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IL-2 production was measured in supernatants from OKT3-stimulated and unstimulated T cell samples using a Beadlyte® human 22-plex cytokine detection system.
Human papillomavirus DNA was detected in cervical cell samples using a GP5+/6+-based PCR assay for 44 HPV types.
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SEM-EDS analysis was performed on air-dried, platinum-coated cell samples using an analytical SEM (JEOL JSM-6360A) equipped with EDS.
Total RNA was extracted from three different treated cell samples using an RNeasy Total RNA Isolation Kit (Qiagen).
This was followed by warming the cells to 37°C and then monitoring the fluorescence changes in the cell sample using a fluorescence spectrophotometer.
In this setting, up to 27 different T-cell specificities can be identified in a single cell sample, using a unique two-color code for each pMHC specificity as reported previously (18).
The frequency of double-positive peripheral MNCs was determined by forward and side-scatter fluorescence dot-plot analysis of a 5 × 105 cell sample using a FACS Calibur analyzer (Becton Dickinson, NJ, USA).
Total RNA extracted from CLL-cell samples using an RNeasy mini kit (Qiagen, Crawley, UK) was reverse transcribed using Moloney murine leukemia virus reverse transcriptase (Promega, Southampton, UK) and an oligo dT 15 primer.
This study was formally approved by Chubu University (approval no.: 2010001) Total RNA was prepared from frozen tumor and human cell line samples using a High Pure RNA Kit (Roche Diagnostics) according to the method previously described [24].
Absorbance spectra were acquired for the standards and the cell culture samples using a plate reader.
The entire data generation and analysis flow is illustrated in Additional file 1. Differentially expressed genes were determined between the pure OCI-Ly8 and HEK293 cell line samples using a false discovery rate (FDR) of less than 5%.
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