CaArray Overview A Quick Start Guide to learning caArray.

caArray Overview

A Quick Start Guide to learning caArray

http://caarray.nci.nih.gov/

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caArray Training Overview

Introductions Brief History of caArray Workflow and Operating Procedures caArray Product Overview Questions and Answers

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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?

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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

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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

http://www.christianet.com/free/clipart/star/index.htm

caArray Workflow - Diagram

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User Accounts

Establishes Access Permissions– Public– Private– Consortium

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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 [email protected]

mailto:[email protected]

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Contacts Order 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 to be affiliated with an organization

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Search Organization

Can use Wildcards

– NCI*– *Cancer*

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Adding a New Organization

If the organization does not exist

– Add the New Organization

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Adding the New Organization Information

Complete the required fields

– Required fields are indicated by *

Submit the New Organization

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Search People

Can use wildcards for either first or last name

– First Name: Jamie– Last Name: *

– First Name: *– Last Name: Keller

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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 yourself as a Contact

NOTE: If you do not see your organization on the list of options you MUST add your organization

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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

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Modifying a Contact continued…

Make all necessary modifications

– Remember to save any modifications

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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

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Two Types of Protocols

Wet Lab Protocols– Hybridization Protocol– Labeling Protocol

Dry Lab Protocols– Image Acquisition

GenePix

– Feature Extraction Affymetrix GCOS

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Protocols Order 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

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Creating a Dry Lab ProtocolMulti-Step Approach

1. Verify Protocol does not already exist: Search Protocol

2. Verify Hardware used in the Dry Lab Protocol exist: Search Hardware

A. If Hardware does NOT exist: Add Hardware

3. Verify the Software used in the Dry Lab Protocol exists: Search Software

A. If the Software does NOT exist: Add Software

4. Once the above steps are completed: New Protocol

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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

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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

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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

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Select New Hardware continued…

– 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

Creating a Dry Lab ProtocolSTEP 2A -- New Hardware continued…

http://www.moleculardevices.com/

http://www.moleculardevices.com/

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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

Creating a Dry Lab Protocol STEP 3 -- Searching Software

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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

Creating a Dry Lab ProtocolSTEP 3A -- New Software

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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

Creating a Dry Lab ProtocolSTEP 3A -- New Software continued…

http://www.axon.com/GN_GenePixSoftware.html




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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

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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


– Public

• Select Submit to continue adding a New Protocol

Adding a Dry Lab ProtocolSTEP 4 -- New Protocol continued…

http://ncicb.nci.nih.gov/

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Add Parameters (if applicable)

Add Hardware– The Hardware added in

Step 2A

Add Software– The Software added in

Step 3A

Adding a Dry Lab ProtocolSTEP 4 -- New Protocol continued…

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Creating a Wet Lab Protocola Two-Step Approach

1. Verify Protocol does not already exist: Search Protocol

2. Add: New Protocol

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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

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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

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Adding A Wet Lab ProtocolSTEP 2 -- 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


– Public

http://ncicb.nci.nih.gov/

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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

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Array DesignOrder of Operations

Verify that the Array exists– If the Array Does not Exist

Add Array...– New Array Design

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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

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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

Search Array Design continued…

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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

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Adding a New Array Design continued…

New Array Design continued…

– 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

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New Array Design continued…

– 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

Adding a New Array Designcontinued…

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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.

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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

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Ontologies

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

Search: Cell Lines, Cell Types, Developmental Stages, Disease Stages, Disease States, Organism Parts, Strain or Line, Tumor Grading

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Search continued…

– Public Databases NCI –Thesaurus ATCC Cultures

OntologiesSearch: Cell Lines, Cell Types, Developmental Stages, Disease Stages, Disease States, Organism Parts, Strain or Line, Tumor Grading continued…

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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

OntologiesAdd: Cell Lines, Cell Types, Developmental Stages, Disease Stages, Disease States, Organism Parts, Strain or Line, Tumor Grading

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Add Ontologies continued…

– 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

OntologiesAdd: Cell Lines, Cell Types, Developmental Stages, Disease Stages, Disease States, Organism Parts, Strain or Line, Tumor Grading continued…

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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

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Biomaterials/Samples

BIOSOURCE

BIOSAMPLE

LABLED EXTRACT

Treatment = Biopsy (what was done to obtain the sample)

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BiomaterialsOrder of Operations

Search to verify the existence of:1. Biosource

2. Biosample related to Biosource

3. Labeled extracts related to Biosources If needed Submit/Add New:

1. Biosource

2. Biosamples related to the newly submitted Biosource

3. Labeled Extracts related to the newly submitted Biosources

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BiomaterialsSearch BioSources

Search by:– Biosource Type

The state of the material when received

– Fresh– Organism

Species from which the sample came

– Homo Sapiens– Visibility

Who can use and view the biomaterial

– Consortium– Biosource Name

The name of the Biosource– Lung Tumor 1

– Provider The name of the

organization or individual who provided the sample

– NIH Clinical Center

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BiomaterialsSearching Biosample

Search Biosamples by:– Sample Name

Name given to biosample– Lung Tumor RNA 1

– Biosource The name of the source

from which the sample is derived

– Lung Cancer Biopsy _1


sample came– Homo Sapiens

– Visibility Who can see the biosample

– Private

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Search Labeled Extracts by:

– Biosample The sample from which

the labeled extract is derived

– Lung_Cancer_1_RNA


sample came from– Homo Sapiens

– Visibility Who can see the labeled

extract– Private

BiomaterialsSearching Labeled Extracts

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BiomaterialsSubmit New Biosource

Submit New Biosource complete:

– Biosource Name What you want to call the

biosource– LungSamplePtX

– Description Short description of the

biosource including how it was obtained (4000 character max)

– Lung sample obtained from female patient age 65 with carcinoma using …


sample came from– Homo Sapiens

– Specify New Organism Type Utilized only if Species is not

on the drop down list in the Organism Field

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Submit New Biosource complete continued…

– Provider The name of the organization

or individual who provided the sample

– NIH Clinical Center– Biosource Type

The state of the material when received

– Fresh– Specify New Biosource Type

Utilized only if biosource is not on the drop down list in the Biosource Type field

– Visibility Who can see the Biosource

– Private Save

BiomaterialsSubmit New Biosource continued…

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BiomaterialsNew BioSample

Three Step Process

1. Identify the Biosource– If the biosource does not exist, it must be created prior

to adding the New Biosample

2. Identify the Treatment– The function performed on the biosource to create the

New Biosample

3. Identify the Protocol– If the Protocol does not exist, it must be created prior

to adding the New Biosample

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Biomaterials New Biosample

Step 1– Identify Biosource New Biosample – Step 1

Identify the Biosource:– Select Biosource

The biosource from which the sample is derived

– Lung_Cancer1– Name of Resulting

Biomaterial What you wish to name

the new biosample– Lung Cancer RNA 1

– Description of Resulting Biomaterial

A short description of how the biosample was derived

– Total RNA from Lung Tumor Biopsy

Select Next – Step 2 Identify Treatment

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New Biosample – Step 2 Identify Treatment :

– Applying a Protocol Protocols were created in

the Protocol tab and should be done prior to submitting biosamples

– Add New Treatment Event How the Biosource was

treated to create the Biosample

Treatment Type– Nucleic_Acid_Extraction


Step 2– Identify Treatment

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Step 2– Identify Treatment continued…

New Biosample – Step 2 Identify Treatment continued…

– Measurement The measurement of the

biosample– 5

– Unit Type The type of measurement used

– Mass Unit– Note that another field may

appear based on the Unit Type selected

• Unit• MG

Add Treatment Select Apply Protocol – Step 3

Identify Protocol

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New Biosample – Step 3 Apply Protocol:


the Protocol tab and should be done prior to adding a New Biosample

– Activity Date– 10/10/04

– Performer– Who performed the

treatment (NOTE: This is a contacts added in the Contact tab if the name is missing it must be added in the Contacts tab prior to completing this section)

• Jane Liu Save


Step 3– Apply Protocol

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Biomaterials New Labeled Extract

Two Step Approach

Identify the treatment of the biosample which results in the New Labeled Extract– If the biosample does not exist, it must be created prior

to adding the New Labeled Extract Apply the Protocol

– If the Protocol does not exist, it must be created prior to adding the New Labeled Extract

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Step 1– Identify Biosample Treatment New Labeled Extract –

Step 1 Identify the Biosample Treatment :

– Name of Resulting Extract The name of the extract

derived from the biosample– Lung_Tumor_1_Cy5

– Select a Biosample to be Labeled

This was created when the new biosample was added

– Lung_Cancer_RNA 1– Label

Detector– Biotin, Cy5

– Amount of Nucleic Acid Labeled

The numeric amount of nucleic acid

– 100

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New Labeled Extract – Step 1 Identify the Biosample Treatment continued…

– Unit of Mass The unit in which the acid is

measured– NG

– Material Type of Resulting Labeled Extract

Labeled Sample – Total RNA

– Visibility Who can use and view the

Labeled Extract– Consortium

Select Apply Protocol


Step 1– Identify Biosample Treatment continued…

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New Labeled Extract – Step 2 Apply Protocol


the Protocol tab and should be done prior to adding a New Labeled Extract

– Activity Date– 10/10/04

– Performer– Who performed the

treatment (NOTE: This is a contacts added in the Contact tab if the name is missing it must be added in the Contacts tab prior to completing this section)

• Jane Liu Save

Biomaterials New Labeled ExtractStep 2– Apply Protocol

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Submitting an Experiment

Complete Contacts Protocols Array Designs Ontologies Bio Materials

Submit Experiment

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Submit Experiment Order of Operations

Verify the Experiment has not been submitted– Search/Modify Experiments

Add New Experiment– Create Hybridizations– Determine Experimental Factors– Upload Experiment

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Search/Modify Experiment

You can Search/Modify Experiment by:– Experiment ID

Unique identification number

– 788918BK

– Experiment Name The name of the

experiment– JLK BLOOD 1.1

– Visibility Who can view the

Experiment– Consortium

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Search/Modify Experiment continued…

You can Search By continued…

– Experiment Type What kind of experiment

are you looking for– RNA_Stability Design

– Principal Investigator Who created the

experiment– Dr. John Maiti


experiment was derived– Mus Musculus

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Import MAGE ML File

MAGE files can be imported as part of the experiment documentation

To Import MAGE ML:– File Name

To locate the MAGE file to be imported Browse to find the file

– Message to Curator A short message to the

data curator regarding the MAGE file, documenting from where the MAGE file came, etc

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ExperimentNew Experiment

Multi-Step Approach1. General Experiment Information2. Experimental Factors3. Publications

– Any Publications that are part of the experiment4. Quality Control Steps

– Measures taken to ensure

5. Additional Qualifiers6. Additional Upload Files7. MAGE ML Download8. Hybridizations

– Protocols 1. Image Acquisition – Dry Lab Protocols2. Feature Extractions – Wet Lab Protocols

9. Upload Hybridization – Submit Experiment

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Step 1 – General Experiment Information New Experiment – Step 1

General Experiment Information

– Title The name of the

experiment– Lung cancer

experimental factors

– Experiment completion date The day the experiment

was completed– 05/25/03

– Experiment design Type High level description of

the kind of experimental design being utilized

– Dose Response

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Step 1 – General Experiment Information continued…

New Experiment – Step 1 General Experiment Information continued…:

– Visibility Who can view, or use the

Experiment– Consortium

– Description A description of the

experiment (max 4000 characters)

– Your white paper for the experiment

– Principal Investigator Who is responsible for the

Experiment (This list comes from the Contacts tab, if the contact is missing you must return to the Contacts tab and enter the New Contact)

– Dr. John Maiti

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New Experiment – Step 1 General Experiment Information continued…

– Contact Person The person to contact if

more information is needed (This list comes from the Contacts tab, if the contact is missing you must return to the contacts tab and enter the New Contact)

– Jamie Keller– Number of Experimental

Factors Parameters of a study that

influence the experimental result

– 2 Next – Step 2 Experimental

Factors


Step 1 – General Experiment Information continued…

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Step 2 – Experimental Factors

New Experiment – Step 2 Experimental Factors

– Factor Name The type of experimental

factors used– Dose

– Factor Type How the experimental

factor is classified– Labeling Protocol

– Scale How the factor is measured

– Linear_Scale– Levels

The amount of factor given– 25 mcg

Next – Step 3 Experimental Factors

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New Experiment – Step 3 Additional Publications

– Add A New Publication if applicable

Any additional supporting publications used or referenced in the experiment


Step 3 – Additional Publications

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Step 4 – Quality Control

New Experiment – Step 4 Quality Control

– Add Quality Control Steps if applicable

Any quality assurance measures taken with the experiment

– Peer Review

– Reverse Fluoresces

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Step 5 – Additional Qualifiers

New Experiment – Step 5 Additional Qualifiers

– Add Additional Qualifiers if applicable

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Step 6 – Additional Upload Files

New Experiment – Step 6 Additional Upload Files

– Add Additional Upload Files if applicable

Any additional materials used in conducting the experiment

– Image File

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Step 7 – Hybridizations

New Experiment – Step 7 Hybridizations

– Protocols Dry Lab Protocol

– Image Acquisition Protocol

– Feature Extraction Protocol

Wet Lab Protocols – Hybridization Protocols

– Labeling Protocols

Batch Upload

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New Experiment – Step 7 Hybridizations continued…

– Common Hybridization Information

Array Design– Created in the Array

Design Tab• NCICB_Mus

musculus_1.1_19K Manufacture

– Who makes the hybridization

• Not Utilized at this time Number of Hybridizations

– How many hybridizations are you going to add to your experiment

Hybridization Protocol– Wet Lab Protocol created

in the Protocol Tab Select Next


Step 7 – Hybridizations continued…

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– Verify the information on the Hybridization is correct

NOTE: This information comes from the completion of the Array Design as well as the Protocol (Hybridization Protocol = Wet Lab Protocol)

– If the Array Design Information has not been completed return to the Array Design tab to complete the information.

– If the Wet Lab/Hybridization Protocol has not been completed return to the Protocol Tab to complete the information

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– Performer The person who

created the hybridization

– Jamie Keller– Activity Date

Date the Experiment is being submitted/added

– 10/18/2004 Select Next

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– Identifying Image Acquisition Protocol

This is the Wet Lab Protocol created in the Protocol Tab

If the Image Acquisition Protocol/Wet Lab Protocol is missing return to the Protocol Tab to create it

Select Next



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– Verify the information on the Protocol is correct

NOTE: This information comes from the completion of the Image Acquisition/ Wet Lab Protocol

– Lab Performer The person who created the

hybridization– Jamie Keller

– Activity Date Date in which the

Experiment is being submitted/added

– 10/18/2004

Select Next



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– Identifying Feature Extraction Protocol

This is the Dry Lab Protocol created in the Protocol Tab

If the Feature Extraction Protocol/Dry Lab Protocol is missing return to the Protocol Tab to create it

Select Next

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– Verify the information on the Protocol is correct

NOTE: This information comes from the completion of the Feature Extraction/ Dry Lab Protocol

– Lab Performer The person who created

the hybridization– Jamie Keller

– Activity Date Date in which the

experiment is being submitted/added

– 10/18/2004 Select Next



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– Identifying Additional Hybridization Information

Associate files, documents, etc. with the Hybridization

Select Next to create New Experiment

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– Verify the Experiment is being processed

This may take a few minutes

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– Continue The Experiment has

now been added/submitted to caArray!!!

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Step 8 – MAGE ML Download

New Experiment – Step 8 MAGE ML Download

– MAGE ML Download Once the Experiment has

been added to caArray a MAGE ML file can be generated

– NOTE: This is a Snap shot in time, if modifications or changes are made to the experiment the MAGE ML must be generated again to capture the updates

CaArray Overview A Quick Start Guide to learning caArray.

Documents

new person contact

new organizationadding

new personadd

new organizationif

contact continuedmake

peopleif contact

required fieldsrequired

data submission