Generation of Inducible shRNAi Human Embryonic Stem Cell Lines

Stuart Avery1

1 Institute of Medical Biology, A*STAR, Singapore
Publication Name:  Current Protocols in Stem Cell Biology
Unit Number:  Unit 5C.1
DOI:  10.1002/9780470151808.sc05c01s18
Online Posting Date:  September, 2011
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This unit describes the generation of tetracycline‐inducible short hairpin RNA interference (shRNAi) human embryonic stem cell (hESC) lines. Using this vector‐based approach enables stable and long‐term expression of target hairpins under the control of doxycycline/tetracycline. Target degradation can be controlled in both a dose‐ and time‐dependent manner that can even be switched off, depending upon the particular requirements of the study. Curr. Protoc. Stem Cell Biol. 18:5C.1.1‐5C.1.14. © 2011 by John Wiley & Sons, Inc.

Keywords: RNA interference; shRNAi; tetracycline; doxycycline; inducible; human embryonic stem cells (hESCs); stable transfection

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Table of Contents

  • Introduction
  • Basic Protocol 1: Design and Cloning of RNAi Targets
  • Basic Protocol 2: Generation and Screening of Stable Clones Expressing TetR Protein and Target shRNA
  • Reagents and Solutions
  • Commentary
  • Literature Cited
  • Figures
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Basic Protocol 1: Design and Cloning of RNAi Targets

  • pSUPERIOR.neo (Oligoengine)
  • Target specific sense and anti‐sense oligonucleotides at 200 µM (see annotations to step 2, below)
  • 5× annealing buffer (see recipe)
  • Restriction endonucleases BglII and XhoI (New England Biolabs)
  • NEBuffer 3 (New England Biolabs)
  • 10× (1 mg/ml) bovine serum albumin (BSA)
  • 1% agarose gel prepared with TAE or TBE buffer (Voytas, )
  • Gel‐extraction kit (Qiagen)
  • 10 mM Tris⋅Cl, pH 8.5 (or elution buffer from Qiagen gel‐extraction kit)
  • T4 DNA ligase (New England Biolabs) and ligase buffer
  • Electrocompetent or chemically competent bacterial host strain such as DH5α
  • LB agar plates (see recipe) containing 100 µg/ml ampicillin
  • PCR primers (use at 0.3 µM each primer):
    • pSUPERIOR sense: agaattcgaacgctgacgtc
    • pSUPERIOR antisense: ggaacaaaagctgggtaccg
  • Taq DNA polymerase (New England Biolabs)
  • DNA miniprep or maxi prep kit
  • Oligoengine 2.0 software (
  • Thermal cycler
  • Spectrophotometer
  • 16°C water bath
  • Additional reagents and equipment for agarose gel electrophoresis (Voytas, ) and transformation of bacteria (Seidman et al., )

Basic Protocol 2: Generation and Screening of Stable Clones Expressing TetR Protein and Target shRNA

  • Human embryonic stem cells (hESCs; unit 1.5)
  • mTeSR1 medium (StemCell Technologies)
  • 10 mM Y‐27632 dihydrochloride monohydrate stock solution (Sigma‐Aldrich, mol. wt. 338.27); dissolve 1 mg in 295.5 µl sterile distilled H 2O and store in aliquots at 70°C
  • Dulbecco's phosphate‐buffered saline (DPBS; Invitrogen, cat. no. 14190)
  • Accutase (Invitrogen)
  • Amaxa Human Stem Cell Nucleofector Kit 1 or 2 (see below; Lonza)
  • pCAGTetRnls vector (Addgene, cat. no. 26599)
  • 10 mg/ml puromycin stock solution (Invitrogen)
  • 1 mg/ml collagenase IV solution (see recipe)
  • DMEM/F12 1:1 medium (Invitrogen)
  • Mouse TET‐02 anti‐TetR (MoBiTec,
  • Donkey anti‐mouse‐HRP conjugated secondary antibody (Santa Cruz Biotechnology)
  • pSUPERIOR vector containing a target‐specific shRNAi sequence ( protocol 1)
  • 50 mg/ml Geneticin stock solution (Invitrogen)
  • Doxycycline working stock (see recipe)
  • Matrigel‐coated (see recipe) 12.5‐cm2 tissue culture flasks and 12‐well plates (6‐cm2 tissue culture dishes optional; BD Falcon)
  • Centrifuge and centrifuge tubes
  • Nucleofector device and cuvettes (Lonza)
  • Extra‐fine tipped Pasteur pipets (Alpha Laboratories;
  • Additional reagents and equipment for generating and passaging hESCs (unit 1.5), counting cells (unit 1.3), and immunoblotting (Gallagher et al., ; Zafarana et al., )
NOTE: All cell culture work should be performed following good aseptic technique in a Class II biological hazard flow hood or laminar‐flow hood.NOTE: All incubations are performed in a 37°C, 5% CO 2 humidified incubator, unless otherwise noted.
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Literature Cited

Literature Cited
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