Submit microarray experiment

GEA submission flow

1. Obtain a submission account

Create a D-way submission account.
To enable GEA submission, register a public key to your account.

2. Register a BioProject and BioSample(s)

BioSample

A description of biologically or physically unique samples used to generate experimental data.

metadata can be submitted as a tab-delimited text file.

3. Upload raw and processed data files

Upload raw and processed data files into the GEA submission directory.
[Optional] When an array design is not available in ArrayExpress/GEA, upload an array design file into the GEA submission directory along with data files.

4. Select a BioProject and BioSample(s)

Select a registed BioProject for the GEA submission.
Select registed BioSample(s) for the GEA submission. Majority of GEA submissions require more than one sample.

5. Prepare IDF and SDRF

IDF

The IDF (Investigation Description Format) file is used to give an overview of the experiment, including the experimental design, protocols and publication information.

SDRF

The SDRF (Sample and Data Relationship Format) describes the sample characteristics and the relationship between samples, arrays, data files etc.
SDRF template is generated from selected BioProject and BioSample(s). Enter additional information.

6. Submit IDF, SDRF and validate data files

After submitting IDF and SDRF in the submission web system, validation of the uploaded data files will automatically begin.
The submission passed validation will be reviewed.

Pre-submission checklist

Two-color microarray experiment

At the moment GEA submission interface only supports one type of two-color workflow (see graphic here), where two samples are connected with one common raw data file, which includes both channels. If you select the dual-channel option in the IDF tab, it will expect that you provide one file for the two samples that were hybridized together. Some recent two-color microarray technologies generate two separate raw data files (usually one for each channel), which will cause validation to fail (if you connect a single file per sample).

If you have separate files for each channel, please contact GEA team.

Single-cell sequencing experiment

Refer to ArrayExpress Single-cell submission guide. Please contact GEA team to upload any additional files for custom spike-ins or to facilitate data analysis.

More than one technology per experiment

GEA will ask you for the technology and name of the array, and applies it to the whole submission. If you have used different types of technologies for the same set of samples, we ask you to create separate submissions. Please make sure that the submissions have distinct titles (even though they may belong to the same study), in order to avoid mistakes. If you have samples from more than one array design in your experiment, it is possible to submit only one experiment. If you wish to do this, please contact GEA team.

Microarray experiment submission

Create a new submission

Create a new microarray experiment submission by selecting “Microarray” and clicking the [New submission]. At the same time, in the DDBJ file server (ftp-private.ddbj.nig.ac.jp), a corresponding subdirectory is created under the submitter’s GEA upload directory. Upload data files to this subdirectory.

If there is no reply from submitters after three months of initial contact, submissions will be cancelled.

The maximum number of assay per submission is 1,000. If you have more than 1,000 assays, please create multiple submissions with the same BioProject reference.

Create a new microarray experiment submission

List of submission status is as follows. The GEA team reviews submission whose status is in “submission_validated” or “data_error”.

List of submission status

Status	Explanation
New	Metadata are not submitted.
Data Submitted	Metadata and data files are submitted.
Data Validating	Validating data files.
Validation Error	Error occurred in data validation process.
Data Validated	Metadata and data are validated.
Curating	Curator is reviewing the submission.
Accession Issued	Accession number is issued to the submission.
Confidential	Archive files are created and submission is kept private
Public	Released to public.

Upload raw and processed data files

Regarding how to upload your data files, please see “Data upload”.

Submission

Set the hold date within four years or choose immediate release when processed. Submitters’ name and affiliation will be public but e-mail address will not be disclosed.

Email regarding GEA submission is sent to addresses entered in the GEA Submission. If you change email address registered in your D-way account, you need to update addresses of GEA Submissions to receive emails regarding the submissions.

BioProject

Select a submitted project registered in your account. If a BioProject is not registered, please go to the BioProject submission site and submit a project.

To use a project obtained in the other account, please contact GEA team.

Select a BioProject for the GEA experiment

BioSample

Select submitted BioSamples registered in your account. If BioSamples are not registered, please go to the BioSample submission site and submit samples.

To use samples obtained in the other account, please contact GEA team.

Select BioSamples for the GEA experiment

IDF

Enter information for IDF (Investigation Description Format).

Example IDF

Protocol: Pre-checked protocols are mandatory.
Publication: Describe associated publications by PubMed ID or DOI. For unpublished manuscript, please inform us the publication ID after assignment.
Array Design: When an array design is available in ArrayExpress/GEA, enter an array design accession number “A-XXXX-n”. When an array design is not available, register a new array design by uploading an array design file into the GEA submission directory.
Data File Type: Raw and processed data files are required for microarray experiment submission. We strongly recommend to submitting raw and processed data file per sample. Accepted Data Files Formats for microarray experiment.

SDRF

Enter information for SDRF (Sample and Data Relationship Format).

Example SDRF

Auto-filled fields.

Name columns and attribute columns for Source Name: Generated from BioSamples.
SDRF rows: 1 row for 1 BioSample.
Protocols: Protocols described in IDF are inserted to appropriate positions of SDRF with temporary protocol IDs (e.g., ESUB000350_Protocol_1)
Technology Type: “array assay” for microarray submission.
Array Design REF: array design accession or filename described in IDF.

Enter required fields by overwriting <Required: fill in the content> tags.

Fields you need to add.

Material Type: Enter controlled terms.
- total RNA
- polyA RNA
- cytoplasmic RNA
- nuclear RNA
- genomic DNA
- protein
- other
Label: Enter label compounds used to label the extracted molecule such as biotin, Cy3 and Cy5.
Array Data File and Comment[Array Data File md5]: Enter filename and md5 checksum pair for each raw data file.
Derived Array Data File and Comment[Derived Array Data File md5]: Enter filename and md5 checksum pair for each processed data file.
A list of filename and its md5 checksum (output of md5sum command) can be provided as a file <GEA submission ID>.md5 (e.g., ESUB000001.md5) (when the checksum values are provided in both SDRF and .md5 file, those in the .md5 are used).
Factor Value[enter experiment factor name here]: A user-defined name for each experimental factor studied by the experiment. These experimental factors represent the variables within the investigation (e.g. growth condition, genotype, organism part). The actual values of these variables will be listed in the “Factor Value []” columns. Example:
- Factor Value[strain]
- AT76
- KU-2003
- KU-PI499262

SDRF template, yellow-highlighted fields need to be filled by submitter

Select the entered SDRF file and continue.

md5 checksum

GEA uses md5 checksum values to detect corruption of files.
When there are many files or you are familiar with command line, provide output of md5sum command as a separate file with the filename <GEA submission ID>.md5 (for example, ESUB000001.md5) and upload it along with the data files. Values of the .md5 file are used over those of the SDRF.

Example: ESUB000001.md5 (checksum values and filenames are delimited by two spaces)

ed3d9b2adb5b29aa476b9d4164e208d5  raw1.txt
3d77463ca6f43416a6c1925b7704d304  raw2.txt
0e5be28700daa6d61ea3351921d6e578  processed1.txt
351fb1324feebe954405ca610e46ae44  processed2.txt
3d5749b63617da9002c7376deee8e0a3  array-design.txt

Overview and submit

You can download the IDF and SDRF files and check them. When correction is necessary, go back to the previous tab and corrent metadata.

Submit the IDF and SDRF metadata by clicking the “Submit” button.

Validation

When data files described in the IDF and SDRF are not found in the submission directory, an error message “Data file is not uploaded” is shown and the submission is aborted.

The validator checks submitted IDF and SDRF files according to the validation rules and gives warning and error messages. Errors need to be resolved for submission.

Accession number

GEA accession numbers are issued to completed GEA experiment.

You can allow reviewers access to private records by communicating a reviewer accesss token.

Update submission

Update in each database

Database	Update
Annotated sequence database	Request updates from web form
Sequence Read Archive (DRA)	Login D-way and update metadata To add or delete sequencing data, request updates from web form
Genomic Expression Archive (GEA)	Request updates from web form
BioProject/BioSample	Request updates from web form

Withdraw archived objects

To withdrawing archived Experiment, please contact us.

MD5 checksum value

See “MD5 checksum value” for how to obtain MD5 checksum values.