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Once we obtained synchronization of the cells as demonstrated by FACS analysis, nascent strand preparations from each one of the time points were prepared as described above, and the copy number at STS36.8 and STS98.4 on chromosome 2q34 was determined by real time PCR as indicated above.
Correlation between array data from fresh and frozen PAXGene preparations from each donor was high across all samples prepared with Methods 1 (no depletion_Affymetrix), 2 (Globin PNAs_Affymetrix) or 4 (no depletion_NuGEN), with the exception of donor A using Method 1, where one of the microarray assays underperformed (Table 3).
Cell preparations from each genotype (passages 2 or 3) were immortalized by retroviral transduction of SV40 LT antigen.
At least three independent RNA preparations from each of the selected time points were processed and hybridized on the arrays.
Clones were amplified in 3 different PCR experiments from 3 different cDNA preparations from each sample of tumour and healthy tissues of patients and from reference and control samples using Taq DNA polymerase (SIGMA, USA) or Expand High Fidelity (Roche, USA), with similar results.
Virus preparations from each of the infected cell lines were analysed for genetic modifications.
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Touch preparations were prepared from each sample for histological assessment and were examined by an experienced pathologist.
In the case of pre-mRNA levels evaluation, at least 4 µg of RNA preparation from each sample, previously treated by DNAseI™ (Promega), were used.
A single cDNA preparation from each specimen was used for each assay.
After 3 days of incubation at 37°C, DNA was extracted by heat-lysis preparation from each isolate and stored at −20°C until ready for use in PCR.
Genomic DNA from strains MG1655, Sakai and EDL933 was digested in an analogous fashion, and 1 μg of the preparation from each strain was combined and labeled with Alexa Fluor 546 dye (Invitrogen, Burlington, ON).
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