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Species: Caenorhabditis elegans
Genetic Insert: Mex-5 (aa1-244) (RNAi resistant)
Vector Backbone Description: Backbone Marker:Addgene plasmid 17247; Backbone Size:6351; Vector Backbone:pCG150; Vector Types:Worm Expression, Gateway Cloning; Bacterial Resistance:Ampicillin
Defining Citation: PMID:21925318
Comments: Dendra::MEX-5 constructs were constructed as follows. A 4.4 kb mex-5 promoter fragment based on Tenlen et al. (2008) was cloned into pDONRP4P1R (Invitrogen). Dendra2/TEV/S-peptide (Gallo et al., 2010) was cloned into pDONR201. A MEX-5 genomic fragment from the start ATG through 648 bp of 3'UTR was cloned into pDONRP2RP3. Exon 2 of mex-5 was recoded to be RNAi-resistant (Gen-Script) so as to allow depletion of endogenous MEX-5/6 without depletion of the transgene. These constructs were assembled into pCG150 using three-way Gateway system (LR reaction) (Invitrogen) (Merritt et al., 2008). Mutations were made by recombinant PCR and all inserts were sequenced verified.
Alternate plasmid name: pCG150 + 4.4kb+Dendra+ gen MEX-5 aa1-245 (RNAi res) +3’UTR
Proper citation: RRID:Addgene_40120 Copy
Species: Caenorhabditis elegans
Genetic Insert: Mex-5 (aa 345 - 468)
Vector Backbone Description: Backbone Marker:Cheeseman lab; Backbone Size:16397; Vector Backbone:pIC26; Vector Types:Worm Expression; Bacterial Resistance:Ampicillin
Defining Citation: PMID:21925318
Comments: MEX-5 transgenes driven by the pie-1 promoter and pie-1 3'UTR were constructed by cloning the mex-5 cDNA as a SpeI fragment downstream of a Dendra2/TEV/S-peptide tag cloned into pIC26 LAP tag (Cheeseman et al., 2004).
Alternate plasmid name: pIC26 Dendra + MEX-5 (aa345-STOP) (Dendra + MEX-5 ORF)
Proper citation: RRID:Addgene_40086 Copy
Species: Synthetic
Genetic Insert: LOV-ipaA
Vector Backbone Description: Backbone Marker:EMD Biosciences; Backbone Size:5442; Vector Backbone:pET-21b(+); Vector Types:Bacterial Expression; Bacterial Resistance:Ampicillin
Defining Citation: PMID:22520757
Comments: This vector encodes a photo-activable caged form of the vinculin binding ipaA peptide.
Regarding the hybridized region, the first ten residues of the ipaA VBS1 helical peptide were identified as a close match to the last ten residues of the AsLOV2 Jα helix; five of the ten positions are identical, and the hydrophobic residues on the Jα helix that make critical contacts with the AsLOV2 domain beta-sheet at residues 539, 542, and 543 are conserved in the alignment with ipaA. Additionally, residues in the ipaA sequence that make extensive contacts with vinculin are conserved in the alignment (Ile 612, Ala 615, Ala 616, and Val 619 in ipaA). Side-chain optimization simulations were used to thread the first ten residues of ipaA onto the last ten residues of the Jα helix. The 540 position on the Jα helix was converted to isoleucine.
The LOV-ipaA gene was synthesized with a six histidine N-terminal tag (Genscript, Piscataway, NJ, USA) and cloned into the pET21b vector.
Protein coding sequence of LOV-ipaA:
MHHHHHHGSLATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVRDAAEREGVMLIKKTANNIIKAAKDVTTSLSKVLKNIN
Proper citation: RRID:Addgene_40236 Copy
Genetic Insert: yEGFP1
Vector Backbone Description: Backbone Size:5667; Vector Backbone:pRS413; Vector Types:Bacterial Expression; Bacterial Resistance:Ampicillin
Comments: yEGFP contains a M233I point mutation. Depositor states that this mutation does not affect yEGFP function.
Proper citation: RRID:Addgene_40235 Copy
Species: Mus musculus
Genetic Insert: CD40L
Vector Backbone Description: Backbone Marker:Addgene plasmid 40569; Vector Backbone:MIEG-hCD4; Vector Types:Retroviral; Bacterial Resistance:Ampicillin
Defining Citation: PMID:19405121
Comments: The CD40-ligand (CD40L)-expressing retroviral vector was constructed by PCR amplification of cDNA from anti-CD3 activated mouse T cells with the following primers for CD40-ligand: sense 5'-CTTTCAGTCAGCATGATAGAAACA-3' and antisense
5'-TCAGAGTTTGAGTAAGCCAAAAGA-3'; these primers were used to amplify the complete coding region of mouse CD40 ligand. The CD40-ligand gene was then reamplified with primers containing XhoI and NotI sites and then cloned via XhoI and NotI sites into a retroviral vector expressing human CD4.
Proper citation: RRID:Addgene_40355 Copy
Species: Homo sapiens
Genetic Insert: Jun dominant negative
Vector Backbone Description: Backbone Marker:David A. Williams (PMID: 10961859); Vector Backbone:pMIEG3; Vector Types:Mammalian Expression, Retroviral; Bacterial Resistance:Ampicillin
Defining Citation: PMID:15699140
Comments: The Jun dominant negative vector was made by first preparing a version of c-Jun with the first 122 aa deleted. This cDNA was amplified by PCR from human c-Jun with the following primers:
sense, 5-AAAAAA-GAATTC-ATGACTAGCCAGAACACGCTGCCCAGCGTC-3;
antisense, 5-AAAAAA-GAATTC-TCAGCTGGCATAGTCAGGCACGTCATAAGGATAGCTAAATGTTTGCAAC-3.
The antisense primer adds a hemagglutinin tag to the C terminus of c-Jun. The PCR product was then cut with EcoRI and cloned into the retroviral vector pMIEG3.
Proper citation: RRID:Addgene_40350 Copy
Species: Homo sapiens
Genetic Insert: RASSF6
Vector Backbone Description: Backbone Marker:Promega; Vector Backbone:pCI-neo (modified); Vector Types:Mammalian Expression; Bacterial Resistance:Ampicillin
Defining Citation: PMID:19797269
Comments: pCIneoFH vector has the sequence NheI-FLAG-His6-EcoRI-MluI-XbaI-SalI-SmaI-NotI.
A digest with NheI and SalI will excise the insert with tags.
Proper citation: RRID:Addgene_40344 Copy
Species: Homo sapiens
Genetic Insert: BCL-6Δ
Vector Backbone Description: Backbone Marker:Masafumi Tanaka and Winship Herr (PMID: 2302733); Backbone Size:7500; Vector Backbone:pCGN; Vector Types:Mammalian Expression; Bacterial Resistance:Ampicillin
Defining Citation: PMID:10973278
Comments: The expression plasmid pCGN-BCL-6Δ was constructed by digesting the BCL-6 cDNA with EcoRI, deleting the 3' region, and cloning the remaining cDNA into pCGN. The BCL-6Δ is missing four of six zinc fingers and does not bind to a consensus BCL-6 probe in a gel shift assay (A. L. Dent, unpublished data).
Note, the cloning and ligation adds the following residues after aa595 of BCL6: RYQAYRYRRPGYR
Proper citation: RRID:Addgene_40338 Copy
Species: Homo sapiens
Genetic Insert: Pumilio homolog 2
Vector Backbone Description: Backbone Size:5372; Vector Backbone:pFRT/FLAG/HA-DEST; Vector Types:Mammalian Expression; Bacterial Resistance:Ampicillin
Defining Citation: PMID:20371350
Comments: Note that there are some cloning scars flanking the insert (see Addgene sequence), but they will not affect plasmid function.
Proper citation: RRID:Addgene_40292 Copy
Species: Synthetic
Genetic Insert: ddYFP-B
Vector Backbone Description: Backbone Marker:Invitrogen; Backbone Size:4100; Vector Backbone:pBad-modified; Vector Types:Bacterial Expression; Bacterial Resistance:Ampicillin
Defining Citation: PMID:23656278
Proper citation: RRID:Addgene_40289 Copy
Vector Backbone Description: Backbone Size:6447; Vector Backbone:JDS94; Vector Types:Mammalian Expression; Bacterial Resistance:Ampicillin
Comments: Backbone contains NNN/G 0.5 Domain
TAL N-terminal: ∆152 (Miller et al. 2011)
TAL C-terminus: +63 (Miller et al. 2011)
FOKI: ELD (-) heterodimer (Doyon et al. 2011)
Proper citation: RRID:Addgene_40322 Copy
Vector Backbone Description: Backbone Size:6447; Vector Backbone:JDS92; Vector Types:Mammalian Expression; Bacterial Resistance:Ampicillin
Comments: Backbone contains SHD/C 0.5 Domain
TAL N-terminal: ∆152 (Miller et al. 2011)
TAL C-terminus: +63 (Miller et al. 2011)
FOKI: ELD (-) heterodimer (Doyon et al. 2011)
Proper citation: RRID:Addgene_40321 Copy
Species: Synthetic
Genetic Insert: ddGFP-B
Vector Backbone Description: Backbone Marker:Invitrogen; Backbone Size:4100; Vector Backbone:pBad-modified; Vector Types:Bacterial Expression; Bacterial Resistance:Ampicillin
Defining Citation: PMID:23656278
Proper citation: RRID:Addgene_40287 Copy
Vector Backbone Description: Backbone Size:6447; Vector Backbone:JDS90; Vector Types:Mammalian Expression; Bacterial Resistance:Ampicillin
Comments: Backbone contains SNI/A 0.5 Domain
TAL N-terminal: ∆152 (Miller et al. 2011)
TAL C-terminus: +63 (Miller et al. 2011)
FOKI: ELD (-) heterodimer (Doyon et al. 2011)
Proper citation: RRID:Addgene_40320 Copy
Genetic Insert: NaChBac
Vector Backbone Description: Backbone Size:8914; Vector Backbone:pUAST; Vector Types:; Bacterial Resistance:Ampicillin
Defining Citation: PMID:16407556
Proper citation: RRID:Addgene_40283 Copy
Vector Backbone Description: Backbone Size:6447; Vector Backbone:JDS88; Vector Types:Mammalian Expression; Bacterial Resistance:Ampicillin
Comments: Backbone contains SNG/T 0.5 Domain
TAL N-terminal: ∆152 (Miller et al. 2011)
TAL C-terminus: +63 (Miller et al. 2011)
FOKI: KKR (+) heterodimer (Doyon et al. 2011)
Proper citation: RRID:Addgene_40319 Copy
Vector Backbone Description: Backbone Size:6447; Vector Backbone:JDS80; Vector Types:Mammalian Expression; Bacterial Resistance:Ampicillin
Comments: Backbone contains SNI/A 0.5 Domain
TAL N-terminal: ∆152 (Miller et al. 2011)
TAL C-terminus: +63 (Miller et al. 2011)
FOKI: KKR (+) heterodimer (Doyon et al. 2011)
Proper citation: RRID:Addgene_40316 Copy
Species: Saccharomyces cerevisiae
Genetic Insert: LEU2
Vector Backbone Description: Backbone Marker:ATCC, Number: 77142; Backbone Size:4967; Vector Backbone:pRS313; Vector Types:Yeast Expression; Bacterial Resistance:Ampicillin
Defining Citation: PMID:23222782
Proper citation: RRID:Addgene_40276 Copy
Species: Homo sapiens
Genetic Insert: LRRK2
Vector Backbone Description: Backbone Marker:Novagen; Vector Backbone:pBACgus; Vector Types:Baculovirus; Bacterial Resistance:Ampicillin
Proper citation: RRID:Addgene_40384 Copy
Species: Homo sapiens
Genetic Insert: LRRK2
Vector Backbone Description: Backbone Marker:Novagen; Vector Backbone:pBACgus; Vector Types:Baculovirus; Bacterial Resistance:Ampicillin
Proper citation: RRID:Addgene_40383 Copy
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