Comparison of microRNA expression using different preservation methods of matched psoriatic skin samples
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Marianne LM-CM-8vendorf
PROVIDER: E-GEOD-28729 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:MicroRNA expression profiling in matched lesional skin samples from 25 patients with psoriasis using the miRNA analysis platform miRCURY LNATM MicroRNA array (v. 11.0) (Exiqon). Aim: To explore the effect of three different preservation methods (Formalin-fixation paraffin-embedding (FFPE), frozen (FS) and OCT-embedding (OCT)) on miRNA expression levels in matched lesional skin samples from 25 patients with psoriasis.
2012-03-22 | GSE28729 | GEO
Project description:Tissue samples in biobanks preserved by formalin-fixation and paraffin-embedding (FFPE) and/or optimal cutting temperature (OCT)-embedded and subsequently freezing are highly valuable in experimental studies where the results can be related to clinical parameters. Today, mass spectrometry (MS)-based proteomics is the method of choice for unbiased and relative comparison of the abundances of thousands of proteins present in biological samples. MS analysis of FFPE- and OCT-preserved tissue has been limited, but it is now approachable using newly developed protocols. However, it has not been clarified how the results from different preservation methods agrees and differ. In this study, we use a unique sample set of urinary bladder cancer tissues of two different tumor stages (Ta/T1 – non-muscle invasive and T2/T3 muscle invasive); upon sampling the tumors were divided and preserved by the two methods. Thereafter a protocol for parallel processing of the samples were applied after which the samples were analyzed with label free quantitative MS analysis. Over 700 and 1200 proteins were quantified in FFPE and OCT samples, respectively. Principal component analysis showed that the largest differences between samples are based on the preservation method, but this analysis could also classify the tumors into different stages in each preservation. The overlap of quantifiable proteins between the preservation methods were 84% when all proteins and full data set were taken into consideration, but only 41% on average when proteins from a specific tumor were analyzed. Proteins involved in mitochondrial function were overrepresented among proteins present in OCT data but missing in the FFPE data, indicating that these proteins are not well preserved by FFPE. Moreover, univariate analysis showed that HMGCS2 protein is uniquely quantified in Ta/T1 tumors in both FFPE and OCT data, and that LGALS1, ANXA5 and plastin proteins are upregulated in T2/T3 tumors compared to Ta/T1 tumors in both FFPE and OCT data, confirming the consistency between the data sets and suggesting these proteins as biomarkers. Finally, LGALS1 data were verified by immunohistochemistry staining of an independent data set.
2021-09-09 | PXD020194 | Pride
Project description:Effect of Oxygen restriction on infection potential of Listeria monocytogenes
2010-07-01 | E-MEXP-2279 | biostudies-arrayexpress
Project description:MicroRNAs regulate several aspects of tumorigenesis and cancer progression. Most cancer tissues are archived formalin-fixed and paraffin-embedded (FFPE). While microRNAs are a more stable form of RNA thought to withstand FFPE-processing and degradation there is only limited evidence for the latter assumption. We examined whether microRNA profiling can be successfully conducted on FFPE cancer tissues using SOLiD ligation based sequencing. Tissue storage times (3-9 years) appeared to not affect the number of detected microRNAs in FFPE samples compared to matched frozen samples (paired t-test p>0.7). Correlations of microRNA expression values were very high across microRNAs in a given sample (PearsonM-bM-^@M-^Ys r=0.71-0.95). Higher variance of expression values among samples was associated with higher correlation coefficients between FFPE and frozen tissues. One of the FFPE samples in this study was degraded for unknown reasons with a peak read length of 17 nucleotides compared to 21 in all other samples. The number of detected microRNAs in this sample was within the range of microRNAs detected in all other samples. Ligation-based microRNA deep sequencing on FFPE cancer tissues is feasible and RNA degradation to the degree observed in our study appears to not affect the number of microRNAs that can be quantified. we analyzed eight matched frozen and FFPE tissues of different histologies for which detailed processing and storage information.
2013-04-15 | E-GEOD-45740 | biostudies-arrayexpress
Project description:The goal of the Optimal Cutting Temperature (OCT) Embedding Media Study was to measure the effect of OCT embedding on peptide identification. One OCT embedded sample and one snap frozen sample were compared. Each sample was analyzed 3 times using label free proteomic profiling. The data sets below contain the raw data files for the 3 replicates, there were 15 fractions assayed per sample for a total of 45 raw data files. No effect has been identified thus far, so concern over OCT embedding of the TCGA samples has been diminished.<ul><li>Dataset imported into MassIVE from <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S014">https://cptac-data-portal.georgetown.edu/cptac/s/S014</a> on 11/02/18</li></ul>
2018-11-02 | MSV000083095 | MassIVE
Project description:Investigation of whole genome gene expression level changes in three S. cerevisiae Y55 mutants, compared to the wild-type strain. The UV-induced mutations enable the mutant strains to ferment high-gravity maltose faster than the WT. The mutants analyzed in this study are further described in Baerends, R.J.S., J.L. Qiu, L. Gautier, and A. Brandt. A high-throughput system for screening of fast-fermenting Saccharomyces cerevisiae strains. Manuscript in preparation. A single-dye 12-plex array chip study using double-stranded DNA prepared from messenger RNA purified from total RNA recovered from three separate Saccharomyces cerevisiae Y55 wild-type cultures and 3x three separate cultures each corresponding to a fast-fermenting UV-induced mutant (mutant 1, 2 and 3), during fermentation of high-gravity maltose at day 2. Each array on the 12-plex chip measures the expression level of 5,777 genes from Saccharomyces cerevisiae S288C with eight 60-mer probes per gene, with three-fold technical redundancy.
2013-10-25 | E-GEOD-25015 | biostudies-arrayexpress
Project description:Background: Psoriasis is a systemic inflammatory skin disease. MicroRNAs (miRNAs) are a class of small non-coding RNA molecules that recently have been found in the blood to be relevant as disease biomarkers. Objective: We aimed to explore miRNAs potential as blood biomarkers for psoriasis. Methods: Using microarray and quantitative real-time PCR we measured the global miRNA expression in whole blood, plasma and peripheral blood mononuclear cells (PBMCs) from patients with psoriasis and healthy controls. Results: We identified several deregulated miRNAs in the blood from patients with psoriasis including miR-223 and miR-143 which were found to be significantly upregulated in the PBMCs from patients with psoriasis compared with healthy controls (FCH=1.63, P<0.01; FCH=2.18, P<0.01, respectively). In addition, miR-223 and miR-143 significantly correlated with the PASI score (r = 0.46, P<0.05; r=0.55, P<0.02, respectively). Receiver-operating characteristic analysis (ROC) showed that miR-223 and -143 have the potential to distinguish between psoriasis and healthy controls (miR-223: Area under the curve (AUC) = 0.80, miR-143: AUC = 0.75). Interestingly, after 3-5 weeks of treatment with methotrexate following a significant decrease in psoriasis severity, miR-223 and miR-143 were significantly downregulated in the PBMCs from patients with psoriasis. Conclusion: We suggest that changes in the miR-223 and miR-143 expressions in PBMCs from patients with psoriasis may serve as novel biomarkers for disease activity in psoriasis; however, further investigations are warranted to clarify their specific roles. In the present study, we compared the global miRNA expression profile between whole blood samples obtained from 24 patients with psoriasis (5 samples were excluded due to poor quality control) compared with 15 healthy controls.
2014-06-10 | E-GEOD-55515 | biostudies-arrayexpress
Project description:Expression profiles of microRNAs in neonatal (isolated from day0 newborn rats) and adult rat cardiomyocytes (isolated from 2month old rats) Two condition experiment; Biological replicates: 7 samples of cardiomyocytes from neonatal rats (from independent isolations); 6 samples of cardiomyocytes isolated from adult animals (from independent isolations)
2012-10-13 | E-GEOD-41537 | biostudies-arrayexpress
Project description:Sixth generation ExiqonM-BM-. locked nucleic acid miRCURYM-bM-^DM-" LNA microarrays were used to search and validate some unidentified miRNAs that regulate EMT in head and neck cancer carcinoma. MiRNA array screening was performed to identify the differential expression of miRNAs involved in EMT in natural epithelial - mesenchymal phenotype cell line pairM-oM-<M-^HHN-4, HN-12) and in TGF-M-NM-2 induced EMT models (HN-4 TGF-M-NM-2,HN-4). HN-4 parental cell was served as the control.One M-BM-5g total RNA from sample and control was labeled with Hy5M-bM-^DM-" and Hy3M-bM-^DM-" fluorescent label, respectively, using the miRCURYM-bM-^DM-" LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer.
2012-06-04 | E-GEOD-38459 | biostudies-arrayexpress
Project description:Results Platelets in non-diabetic patients demonstrated miRNA expression profiles comparable to previously published data. The miRNA expression profiles of platelets in diabetics were similar. Statistical analysis unveiled only three miRNAs (miR-377-5p, miR-628-3p, miR-3137) with high reselection probabilities in resampling techniques, corresponding to signatures with only modest discriminatory performance. Functional annotation of predicted targets for these miRNAs pointed towards an influence of diabetes mellitus on mRNA processing. Conclusions/interpretation We did not find any major differences in platelet miRNA profiles between diabetics and non-diabetics. Minor differences pertained to miRNAs associated with mRNA processing. Thus, previously described differences in plasma miRNAs between diabetic and nondiabetic patients cannot be explained by plain changes in the platelet miRNA profile. Platelet miRNA profiles were assessed in clinically stable diabetic and nondiabetic patients (each n=30). Platelet miRNA was isolated from leucocyte-depleted platelet-rich plasma, and miRNA profiling was performed using LNA micro-array technology (miRBase 18.0, containing 1,917 human miRNAs). Effects of diabetes mellitus were explored by univariate statistical tests for each miRNA, adjusted for potential confounders, and by developing a multivariable signature, which was evaluated by resampling techniques. Platelet phenotype was assessed by light transmission aggregometry and impedance aggregometry.
2014-03-14 | E-GEOD-44093 | biostudies-arrayexpress