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Synopsis

Protein Array data contains information about protein expression and protein concentration. The TCGA DCC is the official repository for all data for this platform. Protein Array data archives submitted to the DCC include original images of protein arrays, calculated raw signals, relative concentration of protein, and normalized protein signals (i.e. protein expression). Protein Array submissions also include MAGE-TAB archives, with some non-standard modification to MAGE-TAB format. These archives contain files that describe the Protein Array experiment and the relationship between the experimental samples and the data files produced by assaying those samples.

This specification covers the validation and deployment of Protein Array submissions to the DCC. The DCC currently accepts Levels 1-3, MAGE-TAB, and auxiliary (aux) archives.

Things to note

  • Biospecimen IDs are tracked using UUID. The primary SDRF column containing TCGA UUIDs for Protein Arrays is the Sample Name column, not the Extract Name column.
  • Biospecimens were shipped at the portion level rather than as aliquots
  • The SDRF contains a "Comment [TCGA File Type]" column after each "* File" column. This column describes the file type to help derive which process was applied.
  • Expect Level 1 data to contain information for multiple disease studies, as one protein array slide will likely contain biospecimens from other disease studies than the one labeled by the archive. Level 2 and 3 will be specific to the labeled disease study.

Overview of Experiment

MD Anderson (MDA) sends tubes containing ceramic beads to the BCRs. The BCRs place 1 portion of tissue into each tube, labels the tubes, and ships the tubes to MDA. MDA extracts the proteins using those tubes. The proteins are denatured, diluted, and then printed onto a nitrocellulose slide. MDA waits for 1,000 sample-portions to accumulate before slide printing happens.

Slides are printed in grids. Each 11x11 grid contains 22 samples and controls. Samples are paired in a row, each with 4 two-fold serial dilutions for a total of 5 spots per sample; a final spot, the last column, contains a control lysate that is part of a 2-fold serial dilution vertically across the grid.

image as described

There may be 1,000 sample-portions per slide. A slide will likely contain more than one tumor project's sample-portions. Each slide-image result (see Level 1 tif below) assays one antibody; slides can only be used one time to produce an image. There will be a minimum of 150 antibodies assayed and a maximum of 500. So there will be a maximum of 150-500 slide images per tumor project. There may be multiple disease studies per slide and possibly multiple/replicate images per disease. Each slide image is measured to produce raw signal data (see Level 1 txt below). The raw signal data is analyzed to create dilution curves for each sample-portion using the SuperCurve R-package (see Level 2 below). The dilution curve data is used to normalize the all the sample-portion antibody results (see Level 3 below).

For more information see RPPA Core Facility - Functional Proteomics.

Design

Centers

Currently, only one center submits proteomic data to the DCC. This is the RPPA Core Facility lead by Gordon Mills:

Code

Center Name

Center Type

Display Name

Short Name

20

mdanderson.org

CGCC

MD Anderson GCC

MDA

Platform

Platform Code

Platform Alias

Platform Name

HTTP Display

MDA_RPPA_Core

MDA_RPPA_Core

M.D. Anderson Reverse Phase Protein Array Core

/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/coad/cgcc/mdanderson.org/mda_rppa_core/protein_exp/

Data Types and Data Levels

image as described

This image models the data types, data levels, and file types we expect to get for Protein Array data. Red rectangles indicate Data Types. Blue rectangles indicate Data Levels. File types are described in the blue boxes.

Data Levels

Level

File Type

Description

Size

1

Array Slide Image (tiff)

black and white, high-resolution image of protein array

7 MB per antibody

1

RPPA Slide Image Measurements (txt)

raw signals from a black and white, high-resolution image of protein array

1 MB per antibody

2

Super Curve Results (tab-delimited, txt)

Supercurve results, use dilution to calculate relative concentration

~2.2 MB for all antibodies

3

Normalized Protein Expression (MAGE-TAB data matrix, txt)

signals for genes

~2.1 MB for all antibodies

Antibody annotations and slide designs are also provided. The annotation file for a particular experiment is listed in the MAGE-TAB archive's SDRF file under the column "Annotation REF".

Data Types

Annotations-Antibodies

Annotations are a data type reserved for metadata about biospecimens (e.g. annotations available in the Annotations Manager), or genomic mappings (i.e. coordinates of a probe/sequence read map to a transcript that maps to a genomic region; e.g. Platform Design Files (ADFs)). For Protein Arrays we are concerned with annotations describing the relationship between antibodies and their gene targets - no protein transcript IDs are provided.

Annotations-Platform Design

For Protein Arrays we are also concerned with annotations describing the design of the slide (i.e. which samples were printed in which locations on the slide).

Expression-Protein

The signal of a protein antibody for a particular sample-portion provides an estimate of the amount of protein contained within that portion (i.e. the protein expression).

  • Level 1 data provides the image of the slide and the raw signals for the images on that slide. 
  • The raw signal data is analyzed to create dilution curves (Level 2) for each sample-portion using the SuperCurve R-package
  • The dilution curve data is used to normalize all the sample-portion antibody results to give the protein expression for a gene (Level 3).

Archive names and structure

There are five archives for protein array submissions: the level (1-3) archives, the aux archives, and the MAGE-TAB (metadata) archive. Naming conventions are similar to typical archives.

<center_domain>_<disease_code>.<platform_code>.Level_3.<index>.<revision>.<series>
<center_domain>_<disease_code>.<platform_code>.mage-tab.1.<revision>.<series>

mdanderson.org_COAD.MDA_RPPA_Core.Level_3.1.0.0
mdanderson.org_COAD.MDA_RPPA_Core.mage-tab.1.0.0
  • Archives are gzipped tars
  • Archives are flat, below a directory named after the archive
  • Archives contain a MANIFEST.txt file; each file in the archive (with the optional exception of the MANIFEST.txt file) will be represented in the MANIFEST.txt as the output of md5sum run against the file.

Archive files

Data Level archives

A complete Protein Array data level archive contains

Level

File Type

Required?

Visibility

1

RPPA Slide Image Measurements

Yes

Open Access

1

Array Slide Image

No: Optional

Open Access

2

Super Curve Results

Yes

Open Access

3

Normalized Protein Expression

Yes

Open Access

All Level Archives

DESCRIPTION.txt

No: Optional

Open Access

All Archives

MANIFEST.txt

Yes

Open Access

Protein Array submissions also include separate MAGE-TAB archives that contain files that describe the Protein Array experiment and the relationship between the experimental samples and the data files produced by assaying those samples.

Data Files

Data File Name Format

<center_token> below means any string that is provided by the center for internal tracking and/or to make the file unique. Any string means every character that Linux allows to be in a file name. The string could include punctuation in some cases.

Level 1 file name format

File Type

File Name

Validation

Example

Array Slide Image (TIFF)

<antibody>_<center_token>.tif

None until Annotation file is normalized

AKT_pS473(V)_GBL901035.tif
<center_token> in this case is a slide ID "GBL901035", but it could be any string.

RPPA Slide Image Measurements

<antibody>_<center_token>.txt

None until Annotation file is normalized

AKT_pS473(V)_GBL901035.txt
<center_token> in this case is a slide ID "GBL901035", but it could be any string.

Level 2 file name format

File Type

File Name

Validation

Example

SuperCurve Results

<center_domain>_<disease_code>.<platform_code>.SuperCurve.Level_2.<center_token>.txt

  • Prefix=<center_domain>_<disease_code>.<platform_code>.SuperCurve.Level_2.
  • Suffix=.txt
  • Disease code = archive disease code
  • center_domain = archive center_domain
  • platform_code = archive platform_code

mdanderson.org_OV.MDA_RPPA_Core.SuperCurve.Level_2.11.28.1.txt
<center_token> in this case is a date "11.28.1", but it could be any string.

Level 3 file name format

File Type

File Name

Validation

Example

Normalized Protein Expression

<center_domain>_<disease_code>.MDA_RPPA_Core.protein_expression.Level_3.<center_token>.txt

  • Prefix=mdanderson.org_<disease_code>.<platform_code>.protein_expression.Level_3.
  • Suffix=.txt
  • Disease code = archive disease code
  • center_domain = archive center_domain
  • platform_code = archive platform_code

mdanderson_OV.MDA_RPPA_Core.protein_expression.Level_3.11.1.3.txt
<center_token> in this case is a date "11.1.3", but it could be any string.

Data File Contents Format

Level 1 file content format

File Type

File Format

Validation

Array Slide Image (TIFF)

TIFF

None

RPPA Slide Image Measurements

  • Tab-delimited
  • column format

None

Level 2 file content format

File Type

File Format

Validation

SuperCurve Results

  • Tab-delimited
  • column format
  • MDA_RPPA_Core specific
  • First two column headers reserved for "Sample REF" and "Order"
  • Rest of headers on X-axis contains Level 1 data file names
  • Y-axis contains sample-portion UUIDs
  • Level 1 file names listed on X-axis must exist in SDRF under the "Array Data File" column
  • Sample REF values must exist in Sample Name column of SDRF
Level 3 file content format

File Type

File Format

Validation

Normalized Protein Expression

  • Tab-delimited
  • MAGE-TAB Data Matrix
  • X-axis contains "Sample REF" values (sample-portion UUIDs) 
  • Y-axis contains Composite Element REFs
  • Sample REF values must exist in Sample Name column of SDRF
  • When Annotation file normalized: Composite Element REFs must be found in Annotations file

Metadata (MAGE-TAB) archives

In addition to the MANIFEST.txt file, Protein Array MAGE-TAB archives contain

  • a DESCRIPTION.txt file
  • an IDF
  • an SDRF

Metadata (MAGE-TAB) Data

SDRF model for Protein Arrays

The DAG below models the processes described by a fictitious experiment. Rectangles are events and edges are protocols. Some events have associated metadata like Files or Comments. The top row associates SDRF column names with the experimental events.

image as described

Metadata (MAGE-TAB) file names

<center_domain>_<disease_code>.<platform_code>.<index>.<revision>.<series>.idf.txt
<center_domain>_<disease_code>.<platform_code>.<index>.<revision>.<series>.sdrf.txt

Metadata (MAGE-TAB) file formats

All files are tab-delimited text.

Investigation Description File (IDF)

Nothing is new for Protein Arrays in IDF files. You could skip over this section if you already know IDFs.

The IDF can be considered as a set of tables that can have variable numbers of rows and columns. The first field in a IDF line is a row header, while subsequent fields are data items corresponding to the row header. Adjacent row lines represent a table. Data items falling in the same column with in tables are related (i.e., columns can be considered records).

Valid row headers in order are as follows (field values are explained in the next section):

Row Headers

Investigation Title

Experimental Design

Experimental Design Term Source REF

Experimental Factor Type

Experimental Factor Type Term Source REF

Person Last Name

Person First Name

Person Mid Initials

Person Email

Person Phone

Person Address

Person Affiliation

Person Roles

Date of Experiment

Public Release Date

Experiment Description

Protocol Name

Protocol Type

Protocol Term Source REF

Protocol Description

Protocol Parameters

SDRF Files

Term Source Name

Term Source File

Term Source Version

Sample-Data Relationship File (SDRF)

What's changed in SDRFs for Protein Arrays?

  1. "Sample Name" will contain the primary TCGA UUID instead of "Extract Name" since the center receives portions of tissues instead of extracted analytes.
  2. "Comment [TCGA Biospecimen Type]" identifies the type of UUID (in this case "Shipped Portion")
  3. There are many Extract Name columns
  4. "Array Name" is a new column
  5. There will be many Array Design Files, one for each antibody, that will be located in the mage-tab archive. These will have a Data Type of "Annotations-Platform Design" and a Level of 0.
  6. "Comment [TCGA Antibody Name]" lists the name of the antibody probed
  7. "Annotations File" is a new column. The file will be located in the mage-tab archive.
  8. "Image File" may be new for you but it is part of the MAGE-TAB specification 
  9. "Data Transformation Name" is relatively new. This column made its first appearance in the RNASeq specification.
  10. Comment [TCGA File Type] is new. The column describes the type of file such that it is easier for someone to know how to process it. This is the first time this column has been used. The DCC will track the file-to-file type values in the future. The values will be controlled.
  11. Each file will also have a corresponding "Comment[TCGA MD5]" column containing the corresponding md5 check sum for that file.

SDRFs have a single header line, followed by records, one record per line.

Valid headers in order are as follows (field values are explained in the next section):

Headers

Source Name

Material Type

Term Source REF

Provider

Sample Name

Material Type

Term Source REF

Comment [TCGA Biospecimen Type]

Protocol REF

Extract Name

Material Type

Term Source REF

Protocol REF

Extract Name

Protocol REF

Extract Name

Protocol REF

Array Name

Array Design File

Comment [TCGA Data Type]

Comment [TCGA Data Level]

Comment [TCGA File Type]

Protocol REF

Comment [TCGA Antibody Name]

Annotations File

Comment [TCGA Data Level]

Comment [TCGA Data Type]

Comment [TCGA File Type]

Hybridization Name

Protocol REF

Scan Name

Image File

Comment [TCGA Include for Analysis]

Comment [TCGA Data Type]

Comment [TCGA Data Level]

Comment [TCGA Archive Name]

Comment [TCGA File Type]

Comment [TCGA MD5]

Array Data File

Comment [TCGA Include for Analysis]

Comment [TCGA Data Type]

Comment [TCGA Data Level]

Comment [TCGA Archive Name]

Comment [TCGA File Type]

Comment [TCGA MD5]

Protocol REF

Data Transformation Name

Derived Array Data File

Comment [TCGA Include for Analysis]

Comment [TCGA Data Type]

Comment [TCGA Data Level]

Comment [TCGA Archive Name]

Comment [TCGA File Type]

Comment [TCGA MD5]

Protocol REF

Normalization Name

Derived Array Data Matrix File

Comment [TCGA Include for Analysis]

Comment [TCGA Data Type]

Comment [TCGA Data Level]

Comment [TCGA Archive Name]

Comment [TCGA File Type]

Comment [TCGA MD5]

The first five columns (Source Name related columns) may not appear in the SDRF if there are no described controls or non-TCGA samples.
Admissible values for the corresponding fields (in the record lines) are given in the next section.

Validation for SDRF Column Headers

The following columns are required, and the archive will fail if they are missing:

  • Sample Name
  • Comment [TCGA Biospecimen Type]
  • Array Design File
  • Annotations File
  • Image File

Other validations:

  • Any column whose name ends with "File" must have the following comment columns IMMEDIATELY after them (in any order);
    • Comment [TCGA Data Level]
    • Comment [TCGA Data Type]
    • Comment [TCGA Archive Name]
    • Comment [TCGA File Type]
    • Comment [TCGA MD5]
  • Any of the following headers must also be followed by a "Comment [TCGA Include for Analysis]" column: "Image File", "Array Data File", "Derived Array Data File", "Derived Array Data Matrix File"
  • If the data level (as determined by the comment column) for a file is Level 2, the file column header must be either "Derived Array Data File" or "Derived Array Data Matrix File"
  • If the data level (as determined by the comment column) for a file is Level 3, the file column header must be "Derived Array Data Matrix File"
  • If the data level (as determined by the comment column) for a file is Level 1, the file column header must be "Image File", "Array Data File", or "Array Data Matrix File"
  • If the data level (as determined by the comment column) for a file is Level 0, the file column header must be "Array Design File",  or "Annotations File"

Metadata (MAGE-TAB) field formats

Investigation Description File (IDF)
IDF field description

Field (row header)

Description

Investigation Title

free text title of study

Experimental Design

standard design terms

Experimental Design Term Source REF

ontological source of terms on previous line

Experimental Factor Type

standard experimental factor terms

Experimental Factor Type Term Source REF

ontological source of terms on previous line

Contact Info 

Person Last Name

list of surnames

Person First Name

list of first names

Person Mid Initials

list of MIs

Person Email

list of emails

Person Phone

list of phone numbers

Person Address

list of mailing addresses

Person Affiliation

list of affiliations

Person Roles

list of roles

Experiment Description

 

Date of Experiment

date in YYYYMMDD format

Public Release Date

date in YYYYMMDD format

Experiment Description

free text description (no tabs or linebreaks)

Protocol Name

tokens serving as references in the SDRF

Protocol Type

list of standard protocol types

Protocol Term Source REF

list of ontological sources of protocol types

Protocol Description

list of free text descriptions (no tabs or linebreaks)

Protocol Parameters

list of <tag>=<value> pairs describing experimental parameters

SDRF Files

The SDRF filename, present in the submitted mage-tab archive

Term Source Name

list of ontological sources in above REF fields

Term Source File

list of urls describing the location of ontological source files

Term Source Version

list of version numbers for ontological sources

IDF example
Investigation Title	Protein Expression for TCGA Ovarian samples using MDA Reverse Phase Protein Array
Experimental Design	is_expressed_design
Experimental Design Term Source REF	MGED Ontology	MGED Ontology
Experimental Factor Type	disease_state_design
Experimental Factor Type Term Source REF	MGED Ontology

Person Last Name	Mills
Person First Name	Gordon
Person Mid Initials
Person Email	gmills@mdanderson.org
Person Phone	713-563-4200
Person Address	"1400 Pressler Street, Unit Number: 1410, Houston, TX 77030 "
Person Affiliation	The University of Texas MD Anderson Cancer Center
Person Roles	PI

Date of Experiment	20110427

Public Release Date	20110427

Experiment Description	Protein Expression for TCGA Ovarian samples using MDA Reverse Phase Protein Array

Protocol Name	mdanderson.org:protein_extraction:01	mdanderson.org:protein_denature:01	mdanderson.org:serial_dilution:01	mdanderson.org:slide_print:01	mdanderson.org:antibody_probe:01	mdanderson.org:slide_scan:01	mdanderson.org:supercurve:01	mdanderson.org:protein_normalization:01
Protocol Type	protein_extraction	protein_denature	serial_dilution	slide_print	antibody_probe	slide_scan	supercurve	protein_normalization
Protocol Term Source REF	NCI EVS	NCI EVS	NCI EVS	NCI EVS	NCI EVS	NCI EVS	NCI EVS	NCI EVS
Protocol Description	protein extracted from shipped portions sent by BCR. Tube contains beads …	denature protein using …	two-fold serial dilution …	print dillutions on slide …	wash antibody over slide …	scanned slide using some scanner	ran supercureve R-package on data	linear noramlization …
Protocol Parameters						version=123;parameter1=wer	version=123;parameter1=wer	version=123;parameter1=wer

SDRF Files	mdanderson.org_OV.MDA_RPPA_Core.1.sdrf.txt
Term Source Name	MGED Ontology	NCI EVS	NCBI Taxonomy
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://evs.nci.nih.gov/	http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/
Term Source Version	1.3.1.1	2010-09	2010-09
Sample-Data Relationship File (SDRF)

Each line in an SDRF describes a control or shipped sample-portion, the processes performed on the portion to obtain data, and the files created which contain data related to the aliquot. Columns named Protocol REF contain values referring to content in the IDF. Columns names * File contain file name values; the files referenced are present in the accompanying data archive. Values of "->" mean null.

Definition

"Print" in the context of an array means adding a sample to a slide.

SDRF field description

Field

Description

Validation

Source Name

Some sort of ID or name describing the source of samples that are not from TCGA

none

Material Type

cell line, cell, or protein, or some term described in the Term Source REF following this column. e.g Material Type in MGED Ontology

none

Term Source REF

The source of the term listed in the previous column. e.g. MGED Ontology. More information about a particular Term Source is found in the IDF file

none

Provider

Who provided the source or sample

none

Protocol REF

token referring to IDF description

validate that IDF contains corresponding Protocol Name

Sample Name

TCGA UUID of the sample-portion if the sample is from TCGA, or some sort of ID/name describing the sample uniquely if the sample is not from TCGA

when "Comment [TCGA Biospecimen Type]" is equal to "Shipped Portion" the value for "Sample Name" is a valid UUID

Comment [TCGA Biospecimen Type]

The type of TCGA UUID (e.g. sample, portion, aliquot)

if UUID, validate that it exists as a portion that was shipped to the center of the archive (e.g. mdanderson.org)

Extract Name

some sort of ID/name describing the sample uniquely

none

Array Name

some sort of ID/name describing the event of printing an array

none

Array Design File

name of the file that describes where samples and dilutions were plated on the array

must be located in the mage-tab directory

Comment [Antibody Name]

the name of the antibody that is assayed on the array

none

Annotations File

name of the file that describes the annotations for antibodies

must be located in the mage-tab directory

Comment [TCGA Data Level]

data level of the file listed in the "* File" column previous

[0-4]

Comment [TCGA Data Type]

data type of the file listed in the "* File" column previous

Expression-Protein or Annotations-Antibodies or Annotations-Platform Design

Comment [TCGA File Type]

file type of the file listed in the "* File" column previous. File Type helps determine how to process the file

Antibody Annotations (txt), MDA_RPPA Slide Design (txt)*, *Array Slide Image (TIFF), RPPA Slide Image Measurements (txt), SuperCurve Results (txt), Normalized Protein Expression (MAGE-TAB data matrix)

Hybridization Name

some sort of ID/name describing the event of probing the array with the antibody

none

Scan Name

some sort of ID/name describing the event of scanning an array

none

Image File

the file produced from the scan

file must exist in specified archive

Comment [TCGA Include for Analysis]

yes|no QC indicator; case non-specific

If the column is included, then it must indicate yes or no.

Comment [TCGA Archive Name]

valid DCC archive name (without .tar.gz extension)

The archive must exist

Comment [TCGA MD5]

The md5 checksum hash of the file

The file's md5 must be listed in the archive's MANIFEST

Array Data File

the numerical interpretation of the file produced from the scan

file must exist in specified archive

Data Transformation Name

some sort of ID/name describing the event of transforming the data in Array Data File

none

Derived Array Data File

a file with the results of the data transformation

file must exist in specified archive

Normalization Name

some sort of ID/name describing the event of normalizing the data in Derived Array Data File

none

Derived Array Data Matrix File

a file with the results of the data transformation

file must exist in specified archive

SDRF example
Source Name	Material Type	Term Source REF	Provider	Sample Name	Material Type	Term Source REF	Comment [TCGA Biospecimen Type]	Protocol REF	Extract Name	Material Type	Term Source REF	Protocol REF	Extract Name	Protocol REF	Extract Name	Protocol REF	Array Name	Array Design File	Comment [TCGA Data Type]	Comment [TCGA Data Level]	Comment [TCGA File Type]	Protocol REF	Comment [TCGA Antibody Name]	Annotations File	Comment [TCGA Data Level]	Comment [TCGA Data Type]	Comment [TCGA File Type]	Hybridization Name	Protocol REF	Scan Name	Image File	Comment [TCGA Include for Analysis]	Comment [TCGA Data Type]	Comment [TCGA Data Level]	Comment [TCGA Archive Name]	Comment [TCGA File Type]	Comment [TCGA MD5]	Array Data File	Comment [TCGA Include for Analysis]	Comment [TCGA Data Type]	Comment [TCGA Data Level]	Comment [TCGA Archive Name]	Comment [TCGA File Type]	Comment [TCGA MD5]	Protocol REF	Data Transformation Name	Derived Array Data File	Comment [TCGA Include for Analysis]	Comment [TCGA Data Type]	Comment [TCGA Data Level]	Comment [TCGA Archive Name]	Comment [TCGA File Type]	Comment [TCGA MD5]	Protocol REF	Normalization Name	Derived Array Data Matrix File	Comment [TCGA Include for Analysis]	Comment [TCGA Data Type]	Comment [TCGA Data Level]	Comment [TCGA Archive Name]	Comment [TCGA File Type]	Comment [TCGA MD5]
->	->	->	->	16211caa-d5f8-4c55-a3a4-be3355122480	cell	MGED Ontology	Shipped Portion	mdanderson.org:protein_extraction:01	TCGA-A3-3306-01A-02.P	protein	MGED Ontology	mdanderson.org:protein_denature:01	TCGA-A3-3306-01A-02.DP	mdanderson.org:serial_dilution:01	TCGA-A3-3306-01A-02.SD	mdanderson.org:slide_print:01	AKT_pS473(V)_GBL9010352	AKT_pS473(V)_GBL9010352.slide_design.txt	Annotations-Platform Design	Level 0	MDA_RPPA Slide Design (txt)	mdanderson.org:antibody_probe:01	AKT_pS473(V)	mdanderson.org_OV.antibody_annotations.txt	Level 0	Annotations-Antibody	Antibody Annotations	AKT_pS473(V)_GBL9010352_H	mdanderson.org:slide_scan:01	AKT_pS473(V)_GBL9010352_S	AKT_pS473(V)_GBL9010352.tif	Yes	Expression-Protein	Level 1	mdanderson.org_OV.MDA_RPPA_Core.Level_1.1.0.0	Array Slide Image (TIFF)	ee00dcf0345b7eb6900737444bf2d8d4	AKT_pS473(V)_GBL9010352.txt	Yes	Expression-Protein	Level 1	mdanderson.org_OV.MDA_RPPA_Core.Level_1.1.0.0	RPPA Slide Image Measurments (txt)	5f8f2396353ec53cfd467079eae49b1e	mdanderson.org:supercurve:01	mdanderson.org_OV.SuperCurve.Level_2.Set29	mdanderson.org_OV.MDA_RPPA_Core.SuperCurve.Level_2.11.28.1.txt	Yes	Expression-Protein	Level 2	mdanderson.org_OV.MDA_RPPA_Core.Level_2.1.0.0	SuperCurve Results	396d7b4a32d1a22be8b422af4d86d275	mdanderson.org:protein_normalization:01	mdanderson_OV.protein_expression.Level_3.Set29	mdanderson_OV.MDA_RPPA_Core.protein_expression.Level_3.11.1.3.txt	Yes	Expression-Protein	Level 3	mdanderson.org_OV.MDA_RPPA_Core.Level_3.1.0.0	Normalizaed Protein Expression (MAGE-TAB Data Matrix)	11b99c73a585be19a0337753bedd0af6
->	->	->	->	462b80e9-9015-43b7-b847-2fe3fdd384ea	cell	MGED Ontology	Shipped Portion	mdanderson.org:protein_extraction:01	TCGA-A3-3311-01A-03.P	protein	MGED Ontology	mdanderson.org:protein_denature:01	TCGA-A3-3311-01A-03.DP	mdanderson.org:serial_dilution:01	TCGA-A3-3311-01A-03.SD	mdanderson.org:slide_print:01	AKT_pS473(V)_GBL9010352	AKT_pS473(V)_GBL9010352.slide_design.txt	Annotations-Platform Design	Level 0	MDA_RPPA Slide Design (txt)	mdanderson.org:antibody_probe:01	AKT_pS473(V)	mdanderson.org_OV.antibody_annotations.txt	Level 0	Annotations-Antibody	Antibody Annotations	AKT_pS473(V)_GBL9010352_H	mdanderson.org:slide_scan:01	AKT_pS473(V)_GBL9010352_S	AKT_pS473(V)_GBL9010352.tif	Yes	Expression-Protein	Level 1	mdanderson.org_OV.MDA_RPPA_Core.Level_1.1.0.0	Array Slide Image (TIFF)	ee00dcf0345b7eb6900737444bf2d8d4	AKT_pS473(V)_GBL9010352.txt	Yes	Expression-Protein	Level 1	mdanderson.org_OV.MDA_RPPA_Core.Level_1.1.0.0	RPPA Slide Image Measurments (txt)	5f8f2396353ec53cfd467079eae49b1e	mdanderson.org:supercurve:01	mdanderson.org_OV.SuperCurve.Level_2.Set29	mdanderson.org_OV.MDA_RPPA_Core.SuperCurve.Level_2.11.28.1.txt	Yes	Expression-Protein	Level 2	mdanderson.org_OV.MDA_RPPA_Core.Level_2.1.0.0	SuperCurve Results	396d7b4a32d1a22be8b422af4d86d275	mdanderson.org:protein_normalization:01	mdanderson_OV.protein_expression.Level_3.Set29	mdanderson_OV.MDA_RPPA_Core.protein_expression.Level_3.11.1.3.txt	Yes	Expression-Protein	Level 3	mdanderson.org_OV.MDA_RPPA_Core.Level_3.1.0.0	Normalizaed Protein Expression (MAGE-TAB Data Matrix)	11b99c73a585be19a0337753bedd0af6
Positive Control	cell line	MGED Ontology	ATCC	Positive Control	->	->	->	->	->	->	->	->	->	mdanderson.org:serial_dilution:01	Positive Control	mdanderson.org:slide_print:01	AKT_pS473(V)_GBL9010352	AKT_pS473(V)_GBL9010352.slide_design.txt	Annotations-Platform Design	Level 0	MDA_RPPA Slide Design (txt)	mdanderson.org:antibody_probe:01	AKT_pS473(V)	mdanderson.org_OV.antibody_annotations.txt	Level 0	Annotations-Antibody	Antibody Annotations	AKT_pS473(V)_GBL9010352_H	mdanderson.org:slide_scan:01	AKT_pS473(V)_GBL9010352_S	AKT_pS473(V)_GBL9010352.tif	Yes	Expression-Protein	Level 1	mdanderson.org_OV.MDA_RPPA_Core.Level_1.1.0.0	Array Slide Image (TIFF)	ee00dcf0345b7eb6900737444bf2d8d4	AKT_pS473(V)_GBL9010352.txt	Yes	Expression-Protein	Level 1	mdanderson.org_OV.MDA_RPPA_Core.Level_1.1.0.0	RPPA Slide Image Measurments (txt)	5f8f2396353ec53cfd467079eae49b1e	mdanderson.org:supercurve:01	mdanderson.org_OV.SuperCurve.Level_2.Set29	mdanderson.org_OV.MDA_RPPA_Core.SuperCurve.Level_2.11.28.1.txt	Yes	Expression-Protein	Level 2	mdanderson.org_OV.MDA_RPPA_Core.Level_2.1.0.0	SuperCurve Results	396d7b4a32d1a22be8b422af4d86d275	mdanderson.org:protein_normalization:01	mdanderson_OV.protein_expression.Level_3.Set29	mdanderson_OV.MDA_RPPA_Core.protein_expression.Level_3.11.1.3.txt	Yes	Expression-Protein	Level 3	mdanderson.org_OV.MDA_RPPA_Core.Level_3.1.0.0	Normalizaed Protein Expression (MAGE-TAB Data Matrix)	11b99c73a585be19a0337753bedd0af6
Negative Control (Buffer)	->	->	->	Negative Control (Buffer)	->	->	->	->	->	->	->	->	->	mdanderson.org:serial_dilution:01	Negative Control (Buffer)	mdanderson.org:slide_print:01	AKT_pS473(V)_GBL9010352	AKT_pS473(V)_GBL9010352.slide_design.txt	Annotations-Platform Design	Level 0	MDA_RPPA Slide Design (txt)	mdanderson.org:antibody_probe:01	AKT_pS473(V)	mdanderson.org_OV.antibody_annotations.txt	Level 0	Annotations-Antibody	Antibody Annotations	AKT_pS473(V)_GBL9010352_H	mdanderson.org:slide_scan:01	AKT_pS473(V)_GBL9010352_S	AKT_pS473(V)_GBL9010352.tif	Yes	Expression-Protein	Level 1	mdanderson.org_OV.MDA_RPPA_Core.Level_1.1.0.0	Array Slide Image (TIFF)	ee00dcf0345b7eb6900737444bf2d8d4	AKT_pS473(V)_GBL9010352.txt	Yes	Expression-Protein	Level 1	mdanderson.org_OV.MDA_RPPA_Core.Level_1.1.0.0	RPPA Slide Image Measurments (txt)	5f8f2396353ec53cfd467079eae49b1e	mdanderson.org:supercurve:01	mdanderson.org_OV.SuperCurve.Level_2.Set29	mdanderson.org_OV.MDA_RPPA_Core.SuperCurve.Level_2.11.28.1.txt	Yes	Expression-Protein	Level 2	mdanderson.org_OV.MDA_RPPA_Core.Level_2.1.0.0	SuperCurve Results	396d7b4a32d1a22be8b422af4d86d275	mdanderson.org:protein_normalization:01	mdanderson_OV.protein_expression.Level_3.Set29	mdanderson_OV.MDA_RPPA_Core.protein_expression.Level_3.11.1.3.txt	Yes	Expression-Protein	Level 3	mdanderson.org_OV.MDA_RPPA_Core.Level_3.1.0.0	Normalizaed Protein Expression (MAGE-TAB Data Matrix)	11b99c73a585be19a0337753bedd0af6
786_0	cell line	MGED Ontology	ATCC	786_0	cell	MGED Ontology	->	->	->	->	->	->	->	mdanderson.org:serial_dilution:01	Negative Control (Buffer)	mdanderson.org:slide_print:01	AKT_pS473(V)_GBL9010352	AKT_pS473(V)_GBL9010352.slide_design.txt	Annotations-Platform Design	Level 0	MDA_RPPA Slide Design (txt)	mdanderson.org:antibody_probe:01	AKT_pS473(V)	mdanderson.org_OV.antibody_annotations.txt	Level 0	Annotations-Antibody	Antibody Annotations	AKT_pS473(V)_GBL9010352_H	mdanderson.org:slide_scan:01	AKT_pS473(V)_GBL9010352_S	AKT_pS473(V)_GBL9010352.tif	Yes	Expression-Protein	Level 1	mdanderson.org_OV.MDA_RPPA_Core.Level_1.1.0.0	Array Slide Image (TIFF)	ee00dcf0345b7eb6900737444bf2d8d4	AKT_pS473(V)_GBL9010352.txt	Yes	Expression-Protein	Level 1	mdanderson.org_OV.MDA_RPPA_Core.Level_1.1.0.0	RPPA Slide Image Measurments (txt)	5f8f2396353ec53cfd467079eae49b1e	mdanderson.org:supercurve:01	mdanderson.org_OV.SuperCurve.Level_2.Set29	mdanderson.org_OV.MDA_RPPA_Core.SuperCurve.Level_2.11.28.1.txt	Yes	Expression-Protein	Level 2	mdanderson.org_OV.MDA_RPPA_Core.Level_2.1.0.0	SuperCurve Results	396d7b4a32d1a22be8b422af4d86d275	mdanderson.org:protein_normalization:01	mdanderson_OV.protein_expression.Level_3.Set29	mdanderson_OV.MDA_RPPA_Core.protein_expression.Level_3.11.1.3.txt	Yes	Expression-Protein	Level 3	mdanderson.org_OV.MDA_RPPA_Core.Level_3.1.0.0	Normalizaed Protein Expression (MAGE-TAB Data Matrix)	11b99c73a585be19a0337753bedd0af6
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