Sample Information Sheet

The Researcher uploading data completes a Sample Information Sheet to identify the samples to be included in TraceBase. Definitions for each term in this worksheet are described below.

See also Labeling and Organizing Data

If you are unsure of how to label something, write whatever you think fits and submit anyway. Indicate what you are unsure about in the submission form or on the information sheet. The developer team will check the data and help you label it properly before adding to the live data on TraceBase.

The key steps to remember for this sheet are to match sample names and animal IDs: Diagram showing how the identifiers between the AccuCor files, Samples Table, and Animals Table must match

Animals Tab

Animal ID

A unique identifier for the animal.

Age

Age in weeks when the infusion started

Sex

"male" or "female"

Animal Genotype

Most specific genotype possible.

Check existing data on TraceBase for common genotypes. If necessary, indicate genotype as "unknown" (e.g. if the animal is a mixed background wildtype).

Animal Body Weight

Weight in grams at time of infusion

Infusate

A description of the infusion solution (aka cocktail) given to this animal.

Individual tracers are formatted: compound_name-[weight element count,weight element count]

  • Examples:
  • valine-[13C5,15N1]
  • leucine-[13C6,15N1]

  • isoleucine-[13C6,15N1]

  • If a tracer is not fully labeled for a given element, the positions of the that element must be included: compound_name-[position,position-weight element count]

  • Example: L-Leucine-[1,2-13C2]

Mixtures of compounds are formatted: tracer_mix_name {tracer; tracer}

  • tracer_mix_name is optional
  • Example: BCAAs {isoleucine-[13C6,15N1];leucine-[13C6,15N1];valine-[13C5,15N1]}

Tracer Concentrations

Concentration(s) of infusate in this infusion solution (in mM)

For multiple tracer compounds, list concentrations in the same order as in "infusate" separated by semicolons

  • Example: 5; 6; 9 to indicate 5 mM, 6 mM, 9 mM

Infusion Rate

Volume of infusate solution infused (microliters (ul) per minute per gram of mouse body weight)

Diet

Description of animal diet used. Include the manufacturer identification and short description where possible. Check data on TraceBase for commonly used diets.

Feeding Status

fasted, fed, or refed

Indicate the length of fasting/feeding in Study Description

Animal Treatment

Short, unique identifier for animal treatment protocol. Details are provided in the Treatment Description field on the Treatments sheet

  • Example: "T3 in drinking water"

Default animal treatment is no treatment.

Note that diets and feeding status are indicated elsewhere, and are not indicated here.

These protocol are designed to be uniquely named so that lab members can share between their studies.

Study Name

An identifier for the "experiment" or collection of animals that this animal belongs to.

Study Description

A long form description of the study.

Describe here experimental design, citations if the data is published, or any other relevant information that a researcher might need to consider when looking at the data from this study.

Samples Tab

Sample Name

Unique identifier for the biological sample. Generally, the sample names should match the sample headers in the AccuCor/IsoCorr files, but if a sample tube was injected multiple times, they can differ. In that case, an LCMS-metadata file should be included in your submission to match the sample names in the database with the headers in the AccuCor/IsoCorr files.

Date collected

Date sample was collected (YYYY-MM-DD).

Researcher Name

Researcher primarily responsible for collection of this sample (FIRST LAST). Secondary people (PI, collaborator, etc) can be mentioned in the study description.

Tissue

Type of tissue, matching the reference list of tissues.

  • See Tissues tab for reference list of tissues, or view a list of Tissues on TraceBase.

  • If you have a tissue that is not listed in Tissues tab, add your new tissue to the Tissues tab.

Collection Time

Minutes after the start of the infusion that the tissue was collected.

Collection Time for samples collected before the infusion should be <= 0.

Animal ID

Matches to the Animal ID that this sample was collected from.

Treatments Tab

Animal Treatment

  • Short, unique identifier for animal treatment protocol.
  • Matches to the same value in "Samples" sheet.

Treatment Description

  • A thorough description of an animal treatment protocol. This will be useful for searching and filtering, so use standard terms and be as complete as possible.

  • Any difference in Treatment should be indicated by a new Animal Treatment

  • Example: different doses of drug

Tissues Tab

TraceBase Tissue Name

  • Short identifier used by TraceBase
  • Use the most specific identifier applicable to your samples
  • If your data contains a tissue not already listed here, create a new TraceBase Tissue Name and Description here.

Description

  • Long form description of TraceBase tissue