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In general, cells after relevant treatments were lysed in lysis buffer of the kit and stored at −70°C prior to RNA extraction which was done to all cells at once, prior to hybridization with the miRNA arrays.
Briefly, the peptide mixture was dried by vacuum centrifugation and resolubilized in the loading buffer of the kit.
Subsequently, cells were washed with PBS, resuspended in lysis buffer of the kit and harvested from the dishes with cell scraper.
Uninfected and infected host cells were washed with PBS, resuspended in the assay buffer of the kit, and detached from dishes with a cell scraper.
Cells were washed in PBS and incubated for 10 15 min at 4°C with the incubation buffer of the kit.
A biotinylated polyclonal anti-C3d antibody (A0063; Dako) diluted 1 1,000 in the conjugate buffer of the kit, was added to the wells, and the plates were incubated for 1 hour at room temperature.
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For preparation of the total cell lysate samples, cells were lysed using the cell lysis buffer of the Proteome Profiler Human Phospho-Kinase Array kit (R&D Systems).
After centrifugation in 12000× g for 10 min, the supernatant was discarded and the pellet resuspended in the ATL buffer of the DNeasy kit (Qiagen).
To reconstitute the dried oral fluid, the foam swab of the GenoTube was re-suspended in a 1.5 ml microcentrifuge tube with 400 μl of the dilution buffer of the ELISA kit which means a 1 2 dilution of the contained oral fluid as is required in manufacturer's instructions.
Labeled gDNA was re-suspended in the universal hybridization buffer of the Pronto kit (Promega, United States), mixed and added to the spotted slide (GEO accession number Platform GPL4980) for overnight hybridization at 42°C in a Tecan HS4800 Pro hybridization station (Tecan Group Ltd ,Switzerland).
The supernatant containing the majority of bacteria were removed carefully and the cell pellet was washed with PBS before adding lysis buffer of the RNeasy Mini Kit (Qiagen, Germany).
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