Strain Descriptor

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Contents

Purpose

The dictyBase curatorial staff proposes the following new field for use in the annotation of strains. Standard Strain Descriptors will be used for display in strain records and on the corresponding Gene Pages. A secondary goal is to eliminate a requirement for formatting. Formats such as superscript, subscript, and bold face require html tags for proper display in an internet browser.

Furthermore, we will encourage researchers to provide all relevant information to create these standard strain descriptors. The relevant information includes:

  • official gene name
  • promoter used to drive expression
  • alterations to the gene sequence expressed
  • molecular markers and location of the fusion (N or C terminus)

Standard format for Strain Descriptors

gene-/[promoter]:gene(substitution or truncation):marker

Explanation

- strain bearing a mutant allele, typically a null or a functional null mutant (e.g. REMI mutants)

/ compound mutant

[ ] promoter gene

( ) substitution and/or truncation

: fusion

Strains with unknown mutation(s)

The Systematic Name is used as the Strain Descriptor.


Additions

[unk]

The letters "unk" designate fusion to an unknown promoter.


[OE]

The letters "OE" are used when a strain is described as an overexpressor but the promoter
used is not specified. 


[KD]

The letters "KD" precede a knockdown strain when the method is unknown.


[AS]

The letters "AS" precede an antisense strain.


[RNAi]

The letters "RNAi" precede an interference RNA strain.


[unsuccessful]

This precedes strains when attempts to delete or mutate the gene failed, but specific tests have not been done.


[inviable]

This precedes strains described and shown as inviable, e.g. by trying creating haploid null strain from heteromorph diploid.



Examples

1) Strain Descriptor for the lvsA null mutant:

lvsA-


2) A rescue experiment would be represented this way; expression of aprA from the actin 15 promoter in an aprA null background:

aprA-/[act15]:aprA


3) A double null mutant of hbxA and warA:

hbxA-/warA-


4) This strain expresses mybE with a C-terminal fusion to GFP; promoter unknown:

[unk]:mybE:GFP


5) This strain expresses a truncated myoE (residues 1-698 only) with a point mutation at residue 336, under control of the actin 15 promoter:

[act15]:myoE(1-698(S336A))


6) This strain expresses an N-terminal YFP fusion to the wipA gene containing two point mutations at residues 93 and 95:

[act15]:YFP:wipA(K93A/S95A)


6) This strain expresses an N-terminal RFP fusion to the gskA gene containing several two groups of identical point mutations; summarize and separate by comma:

[act15]:RFP:gskA(K423,455,484,486A/R711,531A)


8) This strain expresses an C-terminal GFP fusion to the abpC gene containing a deletion from residue 557 to 643, expressed in an abpC null strain:

abpC-/[act15]:abpC(1-556:644-857):GFP


9) This strain expresses an N-terminal GFP fusion to a chimera of racH (residues 1 to 163) and racG (residues 164 to 201):

[act15]:GFP:racH(1-163):racG(167-201)


10) Knockdown of the gsr gene (glutathione reductase) using RNAi:

[RNAi]gsr


11) expressing HA-tagged rab14 from discoidin promoter:

[disc]:HA:rab14

Promotors

1) Genes which contain multiple, naturally-occuring promotors, eg. genes with developmental-stage, or cell-type specific promotors, use the gene name as normal, then add an abbreviated term for the stage or cell type:

[pdsA-agg] (aggregation stage)
[pdsA-ldev] (late development stage)
[acaA-psp] (prespore stage)
[acaA-pst] (prestalk stage)

2) If authors create a man-made fragment of the promotor for experimental purposes, use the gene name as normal followed by -frag:

[ecmB-frag]


Exceptions

1) It is permissible to add the parental strain to the strain descriptor if the curator thinks this is helpful. For example when null strains of the same gene, but from different parental strains, have different phenotypes. Use the following format:

rasG-/AX2
p2xA-/AX4
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