GEO label BASE label Number of allowed labels Allowed values and constraints Content guidelines
^PLATFORM Array design : Name 1 any, must be unique within local file Provide an identifier for this entity. This identifier is used only as an internal reference within a given file. The identifier will not appear on final GEO records.
!Platform_title Array design : Name 1 string of length 1-120 characters, must be unique within local file and over all previously submitted Platforms for that submitter Provide a unique title that describes your Platform. We suggest that you use the system [institution/lab]-[species]-[number of features]-[version], e.g. "FHCRC Mouse 15K v1.0".
!Platform_distribution GEO exporter parameter 1 commercial, non-commercial, custom-commercial, or virtual Microarrays are 'commercial', 'non-commercial', or 'custom-commercial' in accordance with how the array was manufactured. Use 'virtual' only if creating a virtual definition for MS, MPSS, SARST, or RT-PCR data.
!Platform_technology Array design : Platform type 1 spotted DNA/cDNA, spotted oligonucleotide, in situ oligonucleotide, antibody, tissue, SARST, RT-PCR, MS, or MPSS Select the category that best describes the Platform technology.
!Platform_organism Sample : Organism 1 or more use standard NCBI Taxonomy nomenclature Identify the organism(s) from which the features on the Platform were designed or derived.
!Platform_manufacturer GEO exporter parameter 1 any Provide the name of the company, facility or laboratory where the array was manufactured or produced.
!Platform_manufacture_protocol Array design : Configuration
if not
GEO exporter parameter
1 any 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. You can include as much text as you need to thoroughly describe the protocol; it is strongly recommended that complete protocol descriptions are provided within your submission.
!Platform_catalog_number - 0 or more any Provide the manufacturer catalog number for commercially-available arrays.
!Platform_web_link - 0 or more valid URL Specify a Web link that directs users to supplementary information about the array. Please restrict to Web sites that you know are stable.
!Platform_support - 0 or 1 any Provide the surface type of the array, e.g., glass, nitrocellulose, nylon, silicon, unknown.
!Platform_coating - 0 or 1 any Provide the coating of the array, e.g., aminosilane, quartz, polysine, unknown.
!Platform_description Array design : Description 0 or more any Provide any additional descriptive information not captured in another field, e.g., array and/or feature physical dimensions, element grid system.
!Platform_contributor - 0 or more each value in the form 'firstname,middleinitial,lastname' or 'firstname,lastname': firstname must be at least one character and cannot contain spaces; middleinitial, if present, is one character; lastname is at least two characters and can contain spaces. List all people associated with this array design.
!Platform_pubmed_id - 0 or more an integer Specify a valid PubMed identifier (PMID) that references a published article that describes the array.
!Platform_geo_accession - 0 or 1 a valid Platform accession number (GPLxxx) Only use for performing updates to existing GEO records.
!Platform_table_begin - 1 no content required Indicates the start of the data table.
!Platform_table_end - 1 no content required Indicates the end of the data table.
^SAMPLE Raw data set : Name 1 any, must be unique within local file Provide an identifier for this entity. This identifier is used only as an internal reference within a given file. The identifier will not appear on final GEO records.
!Sample_title Raw data set : Name 1 string of length 1-120 characters, must be unique within local file and over all previously submitted Samples for that submitter Provide a unique title that describes this Sample. We suggest that you use the system [biomaterial]-[condition(s)]-[replicate number], e.g., Muscle_exercised_60min_rep2.
!Sample_supplementary_file 1 or more name of supplementary file, or 'none' Examples of supplementary file types include original Affymetrix CEL and EXP files, GenePix GPR files, and TIFF image files. Supplementary files should be zipped or tarred together with the SOFT file at time of submission. Provision of supplementary raw data files facilitates the unambiguous interpretation of data and potential verification of conclusions as set forth in the MIAME guidelines.
!Sample_table - 0 or 1 name of external file to be used as data table At this time, the only allowed external sample table file type is Affymetrix CHP files. This field allows you to specify a native CHP file, rather than supply a tab-delimited data table in the !Sample_table_begin section. Also, there is no need to specify the !Sample_platform_id when CHP files are supplied. CHP files should be zipped or tarred together with the SOFT file at time of submission.
!Sample_source_name_ch[n] Sample : Description 1 per channel any Briefly identify the biological material and the experimental variable(s), e.g., vastus lateralis muscle, exercised, 60 min.
!Sample_organism_ch[n] Sample : Organism 1 or more use standard NCBI Taxonomy nomenclature Identify the organism(s) from which the biological material was derived.
!Sample_characteristics_ch[n] Sample : Annotation(s) 1 or more any 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... You can provide as much text as you need to thoroughly describe your biological samples.
!Sample_biomaterial_provider_ch[n] - 0 or more any Specify the name of the company, laboratory or person that provided the biological material.
!Sample_treatment_protocol_ch[n] - 0 or more any Describe any treatments applied to the biological material prior to extract preparation. You can include as much text as you need to thoroughly describe the protocol; it is strongly recommended that complete protocol descriptions are provided within your submission.
!Sample_growth_protocol_ch[n] - 0 or more any Describe the conditions that were used to grow or maintain organisms or cells prior to extract preparation. You can include as much text as you need to thoroughly describe the protocol; it is strongly recommended that complete protocol descriptions are provided within your submission.
!Sample_molecule_ch[n] Extract : Description 1 per channel total RNA, polyA RNA, cytoplasmic RNA, nuclear RNA, genomic DNA, protein, or other Specify the type of molecule that was extracted from the biological material.
!Sample_extract_protocol_ch[n] Protocol : Description 1 or more any Describe the protocol used to isolate the extract material. You can include as much text as you need to thoroughly describe the protocol; it is strongly recommended that complete protocol descriptions are provided within your submission.
!Sample_label_ch[n] Labeled extract : Label 1 per channel any Specify the compound used to label the extract e.g., biotin, Cy3, Cy5, 33P.
!Sample_label_protocol_ch[n] Protocol : Description 1 or more any Describe the protocol used to label the extract. You can include as much text as you need to thoroughly describe the protocol; it is strongly recommended that complete protocol descriptions are provided within your submission.
!Sample_hyb_protocol Protocol : Description 1 or more any Describe the protocols used for hybridization, blocking and washing, and any post-processing steps such as staining. You can include as much text as you need to thoroughly describe the protocol; it is strongly recommended that complete protocol descriptions are provided within your submission.
!Sample_scan_protocol Scan : scanner
Raw data set : Feature extraction software

Scan : Description
1 or more any Describe the scanning and image acquisition protocols, hardware, and software. You can include as much text as you need to thoroughly describe the protocol; it is strongly recommended that complete protocol descriptions are provided within your submission.
!Sample_data_processing Raw data set : Description 1 any Provide details of how data in the VALUE column of your table were generated and calculated, i.e., normalization method, data selection procedures and parameters, transformation algorithm (e.g., MAS5.0), and scaling parameters. You can include as much text as you need to thoroughly describe the processing procedures.
!Sample_description Hybridization : Description 1 or more any Include any additional information not provided in the other fields, or paste in broad descriptions that cannot be easily dissected into the other fields.
!Sample_platform_id Hybridization : Array design (extraction) 1 a valid Platform identifier Reference the Platform upon which this hybridization was performed. Reference the Platform accession number (GPLxxx) if the Platform already exists in GEO, or reference the ^Platform identifier if the Platform record is being batch submitted within the same SOFT file. To identify the accession number of an existing commercial Platform in GEO, use the FIND PLATFORM tool.
!Sample_geo_accession - 0 or 1 a valid Sample accession number (GSMxxx) Only use for performing updates to existing GEO records.
!Sample_anchor - 1 SAGE enzyme anchor, usually NlaIII or Sau3A Use for SAGE submissions only.
!Sample_type - 1 SAGE Use for SAGE submissions only.
!Sample_tag_count - 1 sum of tags quantified in SAGE library Use for SAGE submissions only.
!Sample_tag_length - 1 base pair length of the SAGE tags, excluding anchor sequence Use for SAGE submissions only.
!Sample_table_begin - 1 no content required Indicates the start of the data table.
!Sample_table_end - 1 no content required Indicates the end of the data table.
^SERIES Experiment : Name 1 any, must be unique within local file Provide an identifier for this entity. This identifier is used only as an internal reference within a given file. The identifier will not appear on final GEO records.
!Series_title Experiment : Name 1 string of length 1-120 characters, must be unique within local file and over all previously submitted Series for that submitter Provide a unique title that describes the overall study.
!Series_summary Experiment : Description 1 or more any Summarize the goals and objectives of this study. The abstract from the associated publication may be suitable. You can include as much text as you need to thoroughly describe the study.
!Series_type Experiment : Type 1 any 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.
!Series_overall_design 1 any 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.
!Series_pubmed_id - 0 or more an integer 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.
!Series_web_link - 0 or more valid URL Specify a Web link that directs users to supplementary information about the study. Please restrict to Web sites that you know are stable.
!Series_contributor Experiment : Authors 0 or more each value in the form 'firstname,middleinitial,lastname' or 'firstname,lastname': firstname must be at least one character and cannot contain spaces; middleinitial, if present, is one character; lastname is at least two characters and can contain spaces. List all people associated with this study.
!Series_variable_[n] - 0 or more 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 Indicate the variable type(s) investigated in this study, e.g.,
!Series_variable_1 = age
!Series_variable_2 = age
NOTE - this information is optional and does not appear in Series records or downloads, but will be used to assemble corresponding GEO DataSet records.
!Series_variable_description_[n] - 0 or more any Describe each variable, e.g.,
!Series_variable_description_1 = 2 months
!Series_variable_description_2 = 12 months
NOTE - this information is optional and does not appear in Series records or downloads, but will be used to assemble corresponding GEO DataSet records.
!Series_variable_sample_list_[n] - 0 or more each value a valid reference to a ^SAMPLE identifier, or all List which Samples belong to each group, e.g.,
!Series_variable_sample_list_1 = samA, samB
!Series_variable_sample_list_2 = samC, samD
NOTE - this information is optional and does not appear in Series records or downloads, but will be used to assemble corresponding GEO DataSet records.
!Series_repeats_[n] - 0 or more biological replicate, technical replicate - extract, or technical replicate - labeled-extract Indicate the repeat type(s), e.g.,
!Series_repeats_1 = biological replicate
!Series_repeats_2 = biological replicate
NOTE - this information is optional and does not appear in Series records or downloads, but will be used to assemble corresponding GEO DataSet records.
!Series_repeats_sample_list_[n] - 0 or more each value a valid reference to a ^SAMPLE identifier, or all List which Samples belong to each group, e.g.,
!Series_repeats_sample_list_1 = samA, samB
!Series_repeats_sample_list_2 = samC, samD
NOTE - this information is optional and does not appear in Series records or downloads, but will be used to assemble corresponding GEO DataSet records.
!Series_sample_id Raw data set : Name 1 or more valid Sample identifiers Reference the Samples that make up this experiment. Reference the Sample accession numbers (GSMxxx) if the Samples already exists in GEO, or reference the ^Sample identifiers if they are being submitted in the same file.
!Series_geo_accession 0 or 1 a valid Series accession number (GSExxx) Only use for performing updates to existing GEO records.

More details on the "SOFT format structure and content", "SOFT submission examples", ... are available [here].

Last modified: Mon Jul 2 15:09:14 CEST 2007