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Submitting Data Files

Note: For large data files or multiple data files, please contact us at mgi-submissions@jax.org and we will provide you with a specific ftp address where your data can be deposited.

Images / Figures

Images and figures can include photographs of mutant mice, images of histopathological sections, and micrographs, as well as charts or graphs showing phenotypic characteristics (e.g. growth curves).

Descriptions or legends should accompany the image file. The description file should contain sufficient information to interpret the image, including relevant genotype and strain information.

Images should preferably be provided as high-resolution TIFF files. The description file should be named in parallel with its associated image. For example, Xyz1image.tiff and Xyz1text.doc.

See these image examples in MGI:




Experimental Data

Data tables can be submitted as tab-delimited text or in Excel format. The first row should include column labels. An accompanying file should describe experimental conditions and the animals used, as well as definitions for each data row and column.

Example 1:

Example data file:
Blood ParametersAge (months)   SexAtr1a<+>/ Atr1a<+>  Number of mice  Atr1a<tm1Ecl>/
Number of mice  p-value compared to wild-type
Hematocrit (%)6.5-9.0combined   36.6 +/- 1.41041.1 +/- 1/210<0.05
RBC (10*6/µl)6.5-9.0combined   7.6 +/- 0.2108.9 +/- 0.310<0.01
Hemoglobin (g/dl)6.5-9.0combined   12.5 +/- 0.41014.1 +/- 0.410<0.05
Plasma proteins (g/l)  6.5-9.0combined   37.9 +/- 1.7838.7 +/- 2.47NS

Example accompanying description file:
Title: Blood parameters for Atr1a wild-type vs. homozygous mutant mice.
Publication: PMID: 17607364. Billet S et al., "Gain-of-function mutant of angiotensin II receptor, type 1A, causes hypertension and cardiovascular fibrosis in mice." J Clin Invest 2007 Jul;117(7):1914-25.

Experimental measurements were done on a mixed genetic background of 129S2 and C57BL/6 using age and sex-matched homozygous mutants and homozygous wild-type littermate controls.

Plasma protein was measured using an Olympus multiparametric autoanalyzer. Hemoglobin, red blood cell concentration, and hematocrit were determined using a Beckman Coulter MAXM automatic analyzer. Values are expressed as mean count +/- SEM.

Definitions for table column labels:
Blood Parameters: name of blood parameter with units of measure in parentheses.
Age: age given in months
Sex: combined; values for males and females were not different, thus results were combined
Atr1a<+> / Atr1a<+>: Allele composition for animals that are wild-type for the Atr1a gene.
Number of mice: given for each assay
Atr1a<tm1Ecl> / Atr1a<tm1Ecl>: Allele composition for animals that are homozygous for the described knock-in p-value compared to wild-type: Indication of significance of the finding.

MP terms for the homozygous mutant, Atr1a<tm1Ecl> / Atr1a<tm1Ecl>:
high hematocrit value
high mean erythrocyte cell number
increased hemoglobin content

Example 2: Mutant data relative to control

Example data file:
GenotypeAllelesSexProcedureParameterTerm (MP)Evidence
129P2/OlaHsd-Fbl3<Gt(CB0226)Wtsi>/H Fbl3<Gt(CB0226)Wtsi/
combined Modified SHIRPA Touch Escape Abnormal response to tactile stimulus (MP:0005316) inferred
129P2/OlaHsd-Fbl3<Gt(CB0226)Wtsi>/H Fbl3<Gt(CB0226)Wtsi/
combined DEXA Bone Mineral Density (excluding skull) Decreased bone density (MP:0000063) inferred

Example accompanying description file
Title: Mutant phenotypes seen in 129P2/OlaHsd-Fbl3<Gt(CB0226)Wtsi>/H homozygotes compared to baseline 129P2/OlaHsd strain.
Publication: Unpublished. Data from Harwell Phenotyping Screen deposited with Euophenome.
Standard operating procedures (SOPs) adopted by EUMODIC/EUMORPHIA were used. These experiments examined mice homozygous for a gene trap mutant allele in the Fbl3 gene (Fbl3<Gt(CB0225)Wtsi>).
Phenotypes were compared to littermate controls under conventional mouseroom conditions. Experimental protocols can be found linked from the Europhenome site for this allele, http://www.europhenome.org/databrowser/lineSummary.jsp?l=125. MP terms describing this phenotype were automatically generated (Evidence = inferred) and have not been scientifically reviewed. Automatic annotations are made when experimental parameters are significantly different by programmatic analysis, but have not yet been reviewed by scientific contributors or curation experts.

Definitions for table column labels:
Genotype: full animal strain designation
Alleles: allele composition of mutant animals, in this case homozygous for Fbl3<Gt(CB0226)Wtsi
Sex: combined; values for males and females were not different, thus results were combined
Procedure: named procedures from EUMODIC/EUMORPHIA. SOPs available at http://empress.har.mrc.ac.uk/
Parameter: named parameter that is being measured
Term (MP): phenotype descriptive term from the Mammalian Phentoype Ontology with its ID
Evidence: inferred evidence indicates that the assignment of the MP term was done automatically based on programmatic analysis.

Text Data

Textual data can be included alone or in conjunction with images and data files. If you prefer to submit text, such as an extended abstract or short paper about your phenotype experiments, we will curate data into MGI format. Your submission will be saved as the original reference.

Other Types of Data

Please contact mgi-submissions@jax.org to discuss other types of data you may wish to submit.

Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
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