Difference between revisions of "WormBase Model:Construct"
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Reference "WBPaper00002968" | Reference "WBPaper00002968" | ||
Reference "WBPaper00031023" | Reference "WBPaper00031023" | ||
− | + | Integrated_from "WBTransgene00002030" | |
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− | |||
Construction_summary "Integrated from BC10030 sEx864." | Construction_summary "Integrated from BC10030 sEx864." | ||
(New) Transgene : "WBTransgene00002030" | (New) Transgene : "WBTransgene00002030" | ||
Public_name "sEx864" | Public_name "sEx864" | ||
+ | Synonym "[pgp-5::gfp]" | ||
+ | Synonym "[C05A9.1::gfp]" | ||
Summary "[rCesC05A9.1::GFP + pCeh361]" | Summary "[rCesC05A9.1::GFP + pCeh361]" | ||
Extrachromosomal | Extrachromosomal | ||
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(New) Construct : "WBConstruct00000017" | (New) Construct : "WBConstruct00000017" | ||
− | Public_name | + | Public_name "[pgp-5::gfp]" |
− | + | Summary "[rCesC05A9.1::GFP]" | |
− | |||
− | Summary "[rCesC05A9.1::GFP | ||
− | |||
Reporter_product "GFP" | Reporter_product "GFP" | ||
Transcriptional_fusion | Transcriptional_fusion | ||
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Summary "[DPY-5::GFP + rol-6(su1006) + pBluescript] | Summary "[DPY-5::GFP + rol-6(su1006) + pBluescript] | ||
Construct "WBConstruct00000003"//pCeh358 | Construct "WBConstruct00000003"//pCeh358 | ||
− | + | Coinjection "WBConstruct00000004"//PCes1943 | |
− | + | Coinjection "WBConstruct00000005"//pBluescript KS | |
− | Construction_summary "Transgenic animals were generated by microinjection of pCeh358 (5 ng/ | + | Construction_summary "Transgenic animals were generated by microinjection of pCeh358 (5 ng/ul) and pBluescript KS (100 ng/ul), or in combination with 50 ng/ul pCes1943, which carries a dominant rol-6 mutation [rol-6(su1006)] used as a morphological marker for successful transformation" |
(New) Construct : "WBConstruct00000003" | (New) Construct : "WBConstruct00000003" |
Revision as of 23:52, 4 March 2014
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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 HR //Homologous_recombination NHEJ //Non-homologous DNA end-joining, imprecise DNA repair MosSci TALENs CRISPR/Cas9 ZFN-NHEJ repair //Zinc-finger nuclease ZFN-HR repair 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. Recombination_site ?Text //LoxP, FRT 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 Derived_from Topic_output_indicator ?WBProcess XREF marker_construct Expression_pattern ?Expr_pattern XREF Construct 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 ==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 <pre> ?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 ?Construct XREF Transgene_construction Coinjection_other ?Text Integration_method UNIQUE ?Text Integrated_from ?Transgene XREF Transgene_derivation 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 Transgene_derivation ?Transgene XREF Integrated_from 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
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 "WBConstruct00000010" Derived_from "WBConstruct00000011" HR //homologous recombination Construct : "WBConstruct00000010" Summary "[nmy-2::gfp] Driven_by "WBGene00003777" Fusion_reporter "GFP" N-terminal_translational_fusion Construct : "WBConstruct00000011" Summary "[LoxP unc-119(+) LoxP] Recombination_site "LoxP" Gene "WBGene00003777"
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.
Variation : "WBVar0200000001" Public_name "e5001" Engineered_allele Variation_summary "[bus-50::gfp]" Derived_from "WBConstruct00000012" CRISPR-Cas9 Construct : "WBConstruct00000012" Summary "[bus-50::gfp]" Gene "WBGene0020000001" Fusion_reporter "GFP" C-terminal_translational_fusion
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.
Variation : "WBVar020000003" Public_name "e5002" Engineered_allele Variation_summary "[bus-50::gfp + loxP unc-119(+) loxP]" Derived_from "WBConstruct00000012" Derived_from "WBConstruct00000011" HR Construct : "WBConstruct00000012" Summary "[bus-50::gfp]" Gene "WBGene0020000001" Fusion_reporter "GFP" C-terminal_translational_fusion Construct : "WBConstruct00000011" Summary "[LoxP unc-119(+) LoxP] Recombination_site "LoxP" Gene "WBGene00003777"
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
Variation : "WBVar020000004" Public_name "e5003" Engineered_allele Variation_summary "[bus-50::gfp + loxP]" Derived_from "WBConstruct00000012" Derived_from "WBConstruct00000011" HR Construct : "WBConstruct00000012" Summary "[bus-50::gfp]" Gene "WBGene0020000001" Fusion_reporter "GFP" C-terminal_translational_fusion Construct : "WBConstruct00000011" Summary "[LoxP unc-119(+) LoxP] Recombination_site "LoxP" Gene "WBGene00003777"
eIs2002 = eIs2002[unc-119::gfp] = eIs2002[unc-119::gfp, III:2992500] Engineered insertions in apparent intergenic region with optional descriptors (nature of the insertion or position in the genome)
Variation : "WBVar020000005" Public_name "eIs2002" Engineered_allele Variation_summary "[unc-119::gfp]" Derived_from "WBConstruct00000013" Identical_transgene "WBTransgene00024514" MosSci Construct : "WBConstruct00000013" Summary "[unc-119::gfp]" Gene "WBGene0020000001" Fusion_reporter "GFP" Translational_fusion Transgene : "WBTransgene00024514" Public_name "eIs2002" Summary "[unc-119::GFP]" Construct "WBConstruct00000013"
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
Variation : "WBVar020000006" Public_name "ozIs909" Engineered_allele Variation_summary "[unc-119::mCherry *eIs2002]" Derived_from "WBConstruct00000015" Identical_transgene "WBTransgene00024515" MosSci Construct : "WBConstruct00000015" Summary "[unc-119::mCherry]" Gene "WBGene0020000001" Fusion_reporter "mCherry" Translational_fusion Transgene : "WBTransgene00024515" Public_name "ozIs909" Summary "[unc-119::mCherry] Construct "WBConstruct00000015"
The following depicts how current transgenes would be redistributed into the proposed Construct and Transgene models
(Original)Transgene : "WBTransgene00000001" Public_name "adEx1256" Summary "[egl-19::sGFP-NLS + lin-15(+)]" Reporter_product "GFP" Driven_by_gene "WBGene00001187" Strain "DA1256" Reference "WBPaper00029359" Reporter_type "Transcriptional fusion" Synonym "[C48A7.1::gfp]" (New)Transgene : "WBTransgene00000001" Public_name "adEx1256" Summary "[egl-19::sGFP-NLS + lin-15(+)]" Construct "WBConstruct00000001" Coinjection_other "lin-15(+)" Extrachromosomal Strain "DA1256" Reference "WBPaper00029359" (New)Construct : WBConstruct00000001 Public_name "adEx1256" Other_name "[C48A7.1::gfp]" Summary "[egl-19::sGFP-NLS]" Fusion_reporter "GFP" Driven_by_gene "WBGene00001187" Reference "WBPaper00029359" Transcriptional_fusion
(Original)Transgene : "WBTransgene00000011" Public_name "adIs1240" Summary "[lin-15(+) eat-4::sGFP]" Reporter_product "GFP" Driven_by_gene "WBGene00001135" Strain "DA1240" Strain "DA1243" Map "X" Map_evidence Paper_evidence "WBPaper00038205" Reference "WBPaper00030960" Reference "WBPaper00032252" Reference "WBPaper00035265" Reference "WBPaper00036277" Reference "WBPaper00036704" Reference "WBPaper00037626" Reference "WBPaper00038205" Reference "WBPaper00044482" Synonym "[eat-4::gfp]" (New)Transgene : "WBTransgene00000011" Public_name "adIs1240" Summary "[lin-15(+) eat-4::sGFP]" Strain "DA1240" Strain "DA1243" Map "X" Map_evidence Paper_evidence "WBPaper00038205" Coninjection_other "lin-15(+)" Reference "WBPaper00030960" Reference "WBPaper00032252" Reference "WBPaper00035265" Reference "WBPaper00036277" Reference "WBPaper00036704" Reference "WBPaper00037626" Reference "WBPaper00038205" Reference "WBPaper00044482" (New)Construct : "WBConstruct00000011" Public_name "adIs1240" Other_name "[eat-4::gfp]" Summary "[eat-4::sGFP]" Fusion_reporter "GFP" Driven_by_gene "WBGene00001135" Reference "WBPaper00030960"
(Original) Transgene : "WBTransgene00000017" Public_name "ajIs1" Summary "[pgp-5::gfp]" Coinjection_marker "pRF4[rol-6(su1006)]" Construction_summary "Integrated from BC10030 sEx864." Reporter_product "GFP" Driven_by_gene "WBGene00003999" Driven_by_gene "WBGene00006767" Integration_method "Gamma_ray" Integrated Reference "WBPaper00002968" Reference "WBPaper00031023" (New) Transgene : "WBTransgene00000017" Public_name "ajIs1" Integration_method "Gamma_ray" Integrated Reference "WBPaper00002968" Reference "WBPaper00031023" Integrated_from "WBTransgene00002030" Construction_summary "Integrated from BC10030 sEx864." (New) Transgene : "WBTransgene00002030" Public_name "sEx864" Synonym "[pgp-5::gfp]" Synonym "[C05A9.1::gfp]" Summary "[rCesC05A9.1::GFP + pCeh361]" Extrachromosomal Construct "WBConstruct00000017" Construct "WBConstruct00000018" Construct "WBConstruct00000002" (New) Construct : "WBConstruct00000018" Public_name "pRF4" Summary "[rol-6(su1006)]" Gene "WBGene00004397" (New) Construct : "WBConstruct00000017" Public_name "[pgp-5::gfp]" Summary "[rCesC05A9.1::GFP]" Reporter_product "GFP" Transcriptional_fusion Driven_by_gene "WBGene00003999" (New) Construct : "WBConstruct00000002" Public_name "pCeh361" Summary "[pCeh::DPY-5]" Construction_summary "A 3.3-kb Nco I fragment containing a predicted cuticle collagen gene was isolated from the cosmid F27C1, and cloned into the Nco I site of pGEM-5 to generate the clone pCeh361" Reference "WBPaper00027361"
(New) Transgene : "WBTransgene00000600" Public_name "hIs2" Summary "[DPY-5::GFP + rol-6(su1006) + pBluescript] Construct "WBConstruct00000003"//pCeh358 Coinjection "WBConstruct00000004"//PCes1943 Coinjection "WBConstruct00000005"//pBluescript KS Construction_summary "Transgenic animals were generated by microinjection of pCeh358 (5 ng/ul) and pBluescript KS (100 ng/ul), or in combination with 50 ng/ul pCes1943, which carries a dominant rol-6 mutation [rol-6(su1006)] used as a morphological marker for successful transformation" (New) Construct : "WBConstruct00000003" Public_name "pCeh358" Summary "[dpy-5::gfp]" Driven_by "WBGene00001067" Gene "WBGene00001067" Translational_fusion Construction_summary "The dpy-5::gfp reporter construct pCeh358 was generated by insertion of a 750 bp Sph I fragment from pCeh361 into the Sph I site of the gfp expression vector pPD95.69 (kindly provided by A. Fire). This fragment contains 5' sequences from an Sph I site in the polylinker of pCeh361 to a site 30 bp downstream from the predicted DPY-5 initiator methionine, resulting in an in-frame fusion of the first 12 codons of dpy-5 with gfp." Reference "WBPaper00027361" (New) Construct : "WBConstruct00000004" Public_name "pCes1943" Summary "[rol-6(su1006)] (New) Construct : "WBConstruct00000005" Public_name "pBluescript KS"