Strain Curation

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Purpose: The Stock Center curation pages allow you to add and modify information in strain records.


Contents

Strain Descriptor

  • See Strain Descriptor documentation.
  • Note: wild type strains have Strain Descriptors like "Dictyostelium bifurcatum UK5," "AX2," or "NC4."
  • Note: DO NOT put parent strains or drug resistance in Strain Descriptors. Avoid descriptors such as "yakA- in AX3" and "CAP-bsr".
  • Note: avoid parentheses like GEG04K11 (tmcB- in KAX3)
  • Note: it is not mandatory to convert all old strain names to a strain descriptor with current gene name. In general, keep 'good' older strain names even if the gene name has changed, but change bad/nonsense strain names. All new strains should be named with as described in Strain Descriptor.

Inviable and Unsuccessful Strains

  • Strain Descriptor : [inviable]GeneName; example [inviable]phlp2-
    • This is when a strain has been shown to be inviable, using diploids, other methods, or seeing cells die after a few days.
    • Add parent
    • Add mutagenesis method
    • Add genotype and genetic modification; genotype is needed for strains with phenotypes.
    • Do NOT add strain characteristic; only stable cell lines should have characteristics.
    • Add DDPHENO:0000302 abolished growth
  • Unsuccessful: [unsuccessful]GeneName; example [unsuccessful]pikD-
    • Make a single unsuccessful strain per gene even if several methods were used (HR, knock down); enter multiple references if necessary
    • Strain summary: attempts to produce a geneA null mutant failed; add specific information as necessary.
    • Add parent (if available)
    • Add mutagenesis method (if available)
    • Do NOT add genotype, genetic modification strain characteristics or any phenotype.

Systematic Name

  • Consists of 2 or 3 capital letters plus a unique serial number (e.g. HM1 or HTY217); see Nomenclature Guidelines for the list of known strain prefixes by laboratory.
  • Note: If the depositor does not provide a systematic name, or a paper does not contain a systematic name, leave the field blank, and the dictyBase Strain ID (DBS + 7 digits) will be automatically assigned as the Systematic Name. This can be modified at a later time if required.
  • Exception: For Laboratory Strains, use the same name as the strain descriptor. For example AX3, JH10.

Synonyms

Add relevant synonyms:

  • Strain name used by authors (if it does not correspond to the Systematic Name or the Name Descriptor). Use super/sub-script and greek letters if the original name contains such. However, also add the name spelled out and/or without html tags, as rp14OE or Δ cannot be searched in the database (add 'rps4OE' and 'delta', respectively).
  • Other names that users are likely to search for, when a synonym is widely used (e.g., car1- for carA-)
  • Do not overuse Gene Name Synonyms as Strain Synonyms (see for example mdrA1-/mdrA2 synonyms: mdrA-/B-, Ax A7-1, mdrA-/mdrB-, mdrA1-/A2-, mdra-b-).

Genetic Modification

  • Genetic Modification is a hierarchical controlled vocabulary used for defining the genetic change in the strain.
  • Choose the LAST modification that the strain was subjected to; for example, a REMI mutant usually has an insertion; a knock out by replacement has a deletion (unless the vector has been integrated in a single site, which then would be an insertion); in all cases, the genetic modification is relative to the parent only. Chimeras between two proteins are insertion or deletion with insertion. The simplest modifications are endogeous mutation and exogenous mutation.
  • The Genetic Modification Ontology is a hierarchical, controlled vocabulary:
    • endogenous mutation
    • endogenous deletion
    • endogenous insertion
    • endogenous deletion with insertion
    • endogenous substitution
    • exogenous mutation
    • exogenous deletion
    • exogenous insertion
    • exogenous deletion with insertion
    • exogenous substitution

Summary

  • Free text field meant to give the user an overview of the important characteristics of the strain.
  • This is a short statement, not a sentence; do not use sentence case: no caps at the beginning and no period at the end.
  • Strain summary should use primary dictyBase Gene Names, e.g., act15, carA, dimA.
  • Strain summary should not contain gene product names or gene name synonyms (like adenosine deaminase REMI mutant for amdA REMI mutant or atg7 (apg7) null)
  • For example, for null strains, the Strain Descriptor is abcD-. The summary can be "acbD null mutant". It may also be helpful to add the strain background, the drug resistance, and/or any other specific characteristics of the strain, especially if more than one strain with the same strain descriptor exists.
  • More Strain Summary Examples

Genotype

  • See Nomenclature Guidelines.
  • Important for proper display of the genotype on the Strains and Phenotype Details Page: Do not add SPACES after comma, as the display issue will be gone after overhaul!
  • Axenic strains:
    AX2 has "axeA2,axeB2,axeC2"
    AX3 and AX4 have "axeA1,axeB1,axeC1"
  • Drug resistance: bleR, bsR, foaR, hygR, neoR
  • Auxotrophic mutants: thy-, ura-
  • Complemented strains: thy+, ura+ (the thy- and ura- are omitted)
  • Endogenous gene mutations:
    (i) abcD- if allele is unknown or not named;
    (ii) alleles can also be given a serial number as recommended by the nomenclature guidelines, and which corresponds to the systematic name (for example, abcD(HM101)) [1];
    (iii) genetic manipulation can be represented by the inserted construct [2]; in that case the construct appears in brackets immediately following the gene in which it is integrated (for example: mhcA-[pTZD1THY])
  • All elements in the genotype should be separated by commas.
  • The formal genotype should be in italics, followed by relevant drug resistance and auxotrophic markers not in italics. (automatically realizable after overhaul, do not add HTML tags)
  • Vectors/constructs should be contained within brackets, following the gene which they modify.
  • Note that it is important to only include the portion of the vector/construct that is actually incorporated into the genome into the genotype, eg:
    • Linear plasmids containing a bsR cassette are often used to create null mutants by homologous recombination. In such cases, only the bsR is actually added to the genome, and this should be displayed in the genotype as [bsRcas].
    • When the mutagenesis method Homologous Recombination has been used to create a null strain, we do not typically add the whole plasmid they used to clone the construct into the genotype (e.g pLPBLP). Instead, if this is a cre-lox plasmid, we add the construct as [bsR-loxP], standing for the floxed bsR cassette, as this is the DNA that gets inserted with help of the homologous flanking sequences.
    • Circular plasmids such as pDNeoII are often used for overexpression of a protein. These are incorporated whole into the genome by random insertion and should be displayed in the genotype as [pDNeoII]. Extrachromosomal plasmids, such as pDM304 should also be displayed in the genotype as [pDM304].
  • When a plasmid is not in the database (or DSC), add to genotype but DO NOT add to the plasmid field.
  • All fusions should be separated by a colon-same as in the strain descriptor, eg. "GFP:wshA". Do not use hypens or double colons


  • Examples of some genotypes:
    • Generic bsR cassette, classic null mutant: axeA1,axeB1,axeC1,dimB-,[bsRcas],bsR
    • Floxed bsR cassette, null mutant: axeA1,axeB1,axeC1,dimB-,[bsR-loxP],bsR
    • Removed floxed bsR cassette, null mutant: axeA1,axeB1,axeC1,dimB-,[loxP]
    • Cre-lox plasmid:, double null mutant: axeA2,axeB2,axeC2,adcC-,[loxP],adcB-,[bsR-loxP],bsR
    • Marker overexpressing null strain: axeA1,axeB1,axeC1,wasB-,[bsRcas],YFP:wasB,[pEXP4(+)],bsR,neoR
    • Laz overexpressed from ecmA promoter, in null strain: axeA1,axeB1,axeC1,mef2A-,[bsR-loxP],lacZ,[pEcmA-Gal],bsR,neoR
    • Auxotroph parents null (here: JH10): axeA1,axeB1,axeC1,pyr5-6-[PYR5-6-SalI-linker],thy-[PYR5-6-THY1],ura+,rasG-[thy1cas],thy+
    • Extrachromosomal plasmid in null background, not in DSC: axeA2,axeB2,axeC2,gpr89-,[bsR-loxP],gpr89:GFP,[p1ANeo8],bsR,neoR
    • Genotype for RNAi strains, knockdown mutant: axeA2,axeB2,axeC2,rrpB-,rrpC-,lacZ,[pDneo2a],RNAi-lacZ,neoR,bsR


  • See the plasmids in dictyBase and/or the wiki page on Vectors for information on the available Dictyostelium vectors.

Plasmid

  • Enter the plasmid used for the transformation if given in the publication.
  • Very important: check vector availability in dictyBase, and only enter what is available! Note bsR resistance constructs added solely for curation:
    • Blasticidin S resistance cassette
    • loxP-Blasticidin S resistance cassette
  • Add parent vector, if users report they did a modification of an available vector for the experiment; this modification can then be added in the genotype and strain characteristics.
  • Vector info is not necessarily the same as the corresponding construct info in the genotype field. For example, when the plasmid is integrating or extrachromosomal, usually the full plasmid name, if available in database, is in both fields and identical. In other cases, the vector might be parental or base vector (e.g. pLPBLP used in homologous recombination), but genotype uses just [bsRcas] (see above).
  • Useful resource: Vectors

Associated dictyBase Genes

  • Using the Search tool, select all genes having modifications.
  • Exception: auxotrophic strains: only link parent strains such as JH10 to the knocked-out genes (in this case thyA). abcD knocked-out in JH10 only gets associated to abcD, NOT to thyA.
  • Exception: do not link genes that are used only as tools. For example, strains utilizing the act15 promoter should not be linked to the act15 gene, unless it is a reporter strain like [act15]:GFP.


PubMed ID

Add the PubMed reference(s) describing the strain. Usually the paper where the strain was created should be the only one cited. Enter extra relevant references in the 'Additional references' field.

Parental Strain

Add the Strain Descriptor of the parental strain, plus the DBS ID in parentheses. If the exact strain used is unknown, use the generic parental strains as follows:

  • AX2 (DBS0237699)
  • AX3 (DBS0237700)
  • AX4 (DBS0237701)
  • NC4 (to be added)
  • JH8 (to be added)
  • JH10 (to be added)
  • DH1 (to be added)

Species

  • Select one species name from the list or add it if it's not there.


Strain Characteristics

  • The purpose of Strain Characteristics is to give the user a list of all relevant information about the strain that cannot be captured in the other structured fields, as well as to allow dictyBase to provide lists based upon one or several of those characteristics.
  • Check all that apply.
  • (The terms in this field will change slightly in the upcoming software release.)

Mutagenesis Method

  • Select the most recent modification that was used to construct the strain.


Strain Comments

  • This field is private. Add any relevant comment about the strain that can not be added to any other field or a note that is for internal use only.


Additional References

  • References judged relevant by the curator, in addition to the one(s) entered in the 'Pubmed ID' field.


Stock Center-Specific Fields

  • Availability in Stock Center: checked NO by default; select YES if the strain is available (Stock Center staff only)
  • Obtained as: frozen, spores, etc.
  • Strain verification: which tests were done when the strain was received
  • Phenotype: phenotype relevant to the stock center; for example, agg-, axe, and drug resistance markers
  • Keywords
  • Depositor: the researcher who submitted the strain
  • Date obtained
  • Franke Reference Library reference ID



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