Abstract
Large repositories of well characterized RNAlater preserved samples and formalin-fixed, paraffin-embedded samples have been generated worldwide. However, the impact on the proteome of the preservation methods remain poorly described. Therefore, we analyzed the impact on the proteome of preserving samples in RNAlater, and by formalin-fixation, paraffin-embedding on human soft tissue, using directly frozen samples as a control (“Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples” [1]). We here report the data from the analysis. The comparative analysis was performed on 24 colon mucosa biopsies, extracted from the sigmoideum of two gastroenterologically healthy participants for the purpose of this study. A set of biopsies were additionally stored for 30 min at room temperature prior to formalin-fixation. The samples were analyzed by high throughput gel free quantitative proteomics. The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PRIDE: PXD002029.
Highlights
Large repositories of well characterized RNAlater preserved samples and formalin-fixed, paraffin-embedded samples have been generated worldwide
We analyzed the impact on the proteome of preserving samples in RNAlater, and by formalin-fixation, paraffin-embedding on human soft tissue, using directly frozen samples as a control (“Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples” [1])
The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PRIDE: PXD002029
Summary
Colon mucosal biopsies were sampled from the sigmoideum of two gastroenterologically healthy participants, by endoscopy at Hospital of Southern Jutland, Aabenraa, Denmark [4]. All biopsies had an approximate size of 1 À 2 mm, and the biopsies were preserved by four different methods: (1) directly frozen biopsies (DF) were immediately transferred to individual cryotubes and snap-frozen with liquid nitrogen followed by storage at À 80 °C for one month prior to sample processing and proteome analysis. (2) RNAlater biopsies were immediately transferred to individual cryotubes prefilled with 0.5 mL RNAlater (Life Technologies, Carlsbad, CA, USA), stored at room temperature for 24 h followed by storage at À 80 °C for one month prior to sample processing and proteome analysis. Additional information about the utilized Uniprot database, e.g. protein count, date ect. The FFPE prepared samples were subsequently stored for three weeks at room temperature prior to sample processing and proteome analysis. The project was approved by The Regional Scientific Ethical Committee (S-20120204) and the Danish Data Protection Agency (2008-58-035), and all participants had given informed consent to participate
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