CRISPR/Cas9‐Directed Genome Editing of Cultured Cells

Luhan Yang1, Joyce L. Yang2, Susan Byrne1, Joshua Pan2, George M. Church1

1 Department of Genetics, Harvard Medical School, Boston, Massachusetts, 2 Biological and Biomedical Sciences Program, Harvard Medical School, Boston, Massachusetts
Publication Name:  Current Protocols in Molecular Biology
Unit Number:  Unit 31.1
DOI:  10.1002/0471142727.mb3101s107
Online Posting Date:  July, 2014
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Human genome engineering has been transformed by the introduction of the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR‐associated) system found in most bacteria and archaea. Type II CRISPR/Cas systems have been engineered to induce RNA‐guided genome editing in human cells, where small RNAs function together with Cas9 nucleases for sequence‐specific cleavage of target sequences. Here we describe the protocol for Cas9‐mediated human genome engineering, including construct building and transfection methods necessary for delivering Cas9 and guide RNA (gRNA) into human‐induced pluripotent stem cells (hiPSCs) and HEK293 cells. Following genome editing, we also describe methods to assess genome editing efficiency using next‐generation sequencing and isolate monoclonal hiPSCs with the desired modifications for downstream applications. Curr. Protoc. Mol. Biol. 107:31.1.1‐31.1.17. © 2014 by John Wiley & Sons, Inc.

Keywords: genome engineering; CRISPR; human stem cells

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Table of Contents

  • Introduction
  • Basic Protocol 1: Preparation of Cas9 and gRNA Plasmids
  • Basic Protocol 2: Transfection of hiPSCs
  • Alternate Protocol 1: Transfection of Human HEK293 Cells
  • Basic Protocol 3: Genotyping Transfected Cells Using Next‐Generation Sequencing
  • Basic Protocol 4: Single‐Cell Isolation of Genome‐Targeted Monoclonal hiPSCs
  • Reagents and Solutions
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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Basic Protocol 1: Preparation of Cas9 and gRNA Plasmids

  • Cas9 plasmid (Addgene, plasmid ID 41815) as bacterial stab in agar
  • LB agar plate containing 100 µg/ml ampicillin (unit 1.1)
  • LB liquid medium containing 100 µg/ml ampicillin (unit 1.1)
  • HiSpeed Plasmid Maxi Kit (Qiagen)
  • PCR‐grade sterile deionized water
  • PCR‐Blunt II‐Topo kit (Invitrogen, cat. no. K2800‐20) including One Shot Top10 Chemically Competent E. coli cells (other competent cells for cloning may also be used)
  • Sterilized glass beads (EMD Millipore, cat. no. 71013‐3)
  • LB agar plate containing 50 µg/ml kanamycin (unit 1.1)
  • M13 Forward (5′‐GTTTTCCCAGTCACGACG‐3′) and M13 Reverse (5′‐AACAGCTATGACCATG‐3′) universal sequencing primers
  • LB liquid medium containing 50 µg/ml kanamycin (unit 1.1)
  • Qiagen plasmid Mini Kit (Qiagen)
  • Sterile pipet tips or toothpicks for picking colonies from agar plates
  • 37°C incubator‐shaker
  • Nanodrop microspectrophotometer (
  • Sequence analysis software (e.g., NCBI BLAST, UCSC Genome Browser BLAT, LaserGene)
  • DNA synthesis facility
  • 42°C incubator for heat‐shocking cells
  • 10‐ml bacterial culture tubes
  • Access to Sanger sequencing facility
  • Additional reagents and equipment for DNA synthesis (unit 2.11) and Sanger sequencing (unit 7.1)

Basic Protocol 2: Transfection of hiPSCs

  • PGP1 hiPSC cells adapted for growth on Matrigel (see personal genome project Web site:
  • Matrigel (hESC‐qualified; BD Sciences, cat. no. 354277)
  • DMEM/F12 medium (Invitrogen)
  • mTeSR1 medium (StemCell Technologies, cat. no. 05850)
  • InSolution Rho kinase (ROCK) inhibitor (Calbiochem, cat. no. Y‐27632)
  • P3 Primary Cell 4D‐Nucleofector X kit containing P3 and Supplement 1 solutions in addition to 16‐well Nucleocuvette Strips (Lonza, cat. no. V4XP‐4032)
  • Cas9 plasmid DNA (see protocol 1)
  • gRNAexpression vector (see protocol 1)
  • Phosphate‐buffered saline (PBS; Life Technologies, cat. no. 20012‐050)
  • TrypLE Express (Invitrogen, cat. no. 12604‐013)
  • 6‐ and 48‐well tissue culture–treated plates
  • 15‐ and 50‐ml conical centrifuge tubes (e.g., BD Falcon)
  • Countess automated cell counter (Invitrogen)
  • Tabletop centrifuge and plate adapter
  • Amaxa 4D‐Nucleofector System (Lonza, cat. no. CD‐MN025)
  • Additional reagents and equipment for culture of hiPSC in mTeSR medium (see Technical Manual Version 3.0.0 from Stem Cell Technologies;

Alternate Protocol 1: Transfection of Human HEK293 Cells

  Additional Materials (also see protocol 2)
  • HEK 293 cells (Invitrogen)
  • Complete DMEM medium (see recipe)
  • Lipofectamine 20000 (Invitrogen, cat. no. 11668027)
  • Opti‐MEM medium (Invitrogen, cat. no. 31985062)
  • Cas9 plasmid DNA (see protocol 1)
  • gRNAexpression vector (see protocol 1)
  • 12‐well tissue culture treated plates

Basic Protocol 3: Genotyping Transfected Cells Using Next‐Generation Sequencing

  • Transfected hiPSCs ( protocol 1 or protocol 3Alternate Protocol) growing in culture
  • Phosphate‐buffered saline (PBS; Life Technologies, cat. no. 20012‐050)
  • mTeSR1 medium (StemCell Technologies, cat. no. 05850)
  • prepGEM gold buffer (ZyGEM)
  • prepGEM tissue protease enzyme (ZyGEM)
  • KAPA Hifi Hotstart Readymix (KAPA Biosystems)
  • Illumina amplification primers (see step 3)
  • Illumina index primers (ScriptSeq Index PCR Primers)
  • 2‐log DNA ladder (New England Biolabs)
  • QIAquick PCR purification kit (Qiagen)
  • Computer running Primer3 software ( for primer identification
  • 15‐ml conical tubes (BD Falcon)
  • Tabletop centrifuge
  • Thermal cycler
  • Access to MiSeq sequencer
  • Additional reagents and equipment for agarose gel electrophoresis (unit 2.5) and measuring DNA concentration ( appendix 3D)

Basic Protocol 4: Single‐Cell Isolation of Genome‐Targeted Monoclonal hiPSCs

  • 0.1% (w/v) gelatin (StemCell Technologies, cat. no. 07903)
  • Irradiated CF‐1 mouse embryonic fibroblasts (Michalska, )
  • hES cell medium (see recipe)
  • Recombinant fibroblast growth factor (Millipore)
  • SMC4 (BD Biosciences; for 1× SMC4, supplement 500 ml of medium with one vial of SMC4 purchased from BD)
  • Fibronectin (StemCell Technologies)
  • Heterogenous pool of edited hiPSC ( protocol 2)
  • mTeSR1 medium (StemCell Technologies, cat. no. 05850) supplemented with SMC4 (BD Biosciences) at final concentration of 1× (one vial per 500 ml medium)
  • mTeSR1 medium (StemCell Technologies, cat. no. 05850), unsupplemented
  • Phosphate‐buffered saline (PBS; Invitrogen, cat. no. 20012‐050)
  • Accutase (Millipore)
  • ToPro‐3 viability dye (Invitrogen)
  • Matrigel (hESC‐qualified; BD Sciences, cat. no. 354277)
  • 96‐well plates
  • BD FACSAria II SORP UV (BD Biosciences) with 100‐mm nozzle
  • Centrifuge for 96‐well plates
  • Access to Sanger sequencing facility
  • Additional reagents and equipment for obtaining amplicons of the targeting region (see protocol 4, steps 4 to 11)
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