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Washing of the wells was performed using a stringent washing buffer, which dissociates and thereby avoids detection of low-avidity Abs.
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A related variation is called CLIP (cross-linking and immunoprecipitation), which was designed to isolate a protein-interacting domain within a given RNA molecule after using a stringent wash to reduce non-specific binding [ 30].
This DNA fragment can be recovered in a separate fraction by a stringent washing when it is not contiguous to the cleaved strand.
A stringent washing step (RIPA buffer) was included in our binding assay to reduce non-specific binding of actin to agarose beads (Fig. 1C).
We used a stringent SVM score threshold of 0.5 to reduce the number of false positives.
Following a stringent wash to remove non-covalent substrate-modifier interactions, the PTM-conjugated substrates are then detected using 'binders' (e.g. antibodies or streptavidin) labeled with fluorescent dyes and the protein microarrays analyzed using a fluorescence slide scanner.
Without a stringent wash with RIPA buffer, substantial amounts of actin were nonspecifically co-precipitated with the agarose beads.
In situ hybridisation was carried out overnight at 37°C, after which the slides were given a stringent wash (20% (v/v) formamide in 0.1× SSC at 42°C).
After hybridisation, the arrays were washed in a GeneChip Fluidics Station 400 with a non-stringent wash buffer at 25°C followed by a stringent wash buffer at 50°C.
After a stringent wash at 65°C for 10 min, the slides were mounted with a fluorescence mounting medium containing 4′,6-diamidino-2-phenylindol dihydrochloride and a coverslip was used.
Post-hybridization processing included a stringent wash to remove unbound and non-specifically hybridized target molecules, a staining step with a Cy™5-Streptavidin conjugate, and several non-stringent washing steps to remove unbound conjugate.
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