SMD Annotating Batch Files

As of Jan 22, 2010, Debby & I (BM) have decided on the following list of potential terms for the key word in the c-4 annotation column for SMD.

• The most important thing is KEY word! Pick the term that BEST suits the sample.
• Annotations are for each sample in an experiment set. The term chosen may vary accordingly in the set, but each sample will be given a term.
• Limit the <c-4> field to a small number of terms, preferably 1 or 2. Examples where you might want to use 2 terms: Parental strain + Autoinducer-2 (AI-2), Parental strain + Aerobic growth, Mutant + Aerobic growth, etc.

Structure

• The field must contain the following syntax:

 <c-anno><c-1></c-1><c-2></c-2><c-3></c-3><c-4></c-4></c-anno>
Experiment Description<c-anno><c-1>Strain</c-1><c-2>Mutations</c-2><c-3>Description of Growth Conditions</c-3><c-4>Condition</c-4></c-anno>

Experiment Description

• A readable brief description of the experiment goes before the <c-anno> tag.
• These names must be unique (meaning no other column can have the exact same name). You can change this by adding rep. 1 which means repitition #1 and go upward if the experiment was the same by repeated.
• These description will be copied and pasted in to column L (SINGLE CHANNEL DESCRIPTION) and column M (Experiment Name)
• Here are some examples

E. coli K-12 MG1655, LB + glucose, rep. 1<c-anno><c-1></c-1><c-2></c-2><c-3></c-3><c-4></c-4></c-anno>
E. coli UTI89, Aerobic 12h
E. coli K-12 MG1655 rpoS(del)::FRT, Biofilm rep. 1
E. coli K-12 MG1655 appY(del) Anaerobic growth, rep. 5 

<c-1> field: Name of the strain

• The name of the organism will be put inbetween the <c-1> tag and the </c-1> tag.
• Do not include if there are any genes deleted or plasmids
• Here are some examples

E. coli O157-H7 str. xxx rpoS(del)::FRT-Kan-FRT   Link for more information about how flipases work

E. coli K-12 xxx

Conventions for the <c-3> field: Describe medium, growth temperature, chemicals added, etc.

37C

biofilm

planktonic

glass wool biofilm

uM for micromolar

ug for microgram

MOPS minimal medium + carbon source

time course

SMD field <c-4> terms

Potential c-4 terms	Example or brief explanation
Biofilm vs planktonic
Biofilm + chemical	Put the actual chemical name in.
Chemical	Again, put the chemical name here.
Control	ie. if sample is replicate 1 vs replicate 2 of same strain and same growth conditions
Ultraviolet (UV) light
Wild type vs mutant
Wild type vs complemented null mutant
Wild type vs overexpression
Null mutant vs complemented null mutant
Strain comparison	ie. E. coli K-12 MG1655 compared to E. coli B REL606
Stationary phase	This includes starvation.
Heat shock
Cold shock
Minimal medium + carbon source	replace carbon source with the actual one (ie. glucose, glycerol, acetate, etc.) use this term ONLY if this is the point!! ie. mutant vs wild type if it fits better than this.
Mutant
Growth curve	Following expression changes as a function of cell density.
Parental strain
Aerobic growth
Anaerobic growth
No treatment
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