Arabidopsis Microarray Experiments
From AFGC (David Finkelstein). http://afgc.stanford.edu/afgc-array-info-forms.html
MIAME concept: MAML element or attribute = AFGC value
Issues:
Treatment/Protocol
sufficient to describe Growth?
Genotype
sufficient to describe Mutant?
Genetic
variation/Treatment/Protocol sufficient to describe Transgenic?
Organism: organism_ncbi = “Arabidopsis thaliana”
Cell source: cell_source = “ABRC” [should be contact info]
Cell type: not applicable
Sex:
sex = “male”
Age: age = “1 day post-imbition” [should make an element with measurement and start point]
Developmental stage: developmental_stage = “embryo, AFGC”
Organism part: tissue = “leaf, AFGC”
Strain or line: strain = “Columbia-0”
Individual:
individual = “plant #9“
Individual genetic characteristics: genotype = “wild type, AFGC”
Disease state: disease = “normal, MGED”
Target cell type: not applicable
Cell line: not applicable
Sample: qualifier, value, source
“genetic variation”, “stable transgenic”, “AFGC”
“vivo_vitro”, “in vivo”, “MGED”
“physiologic
age”, “number of true leaves and macroscopic primordia =1”,
“AFGC”
Treatment: treatment
measurement
action = “seed dormancy”
order = “1”
object
protocol_id = 1
Treatment: treatment
measurement
action = “growth”
order = “2”
object
protocol_id = 2
Treatment: treatment
measurement
action = “environmental treatment”
order = “3”
object = “light stress”
protocol_id = 3
Sample treatment protocol: protocol
Protocol_id = 1
type = “other”,
other_type = “sample_treatment”
name = “seed dormancy”
standard_protocol
Days at 4C: 1
protocol_deviations
protocol_abstract
Sample treatment protocol: protocol
Protocol_id = 2
type = “other”,
other_type = “sample_treatment”
name = “growth”
standard_protocol
Day
Average temperature (C) 1
Average relative humidity (%) 11
Light regime: “short day”
Night
Temperature (C) 1
Relative humidity (%) 1
Duration (hours) 1
Light Conditions
Light intensity at soil level (ueinsteins) 1
Light sources: “natural”
Growth media: one_of list. “soil”
“Mix commercial”
Fertilization type: “complete”
Application rate (units) 2
Plants vernalized? “no”
protocol_deviations
protocol_abstract
hardware
Growth room: “greenhouse”
Sample treatment protocol: protocol
Protocol_id = 3
type = “other”,
other_type = “sample_treatment”
name = “light stress”
standard_protocol
change in duration
UV-A
Increase or decrease relative to control: increase
protocol_deviations
protocol_abstract
Hybridization extract preparation: extract
type = “mrna”
protocol
type = “sample_preparation”
name = “TRIzol”
standard_protocol
protocol_deviations
“Hours after daybreak”
protocol_abstract
Labeling: labeled_extract
type = “cy5”
protocol
type = “extract_labeling”
name = “my favorite kit”
standard_protocol
protocol_deviations
protocol_abstract
Required fields and those related to MIAME concepts are shown using structure from RNA Classification example page. MIAME concepts are given in brackets.
Growth might be considered as a MIAME concept.
Parameter elements (qualifier, value, source tuples) are not sufficient to fully describe genotype and genetic variation.
Taxonomy
Genotype
Genus and Species [organism] Arabidopsis thaliana
Genotype: one_of wild type, mutant, transgenic, other [genetic variation] wild type
Common accession and alias: one_of list [strain] Columbia-0 (Col-0)
Source
[contact]
[cell source]
Growth Conditions: [treatment <growth> with subcategories specified as a protocol].
Growth room
Growth room: one_of list “greenhouse”
Day
Average temperature (C) 1
Average relative humidity (%) 11
Light regime: one_of list “short day”
Night
Temperature (C) 1
Relative humidity (%) 1
Duration (hours) 1
Light Conditions
Light intensity at soil level (ueinsteins) 1
Light sources: one or more of list “natural”
Comments
Growth Media
Media [protocol for <growth> treatment]
Growth media: one_of list. Determines use of soil or agar “soil”
Soil [protocol for <growth> treatment]
If growth media = soil, then one or more of list “Mix commercial”
Agar [protocol for <growth> treatment]
If growth media = agar, then one or more of list
Plus agar concentration, description
Fertilizer [protocol for <growth> treatment]
Fertilization type: one_of list “complete”
Application rate (units) 2
Vernalization treatments [treatment]
Plants vernalized? Yes/no “no”
If yes, describe.
Seed dormancy treatments [treatment]
Days at 4C: 1
Harvest Conditions
Time
Hours after daybreak [extraction protocol] 1
Circadian
experiment [experimental
type] [serial] [serial type] no
Time
course experiment [experimental factors] [ordered] no
Chronological age
Days after imbition [age] 1
Physiologic age
Number of true leaves and macroscopic primordia [sample qualifier] 1
Developmental stage: one_of list [ developmental stage] “embryo”
Anatomy of plant sample
Organ [organism part] “leaf”
RNA sample [extraction protocol]
Sample type: one_of list “polyA RNA”
RNA extraction method “TRIzol”
Treatment of plants
Control of treatment sample
Treatment or reference [sample and arrays list] [primary or derived sample] “treated”
Mutant
[genotype]
Mutant
line
Mutant
type: one_of list
Mutagen:
one_of list
Dominance
of mutant: one_of list
Screening
criteria and phenotype
Chromosome:
one_of list
Genetic
map position or genomic clone ID
Transient
or stable transgenic plant [genetic variation] “stable”
Stable
or transient
Gene
introduction method: one_of list
DNA
type: one_of list
Orientation
of inserted gene: one_of list
Environmental treatment categories
Environmental treatment: each are [treatment]
Light stress type: one_of list
Light stress: choice of wavelengths, direction of change
Temperature stress
Mechanical stress
Atmospheric stress
Osmotic or salt stress
Nutrient treatments: each nutrient is a [treatment]
Choice of nutrient, surplus or deficiency
Environmental subcategories: each is a [treatment]
Choice of pathogen or microbe, microbe class
Choice of toxic metal, concentration
Choice of hormone treatment, concentration
Chemical treatment: one_of list, concentration
Other treatments [treatment] “10”