from Dave Matthews, 12/93
revised 4/96
How to Create Probe Records for GrainGenes
Here is a description of the fields available for Probe data in GrainGenes.
TEMPLATE
Probe : ""
Other_name ""
Locus ""
Reference ""
General_remark ""
Type ""
PCR_primers ""
Amplification_conditions ""
Size
Insert_enzyme ""
Source_gene_class ""
Source_species ""
Source_germplasm ""
Source_tissue ""
Vector ""
Vector_enzyme ""
Excision_enzyme ""
Vector_PCR_primers ""
Vector_amplification ""
Bacterial_strain ""
Antibiotic ""
Location ""
Authority ""
Image ""
Data_source ""
Date ""
Note: this template does not include all of the fields available. The
current list is described in EXPLANATION below, and more will probably be
added. Fields that have no data should be deleted.
EXAMPLE SYNTAX NOTES
Probe : "ABC169" First line must include the " : ".
Locus "abc169A" If a field has multiple values, list
Locus "abc169B" them one after the other like this.
Reference "TAG-86-705"
General_remark "Steptoe malt cDNA"
Type "cDNA"
Size 0.3 Do not use quotes for numeric values.
Source_species "Hordeum vulgare"
Source_germplasm "Steptoe"
Source_tissue Malt If the value of a field does not
Vector pBS contain any blank spaces, the quotes
Excision_enzyme "EcoRI" (") are optional.
Location "Kleinhofs, Andris"
Data_source "ATMI"
Date "92.09"
EXPLANATION
Column heading Sample Entry Description or List of Choices
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Probe PSR177 Name of Probe
Other_name pDEM47x.2a Any other name by which this
Probe is known, esp. if published
Locus Xpsr177 Name of Locus. List all loci
mapped with the probe.
External_DB Sequence L43928 Genbank accession number
Reference GNM-34-362 Reference ID for the reference (see
"Constructing reference IDs").
Include entire reference as a
separate record.
General_remark This probe works Any text
only on odd days.
Type cDNA cDNA, genomic, PCR
PCR_primers AATGCCGAAT Sequence of pcr primers (for
the probe, not the vector)
AFLP_primers E37 Sequence or code for AFLP primers
Amplification_conditions Anneal at 50oC,... Description of conditions
Specificity Adh1 or 3, not 2 Which genes are known to be
recognized or not recognized
Sequence X123429 GENBANK accession #, or other name
of a Sequence
Size 1.2 Sequence length, in kilobases
PCR_size 1.4 Length between Vector_PCR_primers
Background 3/5 Background hybridization
level and scale
Cross_hybridizes_to Zea mays Name of a species
Insert_enzyme EcoRI Name of enzyme used to cut the
source DNA for insertion into the
vector
(Should we change the name "Insert_enzyme" to something more descriptive?
Source_excision_enzyme"? "Library_enzyme"? "Cloning_enzyme"?)
DNA_origin HTF-genomic lib. Library preparation method
Source_gene Adh1 Name of Gene from which the probe
was derived, if known
Source_gene_class Adh Name of Gene_Class from which the
probe was derived, if actual gene
is not known
Source_species Triticum aestivum Name of Species source of DNA.
There should ALWAYS be a value for
this field.
Source_germplasm Chinese Spring Name of Germplasm source of DNA
Source_tissue etiolated leaves Tissue source of DNA
Vector pUC18 Vector in which probe is cloned
Vector_enzyme EcoRI Name of enzyme used to open the
vector
Excision_enzyme EcoRI Name of enzyme used to remove the
insert from vector
Vector_PCR_primers M13F Names of Sequences in vector to
M13R amplify the probe from
Vector_amplification 50uM dATP dCTP... Conditions for amplifying from the
vector
Bacterial_strain XL1 Blue Host for the clone
Antibiotic Ampicillin Resistance carried by the vector
Location Gill, Bikram S. Name of Colleague from whom the
probe can be obtained
Authority Gale, Michael D. Name of Colleague who created the
probe
Subclone_of pPSR77 Name of original Probe from which
PSR177 was subcloned
Subcloned_in pPSR177a Name of Probe that a PSR177 piece
has been subcloned as
Image Survey 2 PSR177 Name of image of autoradiogram or
other picture
Data_source Sorrells, Mark E. Who provided this information
Date 93.12.25 When was the information submitted,
in format yy.mm.dd
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There are a few additional fields that are more complicated, such as
Polymorphism and Wheat_polymorphism. The best way to find out about these
is to look at some examples. Try the query "find probe wheat_polymorphism".