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Sheared chromatin DNA mixture (normalized inputs) was incubated with 4 μg FoxM1 antibody (#Santa Cruz Biotechnology, Santa Cruz, CA, USA) overnight at 4 °C.
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Eluted ChIP samples (and inputs) were incubated at 65°C overnight to reverse cross-links, excess protein was degraded using Proteinase K and DNA was isolated using Zymo columns according to the manufacturer's instructions (Zymo Research).
Rho +/- mouse retinal lysate (Input) was incubated with 1S4 antibody bound to protein A/G beads.
Wild-type (WT) mouse retinal lysate (Input) was incubated with 1D4 antibody and then bound to protein A/G beads.
(F ) RNA from HeLa cells infected with EMCV (input) was incubated with recombinant FLAG-tagged LGP2 protein and anti-FLAG or control IP was performed as in (A ).
In total, 150 µL of the lysis buffer without NP-40 or protease inhibitors (wash buffer) was added to the supernatant and this input was incubated with a mix of 2 µL GFP-TRAP_A beads (ChromoTek) and 8 µL empty Sepharose 4B beads (Sigma), equilibrated in wash buffer, for 1 hr at 4°C.
Briefly, protein samples (Input) were incubated overnight at 4°C with Strep-Tactin Sepharose, and unbound and bound proteins were collected by centrifugation.
Following addition of 0.2 M NaCl, all samples, including input, were incubated at 65°C for 4 h to revert cross-linking.
Following addition of 5 M sodium chloride, all samples, including input, were incubated at 65 °C for 4 h to revert cross-linking.
Following addition of 0.2 M NaCl, all samples, including input, were incubated for 4 h at 65 °C to revert cross-linking.
Supernatant was removed and beads were washed twice with WB. 40 µl 2× SDS-PAGE sample buffer was added to the beads and both beads and input were incubated 10 min at 56°C.
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