GEOarchive submission instructions

GEOarchive
GEOarchive templates and examples
GEOarchive metadata guidelines table
SOFTmatrix
Notes for Microsoft Excel users

GEOarchive

Spreadsheets prepared in GEOarchive format can be transferred directly to GEO by selecting the 'GEOarchive' option on the Direct Deposit page. All files, including any external files (such as CHP, CEL, or GenePix GPR files) should be zipped or tarred together with your spreadsheet files at the time of submission.

GEOarchive is a flexible spreadsheet-based submission format useful for batch deposit of large experiments.

GEOarchive submissions can be created in any spreadsheet software, usually Microsoft Excel.

GEOarchive format supports MIAME-compliant data submissions.

A GEOarchive submission consists of several parts as follows:

Metadata spreadsheet 'Metadata' refers to descriptive information and protocols for the overall experiment and individual Samples.
This information is supplied by completing all fields of the appropriate metadata spreadsheet template (see list of templates).

Matrix table The matrix table is a spreadsheet containing the final, normalized values that are comparable across rows and Samples, and preferably processed as described in any accompanying manuscript.
It is possible to include additional data columns in the table, for example, Affymetrix Detection calls and P-values, or background or flag columns. See the Affymetrix example below.
Affymetrix submitters can submit CHP files instead of a matrix table - but if your manuscript discusses data processed by RMA or another algorithm, we recommend providing a matrix of those values rather than CHP files.

Raw data files In addition to the normalized data provided in the Matrix table, submitters are required to provide raw data, usually in the form of supplementary raw data files. This facilitates the unambiguous interpretation of the data and potential verification of the conclusions as described in the MIAME guidelines.
Affymetrix GEOarchive submissions must include CEL files.
Non-Affymetrix GEOarchive submissions should include the original software-generated scan quantification files, for example, GenePix GPR files.

Platform If your experiments are performed using a commercial array (e.g., Affymetrix GeneChip) or other array already deposited in GEO, please use the FIND PLATFORM tool to find the GEO accession number (GPLxxxx) for inclusion in the 'platform' column in the SAMPLES section of the metadata spreadsheet. Otherwise, please include a PLATFORM section in your metadata spreadsheet and include Platform annotation columns in your matrix table. See the templates and examples.

GEOarchive templates and examples

The following Excel files illustrate the structure of different types of GEOarchive data submissions.
Each Excel file consists of several worksheets, including a metadata template, and metadata and matrix examples.
Click the tabs at the bottom of the worksheet window to switch between worksheets.
Please follow the formatting instructions on the template worksheet carefully.

A template and example for an Affymetrix submission.
A template and example for an Affymetrix submission with CHP files.
A template and example for a single channel submission.
A template and example for a single channel submission with platform.
A template and example for a dual channel submission.
A template and example for a dual channel submission with platform.

Please e-mail us at geo@ncbi.nlm.nih.gov if your data cannot be formatted according to the templates above.

HOW TO UPDATE YOUR SUBMISSION: After curators have uploaded your data and issued accession numbers, you can update individual records by logging in to your account and using the 'UPDATE' button on the Web deposit/update page or the 'UPDATE' button at the top of each of your GEO records. If you have a lot of edits to make, please feel free to e-mail batch edit details to us at geo@ncbi.nlm.nih.gov, and we will process them for you.

GEOarchive metadata guidelines table

Note: For all studies involving human subjects, it is the submitters responsibility to ensure that the data and files supplied to GEO do not in any way compromise patient anonymity. Make sure that all your files, file names, and descriptions are fully de-identified.

Field	Content Guidelines
SERIES
title	Provide a unique title that describes the overall study.
summary	Provide a thorough description of the goals and objectives of this study. The abstract from the associated publication may be suitable. Multiple summary lines can be included.
overall design	Provide a description of the experimental design. Indicate how many Samples are analyzed, if replicates are included, are there control and/or reference Samples, dye-swaps, etc... Multiple lines can be included.
type	Enter keyword(s) that generally describe the type of study. Examples include: time course, dose response, comparative genomic hybridization, ChIP-chip, cell type comparison, disease state analysis, stress response, genetic modification, etc.
contributor	[Optional] List all people associated with this study. Format: 'firstname, middleinitial, lastname' with each contributor on a separate line.
web link	[Optional] Specify a Web link that directs users to supplementary information about the study. Please restrict to Web sites that you know are stable.
pubmed id	[Optional] Specify a valid PubMed identifier (PMID) that references a published article describing this study. Most commonly, this information is not available at the time of submission - it can be added later once the data are published.
variable	[Optional] The format should be "variable type: variable description: list of Sample names" where the variable type can be one of the following: dose, time, tissue, strain, gender, cell line, development stage, age, agent, cell type, infection, isolate, metabolism, shock, stress, temperature, specimen, disease state, protocol, growth protocol, genotype/variation, species, individual, or other. For example: age: 2 months: Sample name 1, Sample name 3 age: 12 months: Sample name 2, Sample name 4 NOTE - this information is optional and does not appear in Series records or downloads, but will be used to assemble corresponding GEO DataSet records.
repeat	[Optional] The format should be "repeat type: list of Sample names" where the repeat type can be one of these three: biological replicate, technical replicate - extract, or technical replicate - labeled-extract. For example: biological replicate: Sample name 1, Sample name 3 biological replicate: Sample name 2, Sample name 4 NOTE - this information is optional and does not appear in Series records or downloads, but will be used to assemble corresponding GEO DataSet records.
SAMPLES
Sample name	A unique name that matches a corresponding header in the matrix file.
title	Provide a unique title that describes this Sample. We suggest that you use the convention [biomaterial]-[condition(s)]-[replicate number], e.g., Muscle_exercised_60min_rep2.
raw data file	Raw data file name, e.g. GPR file. For non-Affymetrix submissions. More than one raw data file column can be included.
CEL file	CEL file name. Affymetrix submissions only.
EXP file	EXP file name. Affymetrix submissions only, if available.
CHP file	CHP file name. Affymetrix submissions only. Use this only if you are planning to submit CHP files instead of a matrix table. If your manuscript discusses data processed by RMA or another algorithm, we recommend providing a matrix of those values rather than CHP files.
source name	Briefly identify the biological material and the experimental variable(s), e.g., vastus lateralis muscle, exercised, 60 min.
organism	Identify the organism(s) from which the biological material was derived.
characteristics	List all available characteristics of the biological source, including factors not necessarily under investigation, e.g., Strain: C57BL/6, Gender: female, Age: 45 days, Tissue: bladder tumor, Tumor stage: Ta. Multiple characteristics columns can be included.
biomaterial provider	[Optional] Specify the name of the company, laboratory or person that provided the biological material.
molecule	Specify the type of molecule that was extracted from the biological material. Include one of the following: total RNA, polyA RNA, cytoplasmic RNA, nuclear RNA, genomic DNA, protein, or other.
label	Specify the compound used to label the extract e.g., biotin, Cy3, Cy5, 33P.
description	Include any additional information not provided in the other fields, or paste in broad descriptions that cannot be easily dissected into the other fields.
platform	Reference the Platform accession number (GPLxxx) if the Platform already exists in GEO. To identify the accession number of an existing Platform in GEO, use the FIND PLATFORM tool. Omit this column if a new Platform is included in your GEOarchive submission.
PROTOCOLS
growth protocol	[Optional] Describe the conditions that were used to grow or maintain organisms or cells prior to extract preparation.
treatment protocol	[Optional] Describe any treatments applied to the biological material prior to extract preparation.
extract protocol	Describe the protocol used to isolate the extract material.
label protocol	Describe the protocol used to label the extract.
hyb protocol	Describe the protocols used for hybridization, blocking and washing, and any post-processing steps such as staining.
scan protocol	Describe the scanning and image acquisition protocols, hardware, and software.
data processing	Provide details of how data in the matrix table were generated and calculated, i.e., normalization method, data selection procedures and parameters, transformation algorithm (e.g., MAS5.0, GCOS, RMA for Affymetrix data), and scaling parameters.
value definition	Provide a short description for the values in the matrix table, for example: - lowess normalized log2 ratio (test/reference) - signal calculated by GCOS1.2 software
PLATFORM
title	Provide a unique title that describes your Platform. We suggest that you use the convention [institution/lab]-[species]-[number of features]-[version], e.g. FHCRC Mouse 15K v1.0.
distribution	Microarrays are 'commercial', 'non-commercial', or 'custom-commercial' in accordance with how the array was manufactured.
technology	Select the category that best describes the Platform technology: spotted DNA/cDNA, spotted oligonucleotide, in situ oligonucleotide, antibody, tissue, SARST, RT-PCR, MS, or MPSS
organism	Identify the organism(s) from which the features on the Platform were designed or derived.
manufacturer	Provide the name of the company, facility or laboratory where the array was manufactured or produced.
manufacture protocol	Describe the array manufacture protocol. Include as much detail as possible, e.g., clone/primer set identification and preparation, strandedness/length, arrayer hardware/software, spotting protocols.
description	[Optional] Provide any additional descriptive information not captured in another field, e.g., array and/or feature physical dimensions, element grid system.
catalog number	[Optional] Provide the manufacturer catalog number for commercially-available arrays.
web link	[Optional] Specify a Web link that directs users to supplementary information about the array. Please restrict to Web sites that you know are stable.
support	[Optional] Provide the surface type of the array, e.g., glass, nitrocellulose, nylon, silicon, unknown.
coating	[Optional] Provide the coating of the array, e.g., aminosilane, quartz, polysine, unknown.
contributor	[Optional] List all people associated with this array design. Each name in the form 'firstname, middleinitial, lastname'.
pubmed id	[Optional] Specify a valid PubMed identifier (PMID) that references a published article that describes the array.

SOFTmatrix

SOFTmatrix was our original spreadsheet-based submission format. GEO will continue to accept SOFTmatrix files, but if you are a new submitter we strongly recommend using GEOarchive format as described above.

Spreadsheets prepared in SOFTmatrix format can be transferred directly to GEO by selecting the 'SOFTmatrix' option on the Direct Deposit page. All files, including any external files (such as CHP, CEL, or GenePix GPR files) should be zipped or tarred together with your spreadsheet files at the time of submission.

The following excel file represents a valid SOFTmatrix submission (data table truncated at 20 rows). An empty template is provided on the second worksheet and an empty template for when referencing CHP files is provided on the third worksheet:

SOFTmatrix file containing three Affymetrix Samples and one Series submission: Affy_data_table_matrix.xls.

Notes for Microsoft Excel users

The following notes draw attention to common Excel-related problems.

Please be aware that Excel may automatically apply irreversible formatting to your data. According to Microsoft support:
- If a number contains a slash mark (/) or hyphen (-), it may be converted to a date format.
- If a number contains a colon (:), or is followed by a space and the letter A or P, it may be converted to a time format.
- If a number contains the letter E (in uppercase or lowercase letters; for example, 10e5), or the number contains more characters than can be displayed based on the column width and font, the number may be converted to scientific notation, or exponential, format.
- If a number contains leading zeros, the leading zeros are dropped.
Certain clone identifiers, gene names, and plate coordinates are particularly susceptible to these issues. To avoid the problem, make sure to first select the whole spreadsheet and Format -> Cells -> Number -> Text when pasting data into Excel (the default is "General"). For more information, see http://www.biomedcentral.com/1471-2105/5/80.
If you Format -> Cells -> Number -> Text as described above, very long data strings (e.g., sequence data) may be converted to hash (#) characters. If this occurs, it is necessary to switch these cells back to "General" format.