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Specimens were digested and decontaminated using the Nalc-NaOH method, and resuspended in 2.0 mL of phosphate buffer.
Mononuclear cell suspension was obtained by the Ficoll-Hypaque density gradient method and resuspended in RPMI-1640 medium with 10% fetal calf serum.
To quantify DNA for real-time qPCR assays, genomic DNA was purified with the standard phenol-chloroform method and resuspended in 10 mM Tris-Cl buffer, pH 8.0, or diluted in distilled, sterile water.
For microarray and real-time PCR analysis, total RNA was extracted from harvested primary BRK cells and transformed cell lines by the Trizol method and resuspended in RNase and DNase-free H2O.
Briefly, spheroplasts were prepared from midlogarithmic phase K. pneumoniae ATCC 13883 cells using the lysozyme-EDTA method, and resuspended in 100 mM phosphate buffer (pH 7.5) containing 20% sucrose to an OD500 nm of ∼1.
For FAC recovery, we prepared ~0.3 mL of 10/mL protoplasts from A. nidulans FAC strains and FAC DNA was isolated by the common alkali lysis method, and resuspended in 10 μL of TE.
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Genomic DNA was extracted from these samples following a standard phenol chloroform method [27] and resuspended in TE buffer (10 mM Tris, 0.1 mM EDTA, pH 8.3).
Total RNA was extracted by phenol-chloroform-isopropanol method, purified, and resuspended in 20 μL of RNase-free water.
Trophozoite-infected erythrocytes were harvested and enriched using the percoll/sorbitol method, washed, and resuspended at 0.1% hematocrit in osmotic lysis solutions containing either 280 mM sorbitol or 150 mM Gdm-Cl buffered with 20 mM HEPES, 0.1 mg/mL BSA, pH 7.4.
DNA is extracted by the phenol/chloroform method, ethanol-precipitated, and resuspended in water.
Genomic DNA was isolated using CTAB-NaCl extraction method [ 97] and resuspended in TE buffer (10 mM Tris pH 8, 1 mM EDTA pH 8).
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