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This analysis guided matched frozen sample selection for ECL.
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A custom-designed 22,000 oligonucleotide array was used in the present study to compare the gene expression profile of colonic epithelial cells isolated by laser capture microdissection from FFPE-archived samples with that of the same cell population from matched frozen samples, the preferred source of RNA.
To investigate any alterations in the metabolic profile that may be induced by a freeze-thaw cycle, 1H-NMR spectra were acquired from both fresh CM samples and matched frozen samples at −20°C for 2 weeks.
Total RNA was extracted from 45 FFPE tumor samples and 10 FFPE matched frozen tumor samples from the same patients.
The results from this processing regimen were compared with those derived from DNA extracted from matched frozen buffy coat samples.
Figure 4 shows one CN change between an FFPE tumor and a matched fresh frozen sample.
The concordance between matched FFPE and frozen samples was evaluated and expressed as a Pearson's correlation coefficient, with values ranging from 0.80 to 0.97.
Only a handful of previous studies have looked at CN in matched FFPE and frozen samples (and generally in less than 20 samples) and while some see much worse performance in FFPE samples, others find the same general patterns of amplifications and gains in matched samples and hence claim similar performance in FFPE and frozen samples [ 5- 7, 9, 10, 27].
A control group of 34 CCs frozen samples matched with SACs for gender, age, location, Dukes' stage, WHO grade and mucinous pattern was selected from the same tumour banks (25 Spanish and nine Finnish cases) accompanied by mucosal tissue in 14 of these (10 Spanish and 4 Finnish).
Truesdale's bank holds more than 1,000 cryogenically frozen samples.
# Analysis of frozen samples.
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