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For bottom-up in vitro SCRaMbLE, 200 ng acceptor vector was mixed with the donor fragments pool (1000 ng in total) in a reaction volume of 50 μl with 1 μl of high concentration Cre recombinase (NEB, M0298M).
Then, 20 µg pGCL vector was mixed with 15 µg pHelper1.0 vector (gag/pol component) and 10 µg pHelper2.0 vector (VSVG component), packed and transfected into 293T cells.
In co-transfection experiments, pCMV-Sp1 or pSG5-Ap1 expression vector was mixed with the luciferase vectors at 1 4 concentration ratio.
100 μl sterile water containing 20 μg/ml vector was mixed with 4 μl FuGENE HD transfection agent (Roche, Basel, Switzerland).
For the annealing process, 1 μl of T4 treated vector was mixed with 2 μl of T4 treated PCR product and allowed to incubate at 22°C for 1 hour. 1 μl of 25 mM EDTA pH 8.0 was then added and the reaction incubated for 5 mins.
200 ng of the linear vector was mixed with insert DNA at equal molar ratio in a 20 µl volume containing Phusion DNA polymerase reaction mixture (Finnzymes).
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In the binomial crossover, the target vector is mixed with the mutated vector, using the following scheme, to yield the trial vector (u_i^G ).
The four pENTR vectors and a pDEST vector were mixed in the presence of LR clonase enzyme to generate the multi-integrase platform plasmid (Fig. 1B).
Around 20 ng of each entry clone and 80 ng of destination vector were mixed with 2 µl of LR clonase II Plus enzyme mix, and made up to 10 µl with TE buffer.
When cells reached about 70% confluence 95 μg of pVSVG, 68 μg of pREV, 176 μg pMDL, and 270 μg transgene containing lentiviral vector were mixed.
For ICAM-5 rescue experiments, plasmid p-EGFP-N1 and ICAM-5 constructs (PEF-BOS-ICAM-5, PEF-BOS-ICAM-5 Δcp or the empty vector) were mixed at 1 10 ratio and co-transfected into neurons.
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