Edinburgh Core Database Group

Capel Group

Cohn Group

Gaido Group

Jain Group

Keast Group

Lessard Group

Little Group

McMahon Group

Mendelsohn Group

Potter Group

Southard-Smith Group

Vezina Group

Editorial Office Protocols

SOFT mapping protocol

GUDMAP cDNA microarray data is formatted into a GEO (Gene Expression Omnibus)-compatible format (SOFT) before being submitted to GEO. The mapping protocol used to render the data compatible with both databases is detailed below.

SOFT (Simple Omnibus Format in Text) format support MIAME-compliant data submissions. For more details see the GEO website.

Ser.   Name in GUDMAP spreadsheet GEO FIELD Name in database: Table Name in database: Column
   

 

SAMPLE INFO SHEET

1   Unique ID MIC_SERIES_SAMPLE SRM_SAMPLE_ID
2   Associated File MIC_GENE_LIST GLT_FILENAME
3   Submitted_By SERIES_CONTRIBUTOR REF_PERSON PER_NAME
4   Submitted_Institution   REF_PERSON PER_LAB
5   Submitted_Mailing_Address   REF_PERSON PER_ADDRESS
6   Submitted_City   REF_PERSON PER_CITY
7   Submitted_Zip_Code   REF_PERSON PER_POSTCODE
8   Submitted_Country   REF_PERSON PER_COUNTRY
9   Submitted_Telephone   REF_PERSON PER_PHONE
10   Submitted_Email   REF_PERSON PER_EMAIL
11   PI_Name   REF_PERSON PER_NAME
12   PI_Institution   REF_PERSON PER_LAB
13   PI_Mailing_Address   REF_PERSON PER_ADDRESS
14   PI_City   REF_PERSON PER_CITY
15   PI_Zip_Code   REF_PERSON PER_POSTCODE
16   PI_Country   REF_PERSON PER_COUNTRY
17   PI_Telephone   REF_PERSON PER_PHONE
18   PI_Email   REF_PERSON PER_EMAIL
19   Sample name SAMPLE_TITLE MIC_SAMPLE SMP_TITLE
20   Tissue/Cell type SAMPLE_SOURCE_NAME_CH MIC_SAMPLE SMP_SOURCE
21   Ontology name   MIC_COMPONENT CPN_COMPONENT_ID
22   Genus / Species SAMPLE_ORGANISM / PLATFORM ORGANISM MIC_SAMPLE SMP_ORGANISM
23   Strain SAMPLE_CHARACTERISTICS MIC_SAMPLE SMP_STRAIN
24   NCBI Taxonomy ID PLATFORM_ORGANISM MIC_PLATFORM PLT_ORGANISM
25   Mutations SAMPLE_DESCRIPTION MIC_SAMPLE SMP_MUTATION
26   Pooled sample SAMPLE_TREATMENT_PROTOCOL_CH MIC_SAMPLE SMP_POOLED_SAMPLE
27   Pool size SAMPLE_CHARACTERISTICS MIC_SAMPLE SMP_POO_SIZE
28   Sex SAMPLE_CHARACTERISTICS MIC_SAMPLE SMP_SEX
29   Developmental stage SAMPLE_CHARACTERISTICS MIC_SAMPLE SMP_DEVELOPMENT_STAGE
30   Theiler Stage SAMPLE_CHARACTERISTICS MIC_SAMPLE SMP_THEILER_STAGE
31   Somite count SAMPLE_CHARACTERISTICS MIC_SAMPLE SMP_SOMITE_COUNT
32   Developmental landmarks SAMPLE_CHARACTERISTICS MIC_SAMPLE SMP_DEVELOPMENT_LANDMARK
33   Dissection method SAMPLE_TREATMENT_PROTOCOL_CH MIC_SAMPLE SMP_DISSECT_METHOD
34   Sample image   MIC_SAMPLE SMP_IMAGE
35   Sample molecule SAMPLE_MOLECULE MIC_SAMPLE SMP_MOLECULE
36   A260/280   MIC_SAMPLE SMP_A260_280
37   Bioanalyzer RIN   MIC_SAMPLE SMP_BIOANALYZER_RIN
38   Platform Technology PLATFORM_TECHNOLOGY MIC_PLATFORM PLT_TECHNOLOGY
39   Platform Distribution PLATFORM_DISTRIBUTION MIC_PLATFORM PLT_DISTRIBUTION
40   Array Manufacturer PLATFORM_MANUFACTURER MIC_PLATFORM PLT_MANUFACTURER
41   Array Manufacturer protocol PLATFORM_MANUFACTURE_PROTOCOL MIC_PLATFORM PLT_MANUFACTURER_PROTOCOL
42   Array Name PLATFORM_TITLE MIC_PLATFORM PLT_NAME
43   RNA extraction protocol SAMPLE_EXTRACT_PROTOCOL_CH MIC_SAMPLE SMP_RNA_EXTRACT_PROTOCOL
44   Target Amplification manufacturer/kit SAMPLE_DESCRIPTION MIC_SAMPLE SMP_TGT_AMP_PROTOCOL
45   Target Amplification protocol SAMPLE_DESCRIPTION MIC_SAMPLE SMP_TGT_AMP_MANUFACT
46   Rounds of amplifcation SAMPLE_DESCRIPTION MIC_SAMPLE SMP_ROUND_OF_AMP
47   Amount labeled target hybridized to array SAMPLE_HYB_PROTOCOL MIC_SAMPLE SMP_AMT_LAB_TGT_HYB_TO_ARY
48   Sample Label SAMPLE_LABEL_CH MIC_SAMPLE SMP_LABEL
49   Array Hyb/Wash/Scan protocol SAMPLE_HYB_PROTOCOL MIC_SAMPLE SMP_ARY_HYB_PROTOCOL
50   GCOS Tgt Value SAMPLE_DATA_PROCESSING MIC_SAMPLE SMP_GCOS_TGT_VAL
51   Data analysis method SAMPLE_DATA_PROCESSING MIC_SAMPLE SMP_DATA_ANA_METHOD
52   Reference used   MIC_SAMPLE SMP_REFERENCE_USED
53   Experimental goals   MIC_EXPERIMENT XMT_GOAL
54   Experimental Design   MIC_EXPERIMENT XMT_DESIGN

 

SERIES INFO SHEET

55   Title (Standard Fields table) SERIES_TITLE MIC_SERIES SER_TITLE
56   Summary (Standard Fields table) SERIES_SUMMARY MIC_SERIES SER_SUMMARY
57   Type (Standard Fields table) SERIES_TYPE (deprecated) MIC_SERIES SER_TYPE
58   Overall design (Standard Fields table) SERIES_OVERALL_DESIGN MIC_SERIES SER_OVERALL_DESIGN
           
59   Sample ID (Sample ID table)   MIC_SERIES_SAMPLE SRM_SAMPLE_ID
60   Description (Sample ID table)   MIC_SERIES_SAMPLE SRM_SAMPLE_DESCRIPTION
           
61   Variable (Variable table)   MIC_SERIES_DETAIL SDL_ITEM
62   Description (Variable table)   MIC_SERIES_DETAIL SDL_VALUE
63   Samples (Variable table)   MIC_SER_DTL_SAMPLE SDS_SAMPLE_FK
           
64   Replicate type (Replicates table)   MIC_SERIES_DETAIL SDL_ITEM
65   Samples (Replicates table)   MIC_SERIES_DETAIL SDL_VALUE