Sample description

This is an example of the information requested for a sample (biomaterial) description for a microarray experiment (kindly provided by M. Hofmann and S. Schmidtke, LION bioscience AG) with notes added by C. Stoeckert, U. Penn.

 

 

Organism: mus musculus [ NCBI taxonomy browser ]

Note that the source of the term "NCBI taxonomy browser" is provided. We will need to come up with a controlled vocabulary of sources and/or IDs.

 

Cell source: in-house bred mice (contact: norma.howells@itg.fzk.de)

 

Cell type: thymocytes (complex mixture of cells isolated from thymus. mostly T-lymphocytes and epithelial cells of different differentiation stage) [no matching for this cell type found in GXD "Mouse Anatomical Dictionary"]

Note: what we are going for here is not really the type of cell but rather the type of cell source as in paraffin sample, biopsy, etc. This will be clarified in the concepts.

 

Sex: female [ MGED ]

 

Age: 3 - 4 weeks after birth [ MGED ]

 

Growth conditions: normal

Note the need for further structuring of this type of information.

 

controlled environment

20 - 22 oC average temperature

housed in cages according to German and EU legislation

specified pathogen free conditions (SPF)

14 hours light cycle

10 hours dark cycle

 

 

Developmental stage: stage 28  (juvenile (young) mice) [ GXD "Mouse Anatomical Dictionary" ]

 

Organism part: thymus [ GXD "Mouse Anatomical Dictionary" ]

 

Strain or line: C57BL/6 [International Committee on Standardized Genetic Nomenclature for Mice]

 

Genetic Variation: Inbr (J) 150. Origin: substrains 6 and 10 were separated prior to 1937. This substrain is now probably the most widely used of all inbred strains. Substrain 6 and 10 differ at the H9, Igh2 and Lv loci. Maint. by J,N, Ola. [International Committee on Standardized Genetic Nomenclature for Mice ]

 

Individual: -

 

Individual genetic characteristics: the same as in "Genetic Variation"

 

Disease state: normal

 

Targeted cell type: primary thymocytes (complex mixture of cells isolated from thymus. mostly T-lymphocytes and epithelial cells of different differentiation stage [ no matching for this cell type found in GXD "Mouse Anatomical Dictionary"]

 

Cell line: no cell line; primary cells

 

Treatment: in vivo [MGED]  intraperitoneal injection of Dexamethasone into mice, 10 microgram per 25 g bodyweight of the mouse

 

Compound: drug [MGED] synthetic glucocorticoid Dexamethasone, dissolved in PBS

 

Clinical Information: -

 

Separation technique:   mice were killed 4 hours post injection and the thymus was taken out. Thymozytes were prepared by meshing the thymus through sterile gauze several times until a suspension of individual cells was obtained.

 

RNA was prepared from thymozytes using a Qiagen RNA preparation kit.