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3 protocols using one shot stbl3 e coli cells

1

Cloning and Validation of Recombinant Plasmids

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All Vector stocks were generated and maintained via transformation of chemically competent One Shot™ Stbl3™ E. coli cells from ThermoFisher (ThermoFisher, #C737303) and isolated from 5 mL cultures using QIAprep Spin Miniprep Kit (Qiagen, #27106) following the manufacturer’s protocol. Where appropriate, restriction digests were conducted using FastDigest restriction enzymes (Thermo Scientific) following manufacturer’s protocol. PCR was conducted in a thermocycler using PrimeSTAR Max (Takara, #R045A) following the manufacturer’s protocol. Restriction digests and PCR products were electrophoresed on 1% agarose gels in TAE buffer (40 mM Tris pH 7.6, 20 mM acetic acid, 1 mM EDTA) and visualised using SYBRSafe DNA stain (Invitrogen, #S33102). Desired bands were excised from the gel and extracted using QIAquick Gel Extraction Kit (Qiagen, #28704) following the manufacturer’s protocol. T4 ligations were performed using T4 DNA Ligase (ThermoFisher, #EL0014) and Gibson assembly via NEBuilder HiFi DNA Assembly (New England Biolabs, #E5520) following respective manufacturers protocols. All constructs were confirmed via Sanger sequencing. A list of primers used in this study is provided in Table S1.
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2

Cloning of Genomic Regions from hPSCs

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hPSCs were cultured in a well of a 6-well plate until reaching 80% confluency. Once reaching this confluency, genomic DNA was then isolated using the ZYMO Quick DNA Miniprep Plus kit (Zymo Research). This genomic DNA was then used as a template for PCR amplification of genomic regions of interest. PCR was carried out using GoTaq DNA polymerase (Promega) with appropriate primers. The resulting amplicons were run through 1% agarose gels, and bands of interest were gel purified using the Zymoclean Gel DNA Recovery kit (Zymo Research) and subsequently run through the Zymo clean and concentrator-5 kit (Zymo Research). The resulting amplicons were then cloned into the TOPO TA cloning plasmid using the TOPO TA Cloning Kit for Sequencing (Thermofisher) according to the manufacturer’s instructions. The resulting cloned plasmids were finally transformed into One Shot Stbl3 E. coli cells (Thermofisher) according to manufacturer’s instructions, plated on Ampicillin agar plates, and cultured at 37°C overnight. Single E. coli colonies were then picked and cultured in LB broth overnight, cultured at 37°C and shaking at 250 rpm. The next day, plasmids were purified using the Zyppy Plasmid Miniprep Kit (Zymo Research) and sent in for sequencing.
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3

Preparation of pHRed DNA Transfer Plasmid

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FUG-W-pHRed DNA transfer plasmid was received as a gift from Dr. Tantama (Purdue University). A glycerol stock of E. coli transformed with the Perceval HR DNA transfer plasmid, FUG-W-Perceval HR, was purchased from Addgene (Cambridge, MA). Bacterial agar stabs carrying the accessory plasmids required for packaging and enveloping the virions, psPAX2 and pMD2.G, were also purchased from Addgene. We prepared a pHRed bacterial glycerol stock by transforming One Shot Stbl3 E. coli cells (Thermo Fisher, Waltham, MA) with FUG-W-pHRed DNA, following the manufacturer’s instructions. All glycerol stocks were then used to inoculate LB Broth (Sigma, St. Louis, MO) cultures grown with 100 μg/ml of ampicillin (Sigma) for about 15 h at 37 °C with a shaking incubator set at 225 rpm. DNA plasmids were extracted from these cultures and purified using the Endotoxin-free Maxiprep kit (Sigma). Their quantity and purity were measured with a Nanodrop spectrophotometer (Thermo Fisher). Plasmid identities were confirmed by 0.8% agarose gel electrophoresis using the E-Gel-iBase system (Thermo Fisher) following standard overnight restriction enzyme digestion by EcoRI (10 units/μg DNA; New England Biolabs, Ipswich, MA).
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