MAGE-TAB example

IDF Example

Full IDF example in spreadsheet (Microarray) Full IDF example in spreadsheet (NGS)

Comment[GEAAccession]	E-GEAD-369
MAGE-TAB Version	1.1
Investigation Title	Transcriptional profiling of Arabidopsis leaves exposed to elevated temperature
Experiment Description	We investigated genome-wide … biological replicates were analyzed.
Experimental Design	stimulus or stress design
Experimental Factor Name	temperature
Experimental Factor Type	temperature
Person Last Name	Test
Person First Name	Tarou
Person Affiliation	DDBJ Center, National Institute of Genetics
Person Roles	submitter
Public Release Date	2018-06-22
PubMed ID	29040613
Protocol Name	P-GEAD-535	…
Protocol Type	sample collection protocol	…
Protocol Description	Plants were sown on GM medium … 22 degrees celsius.	…
SDRF File	E-GEAD-369.sdrf.txt
Comment[Number of channel]	single-channel
Comment[Array Design REF]	A-AFFY-2
Comment[AEExperimentType]	transcription profiling by array
Comment[BioProject]	PRJDB3647
Comment[Public Release Date]	2018-06-22
Comment[Last Update Date]	2018-06-22

A full listing of all supported IDF tags can be found in the IDF section.

SDRF Conceptual Examples

Full SDRF example in spreadsheet (Microarray) Full SDRF example in spreadsheet (NGS)

Example 1: Raw and processed microarray data files for each sample
Example 2: Two-color microarray
Example 3: Next-generation sequencing raw DRA and processed data for each sample

In the below examples, the simplified SDRF (only conceptually-important columns are represented) has been represented by a row in the corresponding table. Column headings in blue denote graph node identifier columns (names).

Example 1: Raw and processed microarray data files for each sample

A simple microarray experiment. Each sample has one raw data file and one processed data file.

Source Name	Protocol REF	Assay Name	Array Data File	Derived Array Data File
Source 1	P-GEAD-10	Hybridization 1	Data1.CEL	Processed1.txt
Source 2	P-GEAD-10	Hybridization 2	Data2.CEL	Processed2.txt
Source 3	P-GEAD-10	Hybridization 3	Data3.CEL	Processed3.txt
Source 4	P-GEAD-10	Hybridization 4	Data4.CEL	Processed4.txt

Raw and processed microarray data files for each sample

Example 2: Two-color microarray

Source Name	Extract Name	Labeled Extract Name	Label	Assay Name
Source 1a	Extract 1a	LabeledExtract 1a Cy3	Cy3	Hybridization 1
Source 1b	Extract 1b	LabeledExtract 1b Cy5	Cy5	Hybridization 1
Source 2a	Extract 2a	LabeledExtract 2a Cy3	Cy3	Hybridization 2
Source 2b	Extract 2b	LabeledExtract 2b Cy5	Cy5	Hybridization 2
Source 3a	Extract 3a	LabeledExtract 3a Cy3	Cy3	Hybridization 3
Source 3b	Extract 3b	LabeledExtract 3b Cy5	Cy5	Hybridization 3

Two-color microarray

Example 3: Raw and processed sequencing data file for each sample, and a processed matrix file

A simple next-generation sequencing experiment. One raw DRA data file and one processed data file for each sample, and one processed matrix file for all samples.

Source Name	Protocol REF	Assay Name	Array Data File	Derived Array Data File	Derived Array Data Matrix File
Source 1	P-GEAD-20	Sequencing 1	DRR000001	Processed1.txt	Processed-matrix.txt
Source 2	P-GEAD-20	Sequencing 2	DRR000002	Processed2.txt	Processed-matrix.txt
Source 3	P-GEAD-20	Sequencing 3	DRR000003	Processed3.txt	Processed-matrix.txt
Source 4	P-GEAD-20	Sequencing 4	DRR000004	Processed4.txt	Processed-matrix.txt

Raw and processed sequencing data file for each sample, and a processed matrix file

MAGE-TAB Real-world Examples

Full SDRF example in spreadsheet.

Following table lists the real-world MAGE-TAB example files of the microarray and sequencing data deposited into the ArrayExpress.

Accession Number	IDF Text	SDRF Text	Experiment Summary	Platform
E-TABM-18	idf text	sdrf text	Transcription profiling of 35 different Arabidopsis thaliana ecotypes	Affymetrix
E-TABM-985	idf text	sdrf text	Transcription profiling by array of mouse testis development, dye swap design	Compugen
E-MEXP-2665	idf text	sdrf text	ChIP-chip by array of mouse cell lines and fresh tissues	Multiple platforms
E-TABM-855	idf text	sdrf text	Genotyping of human lymphoblastoid cell lines from pairs of HapMap indiviudals	Illumina GoldenGate SNP array
E-MTAB-371	idf text	sdrf text	ChIP-seq of human myofibroblasts	Illumina Sequencing
E-MTAB-6311	idf text	sdrf text	Transcription changes in zebrafish embryos of different developmental ages after exposure to cyanide (two factor values)	Affymetrix
E-GEOD-26444	idf text	sdrf text	Deep sequencing-based analysis of the anaerobic stimulon	SOLiD sequencing
E-GEOD-24366	idf text	sdrf text	Global changes following N-deprivation in Chlamydomonas	454 sequencing

MAGE-TAB real-world examples