remove 100 mL of media from each well and transfer it to another plate, maintaining plate format. Use this plate immediately for the LDH assay (see Section 5.5). 5.2.3 Remove remaining media from original plate and discard. 5.2.4 Add 200 mL of fresh media to all wells. 5.2.5 Add 50 mL of MTT to all wells. 5.2.6 Cover in aluminum foil and incubate at 37°C for 4 hours. 5.2.7 Remove plate from incubator and spin at 700 x g for 3 minutes. 5.2.8 Aspirate media and MTT. 5.2.9 Add 200 mL of DMSO to all wells. 5.2.10 Add 25 mL of glycine buffer to all wells. Place on shaker to mix. 5.2.11 Read absorbance at 570 nm on plate reader. | 5.1.1 Harvest cryopreserved cells from prepared flasks (limit to 20 passages). 5.1.2 Count cell concentration using a coulter counter or hemocytometer. 5.1.3 Dilute cells to a density of 2.5 x 105 cells/mL in M199 (3% FBS) cell culture media. 5.1.4 Plate 100 mL cells/well as per plate format (Appendix) for four 96-well plates (time zero, 6 hour sample exposure, 24 hour sample exposure, 48 hour sample exposure). The format indicates no cells in rows D and E as they serve as particle blanks to be subtracted from cell treatment wells. Each plate accommodates two samples (Rows A–C and F–H). Each nanoparticle is tested at nine dilutions. Column 11 receives the APAP positive control and column 12 receives Triton X-100. 5.1.5 Incubate plates for 24 hours at 5% CO2, 37°C and 95% humidity. | 4.1.1 Acetaminophen (APAP) positive control: Add 19 mg to a total volume of 5 mL M199 Cell Culture Media (with 3% FBS) to make a 25 mM solution. Sterile filter using a 0.2 mm filter. | 4.1.2 1% Triton-X-100 positive control: Add 1 mL of Triton-X-100 to 99 mL of media. Sterile filter using a 0.2 mm filter. | 4.2.1 MTT solution: 5 mg/mL MTT in PBS, store for up to one month at 4°C in dark 4.2.2 Glycine Buffer: 0.1 M glycine (MW 75.07), 0.1 M NaCl (MW 58.44), pH 10.5, store at room temperature. | 5.3.1 The highest concentration of nanoparticle tested should be at the limit of solubility. The test sample should be at physiological pH. Neutralization of acidic/basic test samples may be required. 5.3.2 Dilute test compound in media, making a total of 9 1:4 dilutions. 5.3.3 Add 100 mL of each sample dilution and positive control to 6 hour, 24 hour and 48 hour exposure plates as per the plate format (Appendix). | 4.3.1 Reconstitute catalyst in 1 mL dH20 for 10 min with occasional vortexing (stable for 2 weeks at 4°C). 4.3.2 Reaction mixture (for one 96-well plate): Add 250 mL of reconstituted catalyst solution to 11.25 mL of dye solution (stable for 2 weeks at 4°C). |
| Study Protocol URI | NCL_Method_GTA-1.pdf | NCL_Method_GTA-1.pdf | NCL_Method_GTA-1.pdf | NCL_Method_GTA-1.pdf | NCL_Method_GTA-1.pdf | NCL_Method_GTA-1.pdf | NCL_Method_GTA-1.pdf | NCL_Method_GTA-1.pdf | NCL_Method_GTA-1.pdf |
| Study Protocol Version | 1.1 | 1.1 | 1.1 | 1.1 | 1.1 | 1.1 | 1.1 | 1.1 | 1.1 |
| Study Protocol Parameters Name | |||||||||
| Study Protocol Parameters Name Term Accession Number | |||||||||
| Study Protocol Parameters Name Term Source REF | |||||||||
| Study Protocol Components Name | MTT; acetaminophen; dimethyl sulfoxide; glycine; sodium chloride; triton-X-100; M199 cell culture media; fetal bovine serum; nanoparticle; costar 96 well flat bottom cell culture plates; plate reader; centrifuge set at 700-800 x g (Allegra X-15R, Beckman Coulter) with 96 well plate adapter; orbital plate shaker | acetaminophen; dimethyl sulfoxide; glycine; sodium chloride; triton-X-100; M199 cell culture media; fetal bovine serum; biovision LDH-cytoxicity assay kit; nanoparticle; costar 96 well flat bottom cell culture plates; plate reader; centrifuge set at 700-800 x g (Allegra X-15R, Beckman Coulter) with 96 well plate adapter; orbital plate shaker | MTT; acetaminophen; dimethyl sulfoxide; glycine; sodium chloride; triton-X-100; M199 cell culture media; fetal bovine serum; costar 96 well flat bottom cell culture plates; plate reader; centrifuge set at 700-800 x g (Allegra X-15R, Beckman Coulter) with 96 well plate adapter; orbital plate shaker | M199 cell culture media; fetal bovine serum; costar 96 well flat bottom cell culture plates; plate reader; centrifuge set at 700-800 x g (Allegra X-15R, Beckman Coulter) with 96 well plate adapter; orbital plate shaker | acetaminophen; M199 cell culture media; fetal bovine serum | triton-X-100; M199 cell culture media; fetal bovine serum | MTT;glycine; sodium chloride | acetaminophen;glycine; sodium chloride; triton-X-100; M199 cell culture media; fetal bovine serum; nanoparticle; costar 96 well flat bottom cell culture plates; plate reader; centrifuge set at 700-800 x g (Allegra X-15R, Beckman Coulter) with 96 well plate adapter; orbital plate shaker | biovision LDH-cytoxicity assay kit |
| Study Protocol Components Type | reagent; reagent; reagent; reagent; reagent; reagent; reagent; reagent; reagent; material; instrument; instrument; instrument | reagent; reagent; reagent; reagent; reagent; reagent; reagent; reagent; reagent; material; instrument; instrument; instrument | reagent; reagent; reagent; reagent; reagent;reagent; reagent; reagent; material; instrument; instrument; instrument | reagent; reagent;material; instrument; instrument; instrument | reagent; reagent; reagent | reagent; reagent; reagent | reagent; reagent; reagent | reagent; reagent; reagent; reagent; reagent; reagent; reagent; material; instrument; instrument; instrument | reagent |
| Study Protocol Components Type Term Accession Number | NPO_290; NPO_290; NPO_290; NPO_290; NPO_290; NPO_290; NPO_290; NPO_290;NPO_290; ; NPO_1436; NPO_1436; NPO_1436 | NPO_290; NPO_290; NPO_290; NPO_290; NPO_290; NPO_290; NPO_290; NPO_290;NPO_290; ; NPO_1436; NPO_1436; NPO_1436 | NPO_290; NPO_290; NPO_290; NPO_290; NPO_290; NPO_290; NPO_290;NPO_290; ; NPO_1436; NPO_1436; NPO_1436 | NPO_290; NPO_290; ; NPO_1436; NPO_1436; NPO_1436 | NPO_290; NPO_290; NPO_290 | NPO_290; NPO_290; NPO_290 | NPO_290; NPO_290; NPO_290 | NPO_290; NPO_290; NPO_290; NPO_290; NPO_290; NPO_290; NPO_290; ; NPO_1436; NPO_1436; NPO_1436 | NPO_290 |
| Study Protocol Components Type Term Source REF | NPO; NPO; NPO; NPO; NPO; NPO; NPO; NPO; NPO; ; NPO; NPO; NPO | NPO; NPO; NPO; NPO; NPO; NPO; NPO; NPO; NPO; ; NPO; NPO; NPO | NPO; NPO; NPO; NPO; NPO; NPO; NPO; NPO; ; NPO; NPO; NPO | NPO; NPO; ; NPO; NPO; NPO | NPO; NPO; NPO | NPO; NPO; NPO | NPO; NPO; NPO | NPO; NPO; NPO; NPO; NPO; NPO; NPO; ; NPO; NPO; NPO | NPO |
Study Contacts
Example Investigation File Study Contacts Section
| A | B |
|---|---|
| Study Person Last Name | Smith |
| Study Person First Name | Jane |
| Study Person Mid Initials | K |
| Study Person Email | smithj@mail.nih.gov |
| Study Person Phone | 1231231235 |
| Study Person Fax | |
| Study Person Address | Laboratory Street, City, State 111111 |
| Study Person Affiliation | Doe Laboratories |
| Study Person Roles | investigator |
| Study Person Roles Term Accession Number | |
| Study Person Roles Term Source REF | MO |
A
B
INVESTIGATION PUBLICATIONS
Investigation PubMed ID
18095846
Investigation Publication DOI
10.2217/17435889.2.6.789
Investigation Publication Author list
Hall JB; Dobrovolskaia MA; Patri AK; McNeil SE
Investigation Publication Title
Characterization of nanoparticles for therapeutics
Investigation Publication Status
published
Investigation Publication Status Term Accession Number
