CRISPR/Cas Plasmids: Label Genomic Loci

A catalytically inactive Cas9 (dCas9) fused to a fluorescent protein (FP) can be used to visualize specific genomic loci using fluorescent microscopy in living cells. Design your gRNA sequence to direct the dCas9-FP fusion to a specific genomic sequence. Potential target locations can include unique or repetitive regions. If the plasmid that you choose does not also express a gRNA, you will need to use a separate gRNA expression plasmid to target the dCas9-FP protein.

Mammalian

Plasmid	Gene/Insert	Promoter	Selectable Marker	PI	Publication	Hidden Extra Search Info
pHR-SFFV-dCas9-BFP	dCas9-BFP fusion (Homo sapiens)	SFFV		Weissman	CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes. Cell. 2013 Jul 9. pii: S0092-8674(13)00826-X. doi: 10.1016/j.cell.2013.06.044.	Human expression vector containing SFFV promoter, dCas9 that is fused to 2x NLS and tagBFP pHR
pSLQ1658-dCas9-EGFP	dCas9 fuse to EGFP (Homo sapiens)	MSCV LTR promoter	Puromycin	Qi	Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System. Cell. 2013 Dec 19;155(7):1479-91. doi: 10.1016/j.cell.2013.12.001.	Template for NLS-dCas9-NLS-EGFP fusion protein for CRISPR imaging (the recipient vector can be TetON 3G promoter system) pMSCVpuro
pBSKΔB-TRE-dCas9-EGFP	dCas9-EGFP (Synthetic)	TRE		Ochiai	Simultaneous live imaging of the transcription and nuclear position of specific genes. Nucleic Acids Res. 2015 Jun 19. pii: gkv624.	Plasmid for tet-inducible expression of dCas9-EGFP in mammalian cells pBlueScript II SK (+)
pHAGE-EFS-dCas9-GFP	Sp dCas9 (Synthetic)	EFS		Pederson	Multicolor CRISPR labeling of chromosomal loci in human cells. Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):3002-7. doi: 10.1073/pnas.1420024112. Epub 2015 Feb 23.	Expression of Sp dCas9-GFP in mammalian cells pHAGE-DEST
pHAGE-SSFV-dCas9-GFP	Sp dCas9 (Synthetic)	SSFV		Pederson	Multicolor CRISPR labeling of chromosomal loci in human cells. Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):3002-7. doi: 10.1073/pnas.1420024112. Epub 2015 Feb 23.	Expression of Sp dCas9-GFP in mammalian cells pHAGE-DEST
pHAGE-TO-dCas9-GFP	Sp dCas9 (Synthetic)	CMV-TO		Pederson	Multicolor CRISPR labeling of chromosomal loci in human cells. Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):3002-7. doi: 10.1073/pnas.1420024112. Epub 2015 Feb 23.	Expression of Sp dCas9-GFP in mammalian cells pHAGE-DEST
pHAGE-TO-dCas9-3XGFP	Sp dCas9 (Synthetic)	CMV-TO	GFP	Pederson	Multicolor CRISPR labeling of chromosomal loci in human cells. Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):3002-7. doi: 10.1073/pnas.1420024112. Epub 2015 Feb 23.	Expression of Sp dCas9-3XGFP in mammalian cells pHAGE-DEST
pHAGE-TO-dCas9-3XmCherry	Sp dCas9 (Synthetic)	CMV-TO	mCherry	Pederson	Multicolor CRISPR labeling of chromosomal loci in human cells. Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):3002-7. doi: 10.1073/pnas.1420024112. Epub 2015 Feb 23.	Expression of Sp dCas9-3XmCherry in mammalian cells pHAGE-DEST
pHAGE-TO-nmdCas9-3XGFP	Nm dCas9 (Synthetic)	CMV-TO		Pederson	Multicolor CRISPR labeling of chromosomal loci in human cells. Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):3002-7. doi: 10.1073/pnas.1420024112. Epub 2015 Feb 23.	Expression of Nm dCas9-3XGFP in mammalian cells pHAGE-DEST
pHAGE-TO-nmdCas9-3XmCherry	Nm dCas9 (Synthetic)	CMV-TO		Pederson	Multicolor CRISPR labeling of chromosomal loci in human cells. Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):3002-7. doi: 10.1073/pnas.1420024112. Epub 2015 Feb 23.	Expression of Nm dCas9-3XmCherry in mammalian cells pHAGE-DEST
pHAGE-TO-nls-st1dCas9-3nls-3XGFP	St1 dCas9 (Synthetic)	CMV-TO		Pederson	Multicolor CRISPR labeling of chromosomal loci in human cells. Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):3002-7. doi: 10.1073/pnas.1420024112. Epub 2015 Feb 23.	Expression of St1 dCas9-3XGFP in mammalian cells pHAGE-DEST
pHAGE-TO-nls-st1dCas9-3nls-3XGFP-nls	St1 dCas9 (Synthetic)	CMV-TO		Pederson	Multicolor CRISPR labeling of chromosomal loci in human cells. Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):3002-7. doi: 10.1073/pnas.1420024112. Epub 2015 Feb 23.	Expression of St1 dCas9-3XGFP in mammalian cells pHAGE-DEST
pHAGE-TO-nls-st1dCas9-3nls-3XGFP-2nls	St1 dCas9 (Synthetic)	CMV-TO		Pederson	Multicolor CRISPR labeling of chromosomal loci in human cells. Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):3002-7. doi: 10.1073/pnas.1420024112. Epub 2015 Feb 23.	Expression of St1 dCas9-3XGFP in mammalian cells pHAGE-DEST
pHAGE-TO-nls-st1dCas9-3nls-3XTagBFP2	St1 dCas9 (Synthetic)	CMV-TO		Pederson	Multicolor CRISPR labeling of chromosomal loci in human cells. Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):3002-7. doi: 10.1073/pnas.1420024112. Epub 2015 Feb 23.	Expression of St1 dCas9-3XTagBFP2 in mammalian cells pHAGE-DEST
pCDNA3.1- dCas9-2xNLS-EGFP	dCas9-2xNLS-EGFP	CMV		Yeo	Programmable RNA Tracking in Live Cells with CRISPR/Cas9. Cell. 2016 Mar 16. pii: S0092-8674(16)30204-5. doi: 10.1016/j.cell.2016.02.054.	Expresses dCas9-2xNLS-EGFP in mammalian cells pCDNA3.1(-)
pHAGE-TO-MCP-3XBFPnls	MCP (Synthetic)	CMV-TO		Pederson	Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotechnol. 2016 Apr 18. doi: 10.1038/nbt.3526.	MCP-3XBFPnls pHAGE-DEST
pHAGE-EFS-MCP-3XBFPnls	MCP (Synthetic)	EFS		Pederson	Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotechnol. 2016 Apr 18. doi: 10.1038/nbt.3526.	MCP-3XBFPnls pHAGE-DEST
pHAGE-EFS-PCP-3XGFPnls	PCP (Synthetic)	EFS		Pederson	Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotechnol. 2016 Apr 18. doi: 10.1038/nbt.3526.	PCP-3XGFPnls pHAGE-DEST
pHAGE-EFS-N22p-3XRFPnls	N22p (Synthetic)	EFS		Pederson	Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotechnol. 2016 Apr 18. doi: 10.1038/nbt.3526.	N22p-3XRFPnls pHAGE-DEST
pLH-sgRNA1-2XMS2	sgRNA1-2XMS2 (Synthetic)	U6	Hygromycin	Pederson	Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotechnol. 2016 Apr 18. doi: 10.1038/nbt.3526.	sgRNA1-2XMS2 pLKO.1
pLH-sgRNA1-2XPP7	sgRNA1-2XPP7 (Synthetic)	U6	Hygromycin	Pederson	Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotechnol. 2016 Apr 18. doi: 10.1038/nbt.3526.	sgRNA1-2XPP7 pLKO.1
pLH-sgRNA1-2XboxB	sgRNA1-2XboxB (Synthetic)	U6	Hygromycin	Pederson	Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotechnol. 2016 Apr 18. doi: 10.1038/nbt.3526.	sgRNA1-2XboxB pLKO.1
pLH-sgRNA1-MS2-PP7	sgRNA1-2XMS2-PP7 (Synthetic)	U6	Hygromycin	Pederson	Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotechnol. 2016 Apr 18. doi: 10.1038/nbt.3526.	sgRNA1-MS2-PP7 pLKO.1
pLH-sgRNA1-PP7-boxB	sgRNA1-2XPP7-boxB (Synthetic)	U6		Pederson	Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotechnol. 2016 Apr 18. doi: 10.1038/nbt.3526.	sgRNA1-PP7-boxB pLKO.1
pLH-sgRNA1-boxB-MS2	sgRNA1-boxB-MS2 (Synthetic)	U6	Hygromycin	Pederson	Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotechnol. 2016 Apr 18. doi: 10.1038/nbt.3526.	sgRNA1-boxB-MS2 pLKO.1
pLH-sgRNA1-boxB-MS2-PP7	sgRNA1-boxB-MS2-PP7 (Synthetic)	U6	Hygromycin	Pederson	Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotechnol. 2016 Apr 18. doi: 10.1038/nbt.3526.	sgRNA1-boxB-MS2-PP7 pLKO.1

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