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caArray Overview

caArray Overview. A Quick Start Guide to learning caArray. caArray Training Overview. Introductions Brief History of caArray Workflow and Operating Procedures caArray Product Overview Questions and Answers. Introductions. Who are you? What do you know about caArray?

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caArray Overview

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  1. caArray Overview A Quick Start Guide to learning caArray

  2. caArray Training Overview • Introductions • Brief History of caArray • Workflow and Operating Procedures • caArray Product Overview • Questions and Answers Version 1.0

  3. Introductions • Who are you? • What do you know about caArray? • How will you be using caArray? • What is one thing you would like to learn a about caArray? Version 1.0

  4. caArray…The History • Need for standardization • Need for Compliance • caArray is • caBig Compliant • MIAME Compliant • MAGE Compliant • caArray is approved for data submission and publication Version 1.0

  5. caArray…Workflow Step-by-Step • Create User Account • Establishes what access permissions you are granted • Complete Contacts • Complete Protocols • Complete Array Designs • Complete Ontologies (controlled vocabularies) • Complete Biomaterials (sample information) • Submit Experiments • Add Hybridizations • Upload Experiments • Add or Modify Experiments • Publish Data • Lock Final Data Version 1.0

  6. caArray Workflow - Diagram

  7. User Accounts • Establishes Access Permissions • Public • Private • Consortium Version 1.0

  8. Logging In • Type Login ID • Type Password • If you forget your Username and Password contact NCICB Application Support at • 888-478-4423 • 301-451-4384 • NCICB@pop.nci.nih.gov Version 1.0

  9. ContactsOrder of Operations • Verify that a contact exists by using the Search options • Search Either Organization or People • If contact does not exist • Add New Person, New Organization or both • If adding a New Person contact verify the Organization in which the person is affiliated exists • If the Organization does not exist add the New Organization first before adding the New Person as a person is REQUIRED tobe affiliated with an organization Version 1.0

  10. Search Organization • Can use Wildcards • NCI* • *Cancer* Version 1.0

  11. Adding a New Organization • If the organization does not exist • Add the New Organization Version 1.0

  12. Adding the New Organization Information • Complete the required fields • Required fields are indicated by * • Submit the New Organization Version 1.0

  13. Search People • Can use wildcards for either first or last name • First Name: Jamie • Last Name: * • First Name: * • Last Name: Keller Version 1.0

  14. Adding a New Person • Add yourself as a contact • Select New Person • Complete the required fields • Required fields are indicated by an * • When completed, select Submit to add yourselfas a Contact • NOTE: If you do not see your organization on the list of options you MUST add your organization Version 1.0

  15. Modifying a Contact • Occasionally changes or updates may need to be made to either the Organization or Person (e.g. an area code has changed) • Search People or Search Organization • Select Modify Version 1.0

  16. Modifying a Contact continued… • Make all necessary modifications • Remember to save any modifications Version 1.0

  17. Protocols • Steps taken in a Microarray procedure • It is a “recipe” of items used to create the procedure • Well written and documented Protocols can be reused • Affymetrix Labeling and Hybridization Protocol • GenePix Scanning Protocol Version 1.0

  18. Two Types of Protocols • Wet Lab Protocols • Hybridization Protocol • Labeling Protocol • Dry Lab Protocols • Image Acquisition • GenePix • Feature Extraction • Affymetrix GCOS Version 1.0

  19. ProtocolsOrder of Operations • Verify Protocol exists • Search Protocols • If Protocol does not exist • Verify Hardware exists…for Dry Lab Only • Search Hardware • If Hardware does not exist • Add Hardware • Verify Software exists…For Dry Lab Only • Search Software • If Software does not exist • Add Software • Add New Protocol Version 1.0

  20. Creating a Dry Lab ProtocolMulti-Step Approach • Verify Protocol does not already exist: Search Protocol • Verify Hardware used in the Dry Lab Protocol exist: Search Hardware • If Hardware does NOT exist: Add Hardware • Verify the Software used in the Dry Lab Protocol exists: Search Software • If the Software does NOT exist: Add Software • Once the above steps are completed: New Protocol Version 1.0

  21. Verify Protocol ExistsSTEP 1 -- Search Protocol • Can Search by: • Type---Best way to search • The Kind of Protocol • Array_ Manufacturing_ Protocol • Name • Any name given to a created protocol • Dr. Moliuex RNA Labeling Protocol • Visibility • Who can view the protocol • Public Version 1.0

  22. Creating A Dry Lab ProtocolSTEP 2 -- Searching Hardware • Verify Hardware exists • Search Hardware • Hardware Type • Type of Hardware used in Protocol • Array_Scanner • Hardware Manufacturer • Who makes the equipment • Affymetrix • Hardware Model • Visibility • Who can view the Hardware • Public Version 1.0

  23. Creating a Dry Lab ProtocolSTEP 2A -- New Hardware • Select New Hardware • Name • Equipment in the lab • Axon Scanner • Model • Whatever model number is associated with the equipment • GenePix 4000b • Type • What kind of equipment is it • Array_Scanner • Manufacturer • Who makes the equipment • Axon Instruments Version 1.0

  24. Creating a Dry Lab ProtocolSTEP 2A -- New Hardware continued… • Select New Hardwarecontinued… • URI(Uniform Resource Indicator also known as URL) • The website of the Manufacturer • http://www.moleculardevices.com • Visibility • Who can utilize this hardware for their protocols • Public Version 1.0

  25. Creating a Dry Lab Protocol STEP 3 --Searching Software • Verify Software exists • Search Software • Software Type • Type of Software used in Protocol • Array_Manufacture _Software • Software Manufacturer • Who makes the software • GenePix • Visibility • Who can utilize the software in creating a protocol • Public Version 1.0

  26. Creating a Dry Lab ProtocolSTEP 3A --New Software • Select New Software • Name • Software in the lab • Generic Pro 4.0 • Type • What kind of software it is • Array_Manufacture_ Software • Manufacturer • Who makes the software • Generic Version 1.0

  27. Creating a Dry Lab ProtocolSTEP 3A --New Software continued… • Adding New Software continued… • URI (Uniform Resource Indicator also known as URL) • The website of the Software Manufacturer • http://www.axon.com /GN_GenePixSoftware.html • Visibility • Who can utilize this software in creating protocols • Public Version 1.0

  28. Adding a Dry Lab ProtocolSTEP 4 -- New Protocol • New Protocol • Name • The name of the new Protocol • Affymetrix Eukaryotic Sample and Array Processing Protocol • Type • The protocol type • Array_Manufacturing_Protocol • Specify New Type • The protocol type • Option that does not already exist in the Type drop down list Version 1.0

  29. Adding a Dry Lab ProtocolSTEP 4 -- New Protocol continued… • New Protocol continued… • URI (Uniform Resource Indicator also known as URL) • The website of the Organization submitting the Protocol • http://ncicb.nci.nih.gov • Visibility • Who can utilize this software in creating protocols • Public • Select Submit to continue adding a New Protocol Version 1.0

  30. Adding a Dry Lab ProtocolSTEP 4 -- New Protocol continued… • Add Parameters(if applicable) • Add Hardware • The Hardware added in Step 2A • Add Software • The Software added in Step 3A Version 1.0

  31. Creating a Wet Lab Protocola Two-Step Approach • Verify Protocol does not already exist: Search Protocol • Add: New Protocol Version 1.0

  32. Verify Protocol ExistsSTEP 1 -- Search Protocol • Can Search by: • Type---Best way to search • The Kind of Protocol • Array_ Manufacturing_ Protocol • Name • Any Name given to a created protocol • Dr. Moliuex RNA Labeling Protocol • Visibility • Who can view the Protocol • Public Version 1.0

  33. Adding A Wet Lab ProtocolSTEP 2 -- New Protocol • New Protocol • Name • The name of the new protocol • RNA Processing • Type • The protocol type • Grow • Specify New Type • The protocol type • Option that does not already exist in the Type Drop Down List Version 1.0

  34. Adding A Wet Lab ProtocolSTEP 2 -- New Protocol continued… • New Protocolcontinued… • URI (Uniform Resource Indicator also known as URL) • The website of the Organization submitting the Protocol • http://ncicb.nci.nih.gov • Visibility • Who can utilize this software in creating protocols • Public Version 1.0

  35. Array Designs • Descriptions of Microarrays that include • Array Layout • Array Design • Type of technology • Substrate • Surface • Attachment • Strand Type • Gives users ability to add and search record • Allows for replication • Good Array Designs can be reused in future experiments Version 1.0

  36. Array DesignOrder of Operations • Verify that the Array exists • If the Array Does not Exist • Add Array... • New Array Design Version 1.0

  37. Search Array Design • You can Search By: • Technology Type –Best way to Search • What type of technology is being used • In_situ_olgio_ features • Array design name • Name given by creator of the array • NCICB Human1.119K • Visibility • Who can use and view the array • Consortium • Substrate Type • What kind of material is the array made of • Glass Version 1.0

  38. Search Array Design continued… • Searching continued… • Surface Type • What makes the probes stick to the slide • Polylysine • Attachment Type • What is the mechanism that makes the probes attach to the slide • Ionic • Organism • What is the species from which the array comes • Homo Sapiens Version 1.0

  39. Adding New Array Design • When adding New Array Design complete: • Type Upload • If you are using MAGE ML you do not have to complete the the New Array Design Information Section • If you are using GenePix this is a GAL file • Array Design Name • What you are going to call the array • Standard naming convention for caArray is ORGANIZATION_SPICIES NAME_VERSION #_SPOTS ON ARRAY • NCICB__Mus musculus_1.1_19K Version 1.0

  40. Adding a New Array Design continued… • New Array Designcontinued… • Array Version • The print number • 1.1 • Technology Type • The type of probe spotted/printed on the array • cDNA • Substrate Type • Type of surface used for the array • Glass • Surface Type • Type of material used to adhere array to the substrate • Polylysine Version 1.0

  41. Adding a New Array Designcontinued… • New Array Designcontinued… • Attachment Type • How the array is bonded to the substrate and surface • Ionic • Organism • Species from which the array is derived • Homo Sapiens • Array Descriptor • Short description of the array • Can be copied and pasted from outside sources • Max 4000 characters • Visibility • Who can use and view the array • Consortium Version 1.0

  42. Ontologies • Need for Common language • For example, BR CA to some this is brain cancer to other this might be breast cancer…ontology makes it clear that breast cancer will always be referred to as Breast Cancer • Formal specification of the terms in a particular domain, and the relationship among those terms to one another. • The Microarray Gene Expression Data Society (MGED) provides the ontology used by caArray. Version 1.0

  43. OntologiesOrder of Operations • Verify the existence of: • Cell Lines • Cell Types • Developmental Stages • Disease Stages • Disease States • Organism Parts • Strain or Line • Tumor Grading • If missing, add the above ontologies Version 1.0

  44. Ontologies Search:Cell Lines, Cell Types, Developmental Stages, Disease Stages, Disease States, Organism Parts, Strain or Line, Tumor Grading • Search by: • Cell Line Name • Hela • Cell Types Name • Epithelial • Developmental Stage Name • Theiler Stage 3 • Disease Stage Name • Dukes C Colon Cancer • Disease States Name • Lung Cancer • Organism Part Name • Colon • Strain or Line Name • Mouse Strain • Tumor Grading Name • Breast Cancer Stage 2 Version 1.0

  45. Ontologies Search:Cell Lines, Cell Types, Developmental Stages, Disease Stages, Disease States, Organism Parts, Strain or Line, Tumor Grading continued… • Searchcontinued… • Public Databases • NCI –Thesaurus • ATCC Cultures Version 1.0

  46. Ontologies Add:Cell Lines, Cell Types, Developmental Stages, Disease Stages, Disease States, Organism Parts, Strain or Line, Tumor Grading • Add Ontologies: • Cell Line Name • Sm Cell Carcinoma 0312 (Lab identifier) • Cell Type Name • Epidermal • Developmental Stage Name • Embryo • Disease Stage Name • Stage 2 • Disease State Name • Lung Cancer • Organism Part Name • Lung • Strain or Line Name • Mouse X • Tumor Grading Name • Grade 3 Version 1.0

  47. Ontologies Add: Cell Lines, Cell Types, Developmental Stages, Disease Stages, Disease States, Organism Parts, Strain or Line, Tumor Grading continued… • Add Ontologiescontinued… • Public Database(if applicable as private collections will not be found in public databases) • Private • Cell_Ontology • Accession Number • If not part of a public database, no accession number is needed • CL025681 • URI (Uniform Resource Indicator also known as URL) • If not part of a public database, no URI is needed • http://www.atcc.org Version 1.0

  48. Biomaterials/Sample • Your samples that are materials of biological origin • Document all information on your samples  • Biomaterials consist of: • Biosources • This is your sample prior to any treatment • Biopsy • Lung Tumor Biopsy 1 • Biosamples • The sample that resulted from treating the Biosource • RNA extract • Lung Tumor RNA 1 • Labeled Extracts • The labeled sample • RNA Labeling • Lung Tumor 1 Cy5 Version 1.0

  49. Biomaterials/Samples BIOSOURCE Treatment = Biopsy (what was done to obtain the sample) BIOSAMPLE LABLED EXTRACT Version 1.0

  50. BiomaterialsOrder of Operations • Search to verify the existence of: • Biosource • Biosample related to Biosource • Labeled extracts related to Biosources • If needed Submit/AddNew: • Biosource • Biosamples related to the newly submitted Biosource • Labeled Extracts related to the newly submitted Biosources Version 1.0

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