SMD Annotating Batch Files

Experiment Description Column in the Batch File

Overview

This column must contain a brief, readable description of the experiment followed by annotation of the samples and conditions, which are entered using the following syntax: <c-anno><c-1></c-1><c-2></c-2><c-3></c-3><c-4></c-4></c-anno>

• The individual annotation fields contain different classes of information, as shown below. Be sure to include the tags for all four annotation fields, even if some of them are empty.
  • <c-1> Strain
  • <c-2> Mutations (may include plasmids)
  • <c-3>Description of Growth Conditions
  • <c-4>Condition -- need to explain
• An example:

E. coli K-12 MG1655 rpoS(del)::FRT-kan-FRT, rep. 1<c-anno><c-1>E.coli K-12 MG1655</c-1><c-2>rpoS(del)::FRT-kan-FRT</c-2><c-3>LB, 37C, Exponential Phase</c-3><c-4>Mutant vs Wild-type</c-4></c-anno>

Experiment Description

• A brief, readable description of the experiment that must be unique (no other column can have the exact same name). You can add rep. 1, rep. 2, etc. if the same experiment was repeated..
• These description will be copied and pasted in to column L (SINGLE CHANNEL DESCRIPTION) and column M (Experiment Name) ??
• Here are some examples of experiment descriptions
  • E. coli K-12 MG1655, LB + glucose, rep. 1
  • 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

Individual Annotation Fields

Conventions for the <c-1>field

• Put the name of the organism and strain background between the <c-1> and </c-1> tags.
• Do not include mutant alleles or plasmids, because they will be added to the <c-2> field.
• Here are some examples:
  • <c-1>E. coli K-12 MG155</c-1>
  • <c-1>E. coli K-12 BW25113</c-1>
  • <c-1>E. coli K-12 W3110</c-1>
  • <c-1>E. coli O157-H7 EDL933</c-1>
• If the experiment uses another E. coli strain, check whether it has a page in EcoliWiki. If it doesn't, make one or ask someone else to make one.

Conventions for the <c-2>field

• Put the name of relevant mutant alleles or plasmids between the <c-2> and </c-2> tags.

rpoS(del)::FRT-Kan-FRT Link for more information about how flipases work

Conventions for the <c-3> field

• Put information about the experimental conditions between the <c-3> and </c-3> tags. This includes information about the growth medium, growth temperature, growth phase, chemicals added, time points, etc. Here are some examples:
  • biofilm
  • planktonic
  • glass wool biofilm
  • time course
• Don't use special characters. Use the following substitutions, instead.
  • 37C
  • uM for micromolar
  • ug for microgram
• Growth medium information
  • LB
  • MOPS minimal medium + carbon source (xx)

biofilm

planktonic

glass wool biofilm

uM for micromolar

ug for microgram

MOPS minimal medium + carbon source

time course

SMD field <c-4> terms

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.

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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