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DNA amount per sample was normalized to 20 ng/μL.
Data processing includes correction of staining bias, estimation of protein concentration from response curves, normalization for total protein amount per sample and statistical evaluation.
An aliquot of the SDS extract was counted in Ecoscint for S radioactivity in a liquid scintillation spectrometer to determine the amount of S-methionine incorporated into proteins, and the amount per sample was normalized by 1 µg of protein.
Each sample was counted in a Beckman LS 6500 multipurpose scintillation counter to determine the amount of H-uridine incorporated, and the amount per sample was normalized by 1 µg of total RNA.
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Real-time RT-PCRs were conducted in a GeneAmp 7500 Sequence Detection System (Applied Biosystems, Foster City, California, USA) and cDNA amounts per sample were determined using SYBR Green PCR Core Reagents kit (Applied Biosystems).
LR-PCR amplicons were cleaned by column purification and pooled in equimolar amounts per sample.
Nuclei were counted to verify the amount per each sample and resuspended in 135 μl of TE buffer supplemented with 0.1 % Triton X-100 and protease inhibitors.
To fragment DNA, we created a master mix of DNase I (Promega), One-Phor-All BiosciencesrshandBiosciences), Acetylatedated BSA (Invitrogen); the amounts added per sample were 4 µl 10X One-Phor-All, 0.14 µl Acetylated BSA, and approximately 0.085 µl of DNase per ug of DNA.
Starting off from minimal amounts of unamplified total RNA per sample, a reasonable amount of samples can be assayed simultaneously for the quantitative expression of hundreds of genes in an easily customisable and cost-effective manner.
An equal amount of total protein per sample was then loaded into each well, separated by SDS-PAGE electrophoresis and transferred to Immobilon 0.45 µM PVDF membranes (Millipore) using a Semi Dry Electroblotting System (Owl).
EC and OC are expressed as amount of total carbon per sample.
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