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SMD Annotating Batch Files

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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:

K-12 MG1655 rpoS(del)::FRT-kan-FRT, rep. 1<c-anno><c-1>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
  • Here are some examples of what you DO NOT want to put
    • (Don't type WT after the strain name) K-12 BW25113 WT
    • You Don't need to put "bio.rep. 1", just put rep. 1

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 Do include relevant mutant alleles or plasmids; these will also be added to the <c-2> field.Siegele 02:58, 7 June 2011 (UTC)
  • Here are some examples:
    • <c-1>K-12 MG155</c-1>
    • <c-1>K-12 MG155 rpoS::Tn10</c-1>
    • <c-1>K-12 BW25113</c-1>
    • <c-1>K-12 W3110</c-1>
    • <c-1>O157-H7 EDL933</c-1>
    • <c-1>K-12 BW25113 yjgK726(del)::FRT-kan-FRT</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.
  • To find the allele number, go here and type the gene of interest (yjgK for example) in the field labeled "Mutation of gene."

Conventions for the <c-2>field

  • Put the name of relevant mutant alleles or plasmids between the <c-2> and </c-2> tags.
    • <c-2>ygjK726(del)::FRT-kan-FRT</c-2>
  • 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 (0.xx%) (It isn't essential to include the concentration, but DAS usually does because it is information she would want to have.)
    • M9 minimal medium + carbon source (0.xx%) (")
    • M63 minimal medium + carbon source (0.xx%) (")
  • Optical Density
    • OD600=0.3
  • List of things you should NOT PUT:
    • Do not list the number of grams for glass wool
    • Do not list the rpm a solution was shaking at
  • Other Examples
    • LB + glucose (1 g/L), glucose/MgSO4-fed batch culture, OD595=11.5, 50C for 15 min (shifted from 37C)
    • K medium (0.64 osmol/kg H2O) + glucose (20 mM) + met (0.5 mM), 0.3 M NaCl, 1 mM glycine betaine, 43C, OD600=04.-0.5

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

  1. replace carbon source with the actual one (ie. glucose, glycerol, acetate, etc.)
  2. 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

pH

"Acidified medium" or "Alkaline medium"

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.

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