3. Upload Colony Data

Select and Upload Colony Spreadsheet

Data File Format for Uploading.

Download Excel file template

The list of mice and cages should be in an Excel spreadsheet file (".xlxs") with 3 tabs, titled:

• “Genotypes”
• “Breeding Cages”
• “Holding Cages”

Genotypes Tab

Columns for Genotypes Tab

Genotype ID, JAX ID, Full Name, Gene Symbol, WT Symbol, Color, Note

• Genotype ID
  Each genotype in the colony is given a short abbreviated ID, eg tomato used for display and setting the genotype of mice

• JAX ID
  The six digit JAX ID, eg 007676 is included so that the stain can be linked back to the Jackson Labs catalog.

• Full Name
  The full formal name of the strain, eg B6.129(Cg)-Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J.

• Gene Symbol
  A symbol or character abbreviation to indicate the presence of the transgenic allele eg Tg or mutant allele –. See note below.

• WT Symbol
  A symbol or character abbreviation to indicate the presence of the wildtype allele eg + or absence of the transgene eg 0. See note below.

• Color
  Each gene can be assigned a color for its symbol. The color can either be given in hex format, eg. #ff0000, or by webcolor name eg red.

• Note
  Free text comment for your own reference

Gene and WT Allele Symbols

Different genotypes may use different abbreviated symbols indicating the presence/absence of the specific allele. There is no definitive nomenclature for defining allele abbreviations, but we reccommend following the JAX guidelines:

• for spontaneous or targeted (deletion) mutations, the mutant allele is designated "–" and the wildtype allele with "+".

• An randomly inserted transgene allele is represented by the gene symbol “Tg”, and its absence in the wildtype allele is represented by “0” (zero). So a wildtype mouse would be “0/0”

• A knock-in targeted mutation uses an abbreviation for the knocked-in sequence for the mutant allele (eg "cre"), and "+" for the wildtype allele

References

Designating Genotypes: What Does '+' Really Mean? by Jim Yeadon, Ph.D.

Names and Symbols for Variant and Mutant Alleles

Breeding Cages Tab

one row per litter per cage. The genotype and source of the breeding pair are defined in the list of mice.

Columns for Breeding Cages Tab

Cage ID, Cohab Date, Mom ID, Dad ID, Litter Birth Date, Number of Pups, Male Pups, Female Pups,Date Weaned, Date Genotyped, Date Ended, Outcome, Note

• Cage ID

• Cohab Date

• Mom ID

• Dad ID

• Litter Birth Date

• Number of Pups

• Male Pups

• Female Pups

• Date Weaned

• Date Genotyped

• Date Ended

• Outcome

• Note

Holding Cages Tab

The database assumes that each holding cage has mice of the same sex and of the same genotype (or "?/?" if they haven’t been genotyped yet.) In other words, holding cages never have mixed genotypes or sexes.

The genotype of a mouse is specified with the genotype ID (eg abbreviated name) followed by its allelic composition in parantheses. For example, a mouse hemizygous for the dtTomato transgene would have the genotype ID tomato(Tg/0). Mice can have multiple genotypes, which are entered as a list of genotypes separated by semicolons, e.g. tomato(Tg/0);foscre(Tg/Tg)

Columns for Holding Cages Tab

Cage ID, Date Started, Source, Mom ID, Dad ID, Number of Mice, Mouse IDs, Date of Birth,Sex, Genotype IDs,  Date Ended, Outcome, Note

• Cage ID

• Date Started

• Source

• Mom ID

• Dad ID

• Number of Mice

• Mouse IDs

• Date of Birth

• Sex

• Genotype IDs

• Date Ended

• Outcome

• Note