MAGE-TAB example

IDF Example

Full IDF example in spreadsheet.

Comment[GEAAccession]E-GEAD-369
MAGE-TAB Version1.1
Investigation TitleTranscriptional profiling of Arabidopsis leaves exposed to elevated temperature
Experiment DescriptionWe investigated genome-wide ... biological replicates were analyzed.
Experimental Designstimulus or stress design
Experimental Factor Nametemperature
Experimental Factor Typetemperature
Person Last NameTest
Person First NameTarou
Person AffiliationDDBJ Center, National Institute of Genetics
Person Rolessubmitter
Public Release Date2018-06-22
PubMed ID29040613
Protocol NameP-GEAD-535...
Protocol Typesample collection protocol...
Protocol DescriptionPlants were sown on GM medium ... 22 degrees celsius....
SDRF FileE-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.

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.

Raw and processed microarray data files for each sample
Raw and processed microarray data files for each sample
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

Example 2: Two-color microarray

Two-color microarray
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

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.

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

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.

MAGE-TAB real-world examples
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