SMD Annotating Batch Files

Using the Batch Creator Script

If you would like to use the Batch Creator Script to create your batch file visit this tutorial.

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
  • UTI89, Aerobic 12h
  • K-12 MG1655, LB + glucose, rep. 1
  • K-12 MG1655 rpoS(del)::FRT, Biofilm rep. 1
  • K-12 BW25113 hha-745(del)::FRT-Kan-FRT, 4 hr Biofilm, LB
  • K-12 ATCC 25404 + R1drd19 Plasimd, 24 h biofilm

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> Siegele 21:44, 12 September 2010 (UTC) recommend leaving out E. coli: <c-1>K-12 MG1655</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 an E. coli strain other than MG1655, BW25113, or W3110, 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.
• Don't use special characters because the database won't accept them. Some of our substitutions are listed below:
  • Instead of ∆ for deletion, put (del) after the gene name and allele number.
• If a mutation from the Keio collection was used, look up the allele number at the Coli Genetics Stock Center. If the kanamycin resistance gene is still present, describe the strain as yfgA000(del)::FRT-kan-FRT. If the kanR gene was "flipped out", describe the strain as yjgA000(del)::FRT.

Paper about how flipase experiments work: (One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products by Kirill A. Datsenko and Barry L. Wanner)

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
• Use commas to separate conditions listed in the <c-3> field.
  • For example, <c-3>LB, 0.3 ug/ml Mecillinam, 60 ug/ml Cefsulodin, 37C, 40 min</c-3>
• Don't use special characters. Use the following substitutions instead.
  • 37C for 37°C
  • uM for micromolar
  • ug for microgram
• Growth medium information
  • LB
  • MOPS minimal medium + carbon source (You don't need to include the concentration of carbon source, unless it is a variable in the experiment.)
  • M9 minimal medium + carbon source (")
  • M63 minimal medium + carbon source (")

Conventions for the <c-4> field

• The most important thing is KEY word! Pick the term that BEST suits the sample.
• 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
• The table below contains a list of potential keywords for the <c-4> field that DAS and BDM chose on 1/22/2010. This table can be updated or modified.

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 main point! ie. Use 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
edit table

Related Tutorials and Resources

• [Step 1] List of microarray papers to be annotated.
• [Step 2] Guide on how to set up a batch file.
• [ Step 3 ] Guide on how to Annotate batch files.
• [Step 4] Tutorial on how to load batch files into SMD.
• [Step 5] Guide on how to make a publication.