Genome-scale exon perturbation screens uncover exons critical for cell fitness
Xiao M-S, Damodaran AP, Kumari B, Dickson E, Xing K, On TA, Parab N, King HE, Perez AR, Guiblet WM, Duncan G, Che A, Chari R, Andresson T, Vidigal JA, Weatheritt RJ, Aregger M, Gonatopoulos-Pournatzis T
Mol Cell. 2024 June 24. doi: 10.1016/j.molcel.2024.05.024.
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Article
Plasmids from Article
| ID | Plasmid | Purpose |
|---|---|---|
| 209020 | pLenti-LbCas12a-8xNLS | Lentiviral vector expressing human codon-optimized LbCas12a with 8xNLS |
| 209021 | pLenti-enCas12a-2xNLS | Lentiviral vector expressing human codon-optimized enCas12a with 2xNLS |
| 209022 | pLenti-opCas12a-6xNLS | Lentiviral vector expressing human codon-optimized OpCas12a with 6xNLS |
| 209023 | pLenti-UltraCas12a-6xNLS | Lentiviral vector expressing human codon-optimized UltraCas12a with 6xNLS |
| 209024 | pLenti-opCas12a-Ultra-6xNLS | Lentiviral vector expressing human codon-optimized opCas12a-Ultra with 6xNLS |
| 209025 | pLCHKOv3 | Lentiviral backbone for expressing U6 driven hybrid guide (hg)RNAs with BveI cloning sites and puromycin selection marker |
| 209026 | pLCHKOv3-intergenic-As | Lentiviral vector expressing U6 driven hybrid guide (hgRNA) targeting two intergenic sites in the human genome using SpCas9 and AsCas12a nucleases (CHyMErA system), respectively |
| 209027 | pLCHKOv3-CD46 Ex3_1-Lb | Lentiviral vector expressing U6 driven hybrid guide (hgRNA) targeting human CD46 Exon 3 for deletion using SpCas9 and LbCas12a nucleases (CHyMErA system) |
| 209028 | pLCHKOv3-CD46 Ex3_2-Lb | Lentiviral vector expressing U6 driven hybrid guide (hgRNA) targeting human CD46 Exon 3 for deletion using SpCas9 and LbCas12a nucleases (CHyMErA system) |
| 209029 | pLCHKOv3-CD46 Ex3_3-Lb | Lentiviral vector expressing U6 driven hybrid guide (hgRNA) targeting human CD46 Exon 3 for deletion using SpCas9 and LbCas12a nucleases (CHyMErA system) |
| 209030 | pLCHKOv3-intergenic-Lb | Lentiviral vector expressing U6 driven hybrid guide (hgRNA) targeting two intergenic sites in the human genome using SpCas9 and LbCas12a nucleases (CHyMErA system), respectively |
| 209031 | pLCHKOv3-CD46 Ex3_1-As | Lentiviral vector expressing U6 driven hybrid guide (hgRNA) targeting human CD46 Exon 3 for deletion using SpCas9 and AsCas12a nucleases (CHyMErA system) |
| 209032 | pLCHKOv3-CD46 Ex3_2-As | Lentiviral vector expressing U6 driven hybrid guide (hgRNA) targeting human CD46 Exon 3 for deletion using SpCas9 and AsCas12a nucleases (CHyMErA system) |
| 209033 | pLCHKOv3-CD46 Ex3_3-As | Lentiviral vector expressing U6 driven hybrid guide (hgRNA) targeting human CD46 Exon 3 for deletion using SpCas9 and AsCas12a nucleases (CHyMErA system) |
| 209034 | pLCHKOv3-mClover3 | Lentiviral backbone for expressing U6 driven hybrid guide (hg)RNAs with BveI cloning sites, mClover3 and puromycin selection marker |
| 209035 | pLCHKOv3-mCherry | Lentiviral backbone for expressing U6 driven hybrid guide (hg)RNAs with BveI cloning sites, mCherry and puromycin selection marker |
| 209036 | pLCHKOv3-mClover-intergenic-As | Lentiviral vector expressing mClover3 along with U6 driven hybrid guide (hgRNA) targeting two intergenic sites in the human genome using SpCas9 and AsCas12a nucleases (CHyMErA system), respectively |
| 209037 | pLCHKOv3-mCherry-intergenic-As | Lentiviral vector expressing mCherry along with U6 driven hybrid guide (hgRNA) targeting two intergenic sites in the human genome using SpCas9 and AsCas12a nucleases (CHyMErA system), respectively |
| 209038 | pLenti-nSpCas9-NoCBE | Lentiviral vector expressing doxycycline-inducible human codon-optimized SpCas9(D10A)-6xNLS (Cas9 nickase) linked to ssDNA binding domain from RAD51 and uracil DNA glycosylase inhibitor (UGI) |
| 209039 | pLenti-nSpCas9-APOBEC1 | Lentiviral vector expressing doxycycline-inducible human codon-optimized cytosine base editor where APOBEC1 is fused to the N-terminus of SpCas9(D10A)-sDNA Rad51-2xUGI-6xNLS |
| 209040 | pLenti-nSpCas9-APOBEC3A | Lentiviral vector expressing doxycycline-inducible human codon-optimized cytosine base editor where APOBEC3A is fused to the N-terminus of SpCas9(D10A)-sDNA Rad51-2xUGI-6xNLS |
| 209041 | pLenti-nSpCas9-BEACON2 | Lentiviral vector expressing doxycycline-inducible human codon-optimized cytosine base editor where BEACON2 is fused to the N-terminus of SpCas9(D10A)-sDNA Rad51-2xUGI-6xNLS |
| 209042 | pLenti-nSpCas9-evoCDA1 | Lentiviral vector expressing doxycycline-inducible human codon-optimized cytosine base editor where evoCDA1 is fused to the N-terminus of SpCas9(D10A)-sDNA Rad51-2xUGI-6xNLS |
| 209043 | pLenti-nSpCas9-NoABE | Lentiviral vector expressing doxycycline-inducible human codon-optimized SpCas9(D10A)-6xNLS (Cas9 nickase) |
| 209044 | pLenti-nSpCas9-TadA8e | Lentiviral vector expressing doxycycline-inducible human codon-optimized adenine base editor where TadA8e (ABE8e) is fused to the N-terminus of SpCas9(D10A)-6xNLS |
| 209045 | pLenti-nSpCas9-TadA8.20m | Lentiviral vector expressing doxycycline-inducible human codon-optimized adenine base editor where TadA8.20m is fused to the N-terminus of SpCas9(D10A)-6xNLS |
| 209046 | pLCKOv3 | Lentiviral backbone for expressing U6 driven SpCas9 sgRNAs with BveI cloning sites, SpCas9 tracrRNAv1 (Dang et al., 2015; PMID: 26671237) and puromycin selection marker |
| 209047 | pDONR223-TAF5-FL | Gateway-compatible entry vector, with insert of the full length TAF5 gene |
| 209048 | pDONR223-TAF5-∆ex8 | Gateway-compatible entry vector, with insert of the TAF5 isoform lacking the alternative exon-8 (∆ex8) |
| 209049 | pcDNA5-3xFLAG-TAF5-FL | Vector for generating Flp-In cell lines allowing dox-inducible mammalian expression of 3xFlag-tagged full length TAF5 isoform |
| 209050 | pcDNA5-3xFLAG-TAF5-∆ex8 | Vector for generating Flp-In cell lines allowing dox-inducible mammalian expression of 3xFlag-tagged TAF5 isoform lacking the alternative exon-8 (∆ex8) |
| 209051 | pcDNA5-miniTurbo-TAF5-FL | Vector for generating Flp-In cell lines allowing dox-inducible mammalian expression of miniTurbo fused to full length TAF5 isoform |
| 209052 | pcDNA5-miniTurbo-TAF5-∆ex8 | Vector for generating Flp-In cell lines allowing dox-inducible mammalian expression of miniTurbo fused to TAF5 isoform lacking the alternative exon-8 (∆ex8) |
| 209053 | pDONR223-TAF5-FL_WobbleMut | Gateway-compatible entry vector, with insert of the full length TAF5 gene mutated to be resistant to TAF5 siRNA |
| 209054 | pDONR223-TAF5-∆ex8_WobbleMut | Gateway-compatible entry vector, with insert of the TAF5 isoform lacking the alternative exon-8 (∆ex8) mutated to be resistant to TAF5 siRNA |
| 209055 | pcDNA5-3xFLAG-TAF5-FL_WobbleMut | Vector for generating Flp-In cell lines allowing dox-inducible mammalian expression of 3xFlag-tagged full length TAF5 isoform mutated to be resistant to TAF5 siRNA |
| 209056 | pcDNA5-3xFLAG-TAF5-∆ex8_WobbleMut | Vector for generating Flp-In cell lines allowing dox-inducible mammalian expression of 3xFlag-tagged TAF5 isoform lacking the alternative exon-8 (∆ex8) mutated to be resistant to TAF5 siRNA |
| 209057 | pDONR223-EGFP | Gateway-compatible entry vector, with insert of the EGFP gene |
| 209058 | pcDNA5-3xFLAG-EGFP | Vector for generating Flp-In cell lines allowing dox-inducible mammalian expression of 3xFlag-tagged EGFP |
| 209059 | pcDNA5-miniTurbo-EGFP | Vector for generating Flp-In cell lines allowing dox-inducible mammalian expression of miniTurbo fused to EGFP |
| 209734 | CHyMErA LbCas12a Nuclease Optimization hgRNA Library | CHyMErA Cas12a Nuclease Optimization hgRNA Libraries allows assessment and comparison of the efficacy of different LbCas12a nucleases in the context of the Cas9-Cas12a CHyMErA system. |
| 209735 | CHyMErA AsCas12a Nuclease Optimization hgRNA Library | CHyMErA Cas12a Nuclease Optimization hgRNA Libraries allows assessment and comparison of the efficacy of different AsCas12a nucleases in the context of the Cas9-Cas12a CHyMErA system. |
| 209736 | CHyMErA Large-Scale Exon Deletion hgRNA Library | CHyMErA Exon Deletion hgRNA Library allows identification of frame-preserving exons that affect cell fitness in human cells using the CHyMErA screening platform. |
| 218814 | pLCHKOv3-mClover-intergenic_2-As | Lentiviral vector expressing mClover3 along with U6 driven hybrid guide (hgRNA) targeting two intergenic sites in the human genome using SpCas9 and AsCas12a nucleases (CHyMErA system), respectively |
| 218815 | pLCHKOv3-mClover-intergenic_3-As | Lentiviral vector expressing mClover3 along with U6 driven hybrid guide (hgRNA) targeting two intergenic sites in the human genome using SpCas9 and AsCas12a nucleases (CHyMErA system), respectively |
| 218816 | pLCHKOv3-mClover-intergenic_4-As | Lentiviral vector expressing mClover3 along with U6 driven hybrid guide (hgRNA) targeting two intergenic sites in the human genome using SpCas9 and AsCas12a nucleases (CHyMErA system), respectively |
| 218972 | PET01-TAF5-ex8-Minigene-SRSF1 motif WT | Vector for constitutive expression of TAF5 alternative exon-8 mini gene with wild type SRSF1 motif (TCAGAGGA) |
| 218973 | pET01-TAF5-ex8-Minigene-SRSF1 motif MUT | Vector for constitutive expression of TAF5 alternative exon-8 mini gene with mutated SRSF1 motif (AGTCTCCT) |
| 218974 | pcDNA5-3xFLAG-SRSF1 siRNA-resitant | Vector for expressing siRNA-resistant SRSF1 cDNA (siRNA sequence: CGUGGAGUUUGUACGGAAA) |