Difference between revisions of "WormBase Model:Construct"
m (→Variation) |
|||
Line 123: | Line 123: | ||
=Test data= | =Test data= | ||
==Variation== | ==Variation== | ||
+ | |||
+ | Example data | ||
+ | LP132 nmy-2(cp7[nmy-2::gfp + LoxP unc-119(+) LoxP]) I; unc-119(ed3) I | ||
+ | |||
+ | Variation : WBVar020000000 | ||
+ | Public_name "cp7" | ||
+ | Engineered_allele | ||
+ | Variation_summary "[nmy-2::gfp + LoxP unc-119(+) LoxP]" | ||
+ | Derived_from WBConstruct | ||
+ | Identical_transgene "cp7" | ||
+ | CRISPR-Cas9 | ||
+ | |||
+ | Construct : "WBConstruct00000010" | ||
+ | Summary "[nmy-2::gfp + LoxP unc-119(+) LoxP] | ||
+ | Driven_by "WBGene00003777" | ||
+ | Fusion_reporter "GFP" | ||
+ | |||
+ | |||
+ | ------------------------------- | ||
+ | bus-50(e5000[T110E]) = An engineered missense mutation | ||
+ | |||
+ | bus-50(e5001[bus-50::gfp]) aka bus-50::gfp = An engineered fusion of GFP to the C-terminus of BUS-50 bus-50::gfp. | ||
+ | |||
+ | bus-50(e5002[bus-50::gfp + loxP unc-119(+) loxP]) An engineered insertion of GFP plus the unc-119(+) selectable marker, flanked by loxP sites. | ||
+ | |||
+ | bus-50(e5003[bus-50::gfp +loxP]) aka bus-50(e5003) = bus-50(e5002) following Cre-mediated recombinase removal of unc-119(+) leaving a single loxP site | ||
+ | |||
+ | eIs2002 = Engineered insertions in apparent intergenic region with optional descriptors eIs2002[unc-119::gfp] or eIs2002[unc-119::gfp, III:2992500] that include the nature of the insertion or position in the genome | ||
+ | |||
+ | ozIs909, or ozIs909[unc-119::mCherry *eIs2002] = Engineered changes to existing Is (or Si) insertions, which should receive new Is numbers using originating lab’s prefix. The original Is insertion is indicated in brackets with a preceding asterisk (*), in order to allow searches for all derivatives from a given insertion. In this case, an engineered change from GFP to mCherry in eIs2002 | ||
==Construct== | ==Construct== | ||
==Transgene== | ==Transgene== |
Revision as of 21:16, 4 March 2014
back to WormBase_Models
Contents
Proposed model changes
Purpose: the technology of engineering mutations and gene replacement has been developed in C. elegans. With these new research tools, capture and display of the molecular information of these alleles needs to be updated. We propose a new class, Construct, to capture the specifics of the DNA tool used to perform the replacement or engineering, while the Variation model gets updated to record the engineering event itself and its impact on the genome. As a side benefit to the creation of the Construct model, we can use this new class to also capture the genomic arrays used create transgenes.
Variation
Proposed additions
?Variation Variation_type Engineered_allele Variation_summary //to house final engineered construct Derived_from ?Construct XREF Variation Identical_transgene Unique ?Transgene XREF Identical_variation Method Homologous_recombination NHEJ MosSci Cas9 Crispr Expr_pattern ?Expr_pattern XREF Variation #Evidence
notes on variation model changes
see discussion tab
Construct (new)
Class itself is new
?Construct // any single contiguous stretch of engineered DNA sequence Public_name ?Text Other_name ?Text Summary ?Text //genotype like [Pmyo-2::GFP] Sequence feature ?Feature XREF Construct Driven_by ?Gene XREF Drives_transgene Gene ?Gene XREF Transgene_product Fusion_reporter ?Text //fluorescent proteins GFP, RFP, mCherry, etc. Other_reporter ?Text //to add reporters, tags that aren’t included in model Purification_tag ?Text //FLAG, HA, Myc, TAP, etc. Type_of_construct Chimera Domain_swap Engineered mutation Fusion Complex // complex changes (e.g. GFP fusion plus point mutations) Transcriptional_fusion Translational_fusion N-terminal_translational_fusion C-terminal_translational_fusion Internal_coding_fusion Selection_marker ?Text //for elements stitched into contiguous sequence, coinjected elements will get their own construct ID, these will be joined together to create transgene Construction_summary ?Text //Backbone vector, mol bio DNA_text ?text // for mapping to genome, can include entire construct sequence Used_for Transgene_construction ?Transgene XREF Construct Variation ?Variation XREF Engineered_allele Topic_output_indicator ?WBProcess XREF marker_construct Expression_pattern ?Expr_pattern XREF Construct (redundant tag in ?Feature model?) Reference ?Paper XREF Construct Person ?Person XREF Construct Laboratory ?Laboratory #Lab_Location Remark ?Text #Evidence
notes on construct model
see discussion tab
Expression_pattern
proposed addition
Variation ?Variation XREF Expression_pattern ==Gene== proposed change <pre> Drives_Transgene ?Transgene XREF Driven_by_gene
changed to
Drives_construct ?Construct XREF Driven_by_gene ==Clone== proposed addition <pre> Construct ?Construct XREF Clone
Transgene
Proposed changes: Many of the transgene tags have been moved to the proposed ?Construct model, the remaining tags as well as some additions are shown below in the proposed updated ?Transgene model
?Transgene Summary UNIQUE ?Text Synonym ?Text Identical_variation Unique ?Variation XREF Identical_transgene //put in to unambiguously associate the allele/transgene object - see discussion Construction //Strain_construction Construct ?Construct XREF Transgene_construction Coinjection_marker ?Construct XREF Transgene_construction Integration_method UNIQUE ?Text Laboratory ?Laboratory #Lab_Location Author ?Author Genetic_information Extrachromosomal Integrated Map ?Map #Map_position //needed for transgenes with no granular mapping, e.g., just mapped to a LG Phenotype ?Phenotype XREF Transgene #Phenotype_info Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info Used_for Expr_pattern ?Expr_pattern XREF Transgene Marker_for ?Text #Evidence Gene_regulation ?Gene_regulation XREF Transgene Interactor ?Interaction Topic_output_indicator ?WBProcess XREF marker_transgene Associated_with Marked_rearrangement ?Rearrangement XREF By_transgene Strain ?Strain XREF Transgene Reference ?Paper XREF Transgene Species UNIQUE ?Species Remark ?Text #Evidence
Test data
Variation
Example data
LP132 nmy-2(cp7[nmy-2::gfp + LoxP unc-119(+) LoxP]) I; unc-119(ed3) I
Variation : WBVar020000000 Public_name "cp7" Engineered_allele Variation_summary "[nmy-2::gfp + LoxP unc-119(+) LoxP]" Derived_from WBConstruct Identical_transgene "cp7" CRISPR-Cas9
Construct : "WBConstruct00000010" Summary "[nmy-2::gfp + LoxP unc-119(+) LoxP] Driven_by "WBGene00003777" Fusion_reporter "GFP"
bus-50(e5000[T110E]) = An engineered missense mutation
bus-50(e5001[bus-50::gfp]) aka bus-50::gfp = An engineered fusion of GFP to the C-terminus of BUS-50 bus-50::gfp.
bus-50(e5002[bus-50::gfp + loxP unc-119(+) loxP]) An engineered insertion of GFP plus the unc-119(+) selectable marker, flanked by loxP sites.
bus-50(e5003[bus-50::gfp +loxP]) aka bus-50(e5003) = bus-50(e5002) following Cre-mediated recombinase removal of unc-119(+) leaving a single loxP site
eIs2002 = Engineered insertions in apparent intergenic region with optional descriptors eIs2002[unc-119::gfp] or eIs2002[unc-119::gfp, III:2992500] that include the nature of the insertion or position in the genome
ozIs909, or ozIs909[unc-119::mCherry *eIs2002] = Engineered changes to existing Is (or Si) insertions, which should receive new Is numbers using originating lab’s prefix. The original Is insertion is indicated in brackets with a preceding asterisk (*), in order to allow searches for all derivatives from a given insertion. In this case, an engineered change from GFP to mCherry in eIs2002