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Mice simulations were performed to produce a normal mouse sample and to complement the relatively small experimental mouse sample size by increasing the overall sample size.
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Since the putative serum SEPs might show very low abundance and high dynamics, 11 WT mouse samples and four ob/ob mouse samples were chosen for the following MS detection, respectively (Fig. 3B, C).
Primers to ribosomal protein S16 (for mouse samples) and RPL13 (for human samples) were used to normalize cDNA loading.
A similar experiment was undertaken using mouse samples and Illumina mouse WG-6 V2 BeadChips.
KV assisted in collection of mouse samples and carried out the immunoassays.
Thus, we achieved a sequencing success rate of 94% for the mouse samples and 89% for the human samples.
Plasma miRNAs were analyzed in an independent set of 20 wild-type mouse samples and 20 GEMM samples (10 localized and 10 metastatic).
PGP and N-Ac-PGP levels in mouse samples and the ex vivo PGP generation assay were analysed as described previously.
Changes in expression levels of bovine or mouse Prg4, Papss2, and Plod2 were determined using hypoxanthine ribosyltransferase (Hprt) as the normalization gene in mouse samples and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in bovine samples.
Fasting insulin determination was done using a rat/mouse insulin ELISA kit (Millipore) for the mouse samples, and a hamster-specific insulin ELISA kit (Crystal Chem Inc., Downers Grove, IL, USA) was used for the hamster samples.
Dye-swap experiments were performed for intraspecific (i.e. human samples and a human cDNA platform) and interspecific (i.e. mouse samples and a human cDNA platform) hybridizations for dye bias control.
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