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Species: Saccharomyces cerevisiae
Genetic Insert: YKU70 sgRNA
Vector Backbone Description: Backbone Marker:John Wyrick lab; Backbone Size:11240; Vector Backbone:pML104; Vector Types:Yeast Expression, CRISPR; Bacterial Resistance:Ampicillin and Kanamycin
Defining Citation: PMID:42519825
Comments: This plasmid contains an example guide sequence targeting **YKU70**. As described in our protocol paper, the guide sequence can be easily changed by designing forward and reverse primers for a new target and then using PCR and seamless plasmid recircularization.
Proper citation: RRID:Addgene_254712 Copy
Species: Exaiptasia diaphana
Genetic Insert: AIPGENE865 promoter
Vector Backbone Description: Backbone Marker:Lab of Ulrich Technau; Backbone Size:4115; Vector Backbone:pNvT-MHC::mCh; Vector Types:Expression of NLS-Kaede in Exaiptasia diaphana; Bacterial Resistance:Ampicillin and Kanamycin
Comments: The whole intergenic region between AIPGENE865 (KXJ12416.1; Elongation Factor 1alpha) and AIPGENE899 was cloned as promoter fragment. The original gene annotation for AIPGENE865 is incorrect, the automatic NCBI annotation is correct in regards of exons, introns and translation start site. We found that Aiptasia strain CC7 was actually heterozygous for that locus: one allele was mostly in agreement with the genome sources but the other one had a couple of SNPs and a large, 749-bp insert in the intergenic region. The longer version with insert was used as promoter for this plasmid.
Proper citation: RRID:Addgene_240639 Copy
Species: Hymenolepis diminuta
Genetic Insert: pogzl
Vector Backbone Description: Vector Backbone:pJC53.2; Vector Types:RNAi, riboprobe synthesis; Bacterial Resistance:Ampicillin and Kanamycin
Defining Citation: PMID:31549962
Comments: contig listed under transcriptome: GHNR00000000.1
Proper citation: RRID:Addgene_239145 Copy
Species: Hymenolepis diminuta
Genetic Insert: hnf4
Vector Backbone Description: Vector Backbone:pJC53.2; Vector Types:RNAi, riboprobe synthesis; Bacterial Resistance:Ampicillin and Kanamycin
Defining Citation: PMID:31549962
Comments: contig listed under transcriptome: GHNR00000000.1
Proper citation: RRID:Addgene_239143 Copy
Species: Schistosoma mansoni
Genetic Insert: h2b (Smp_108390)
Vector Backbone Description: Backbone Size:3239; Vector Backbone:pJC53.2; Vector Types:T/A Cloning Vector for dsRNA generation and the generation of sense and anti-sense probes; Bacterial Resistance:Ampicillin and Kanamycin
Defining Citation: PMID:32737161
Comments: Cloning Primers: Forward-GCCTCCTAAAGTTGTGTCTGG, Reverse-GACCCACTGTACTTCGTCACTG
Proper citation: RRID:Addgene_239174 Copy
Species: Hymenolepis diminuta
Genetic Insert: cel135
Vector Backbone Description: Vector Backbone:pJC53.2; Vector Types:RNAi, riboprobe synthesis; Bacterial Resistance:Ampicillin and Kanamycin
Defining Citation: PMID:31549962
Comments: contig listed under transcriptome: GHNR00000000.1
Proper citation: RRID:Addgene_239166 Copy
Genetic Insert: Kaede
Vector Backbone Description: Vector Backbone:pCRII-TOPO plasmid; Vector Types:Transgenesis in Hofstenia miamia; Bacterial Resistance:Ampicillin and Kanamycin
Defining Citation: PMID:34752780
Proper citation: RRID:Addgene_176423 Copy
Species: Vibrio fischeri
Genetic Insert: Acyl-homoserine-lactone synthase, 3OC6-HSL
Vector Backbone Description: Backbone Size:9691; Vector Backbone:pAM1579; Vector Types:Bacterial Expression, Synthetic Biology; Bacterial Resistance:Ampicillin and Kanamycin
Defining Citation: PMID:40716565
Comments: Please visit https://doi.org/10.1101/2025.04.03.647055 for bioRxiv preprint.
Proper citation: RRID:Addgene_239010 Copy
Species: Azotobacter vinelandii
Genetic Insert: Deoxyviolacein Operon
Vector Backbone Description: Vector Backbone:pUC19; Vector Types:Bacterial Expression; Bacterial Resistance:Ampicillin and Kanamycin
Proper citation: RRID:Addgene_260269 Copy
Genetic Insert: ParsR-arsR-cre[LVA] + PrpsL-loxP-TT-loxP-syfp2
Vector Backbone Description: Backbone Marker:Christopher Voigt (Addgene plasmid #108517); Vector Backbone:p15A-Kan; Vector Types:Bacterial Expression; Bacterial Resistance:Ampicillin and Kanamycin
Defining Citation: PMID:40949998
Comments: Please visit https://doi.org/10.1101/2024.10.02.616356 for bioRxiv preprint.
Proper citation: RRID:Addgene_252621 Copy
Species: Human Merkel Cell polyomavirus
Genetic Insert: MCV replication region
Vector Backbone Description: Backbone Marker:Invitrogen; Backbone Size:3900; Vector Backbone:pCR2.1-TOPO; Vector Types:Bacterial Expression; Bacterial Resistance:Ampicillin and Kanamycin
Defining Citation: PMID:18812503
Proper citation: RRID:Addgene_28192 Copy
Species: Synthetic
Genetic Insert: GLT1 POL1 24xPP7SL
Vector Backbone Description: Vector Backbone:pHIS; Vector Types:; Bacterial Resistance:Ampicillin and Kanamycin
Defining Citation: PMID:21512033
Comments: Note that Addgene NGS results found 22xPP7 stem loop repeats rather than expected 24. It is not known how this impacts plasmid function.
This plasmid was designed to construct mRNAs that contain multiple copies of an RNA sequence (the 24xPP7 stem-loops) that can be recognized by a chimeric RNA-binding protein fused to GFP, encoded in plasmid pDZ276 (Addgene plasmid #35194). See associated publication for detailed methods and use of this plasmid.
Please note that the LacZa-ccdB fusion in this plasmid is not functional and was originally present in the vector backbone to aid in screening for insert.
Proper citation: RRID:Addgene_35196 Copy
Species: S. mediterranea
Genetic Insert: Protein arginine methyltransferase 1 homolog
Vector Backbone Description: Backbone Marker:Jim Collins, Newmark lab; Vector Backbone:pJC53.2; Vector Types:; Bacterial Resistance:Ampicillin and Kanamycin
Defining Citation: PMID:22318224
Comments: There are several mismatches between Addgene's quality control sequence and the available NCBI sequence. Depositing lab believes these mismatches will not affect plasmid function.
Proper citation: RRID:Addgene_35694 Copy
Species: S. mediterranea
Genetic Insert: Protein arginine methyltransferase 5
Vector Backbone Description: Backbone Marker:Jim Collins, Newmark lab; Vector Backbone:pJC53.2; Vector Types:; Bacterial Resistance:Ampicillin and Kanamycin
Defining Citation: PMID:22318224
Comments: There are several mismatches between Addgene's quality control sequence and the best match available NCBI sequence (AEX33822.1). Depositing lab believes these mismatches will not affect plasmid function.
Proper citation: RRID:Addgene_35692 Copy
Species: Saccharomyces cerevisiae
Genetic Insert: rRNA 5'ETS ntds 923 to 1179
Vector Backbone Description: Backbone Marker:Invitrogen; Backbone Size:4000; Vector Backbone:pTOPO; Vector Types:Bacterial Cloning - TOPO; Bacterial Resistance:Ampicillin and Kanamycin
Defining Citation: PMID:15489292
Proper citation: RRID:Addgene_23995 Copy
Species: Saccharomyces cerevisiae
Genetic Insert: 25S rRNA from +5270 to oligo y
Vector Backbone Description: Backbone Marker:Invitrogen; Backbone Size:4000; Vector Backbone:pTOPO; Vector Types:Bacterial Cloning - TOPO; Bacterial Resistance:Ampicillin and Kanamycin
Defining Citation: PMID:15489292
Proper citation: RRID:Addgene_23996 Copy
Species: Saccharomyces cerevisiae
Genetic Insert: rDNA 5'ETS ntds 1 to 177
Vector Backbone Description: Backbone Marker:Invitrogen; Backbone Size:4000; Vector Backbone:pTOPO; Vector Types:Bacterial Cloning - TOPO; Bacterial Resistance:Ampicillin and Kanamycin
Defining Citation: PMID:15489292
Proper citation: RRID:Addgene_23993 Copy
Genetic Insert: GFP4m
Vector Backbone Description: Vector Backbone:p2attNG; Vector Types:Mammalian Expression, Human Targeting; Bacterial Resistance:Ampicillin and Kanamycin
Defining Citation: PMID:24304893
Proper citation: RRID:Addgene_51545 Copy
Species: Bacterial origin
Genetic Insert: Kanamycin cassette
Vector Backbone Description: Backbone Size:7145; Vector Backbone:pLKO.1; Vector Types:Mammalian Expression, Lentiviral, CRISPR; Bacterial Resistance:Ampicillin and Kanamycin
Comments: This is a second generation plasmid that increases the efficiency of sgRNA guide cloning over the original "pLKO.1-puro U6 sgRNA BspMI stuffer" vector.
"pLKO.1-puro U6 sgRNA BfuAI large stuffer" was created to simplify the cloning of the sgRNA guide cassette into pLKO.1-puro U6 sgRNA BspMI stuffer vector originally described in the manuscript “Kearns, NA, etal. Development 2014, 141(1):219-23”. The original vector has a small intervening sequence that presents two problems: 1) the efficiency of excision by BfuAI is moderate, and 2) the size of this spacer is similar to the guide sequence, which makes distinguishing positive clones from reclosures challenging. Consequently, we have inserted a Kanamycin cassette between these sites at a unique Bcl1 site. This element is more efficiently excised by BfuAI and makes distinguishing vectors containing the desired guide sequence easy to distinguish from the parent vector. The excision of the Kan cassette by BfuAI cuts this cassette into 3 fragments due to two internal BfuAI sites within the Kan cassette. Otherwise the cloning of the guides is carried out as described in the manuscript.
Proper citation: RRID:Addgene_52628 Copy
Species: Mus musculus
Genetic Insert: mouse Ins2 gene partial
Vector Backbone Description: Backbone Marker:Life Technologies; Vector Backbone:pCR2.1-TOPO; Vector Types:Bacterial Expression; Bacterial Resistance:Ampicillin and Kanamycin
Defining Citation: PMID:23144715
Proper citation: RRID:Addgene_53969 Copy
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