We aimed to compare the gene expression profiles of patients with degenerative MR in SR and AFib. We used Affymetrix human gene expression microarrays for each atrium sample. We chose most homogenous groups to compare, cause of the noise overshadows in high-throughput analysis when investigating complex diseases.
No associated publication
Specimen part, Disease, Disease stage
View SamplesToll-like receptors (TLR), pattern-recognition receptors responsible for the recognition of various microorganisms and tissue-derived danger signals, are indispensable components of the innate immune system. It is important to note that the expression of TLRs during fetal period is developmentally regulated in such a way that the expression of TLRs increases in a steady-state manner with increasing fetal weight. Although it is well established that assisted reproduction is associated with reduced fetal growth in various species, it remains to be determined whether or not ART alters the expression of TLRs as well as genes involved in TLR-signaling pathway within this critical period of life. Given that the portal of pathogen entry into a neonate is primarily through the respiratory tract, we aimed in the present study to test if the expression of genes involved in TLR-signaling pathway is altered in the lung tissue of fetuses generated through in vitro culture and embryo transfer.
No associated publication
Sex, Specimen part
View SamplesThe use of nucleic acids from formalin-fixed paraffin-embedded (FFPE) tissues for high-throughput molecular techniques, such as microarray gene expression profiling has become widespread in molecular research area. However, working with FFPE tissues is challenging because of degradation, cross-linking with proteins, and RNA chemical modifications. Also, there is no generally accepted procedure for RNA extraction to microarray analysis. Thus, there is a need for a standardized workflow for FFPE samples to study microarray transcriptome profiling. Therefore, the main purpose of this study was to conduct a standardized process from deparaffinization to RNA extraction and microarray gene expression analysis. Firstly, deparaffinization procedure was optimized for FFPE samples and then Trizol, PicoPure RNA isolation kit, and Qiagen RNeasy FFPE kit performances were compared in terms of yield and purity. Finally, two different cRNA/cDNA preparation and labeling protocols with two different array platforms (Affymetrix Human Genome U133 Plus 2.0 and U133_X3P) were also evaluated to determine which combination gives the best percentage of present call. Our optimization study shows that the Qiagen RNeasy FFPE kit with modified deparaffinization step gives better results (RNA quantity and quality) than the other two isolation kits. The Ribo-SPIA protocol and U133_X3P array combination gave a significantly higher percentage of present calls than the 3 IVT cDNA amplification and labeling system. However, no significant differences were found between the two array platforms. These results present a workflow for microarray gene expression profiling of FFPE tissues. The findings also indicate that sufficient quality gene expression data can be obtained from FFPE-derived RNA.
Optimization of gene expression microarray protocol for formalin-fixed paraffin-embedded tissues.
Specimen part
View SamplesGrapevine rootstock 1616C shoots were sterilized and cultured on Murashige & Skoog (MS) medium containing 2% sucrose (w/v). Plantlets were grown in a growth chamber with a 16-h light/8-h dark cycle for 10 weeks at 25 °C.
Salt stress induces endoplasmic reticulum stress-responsive genes in a grapevine rootstock.
Specimen part, Time
View SamplesThe purpose of this study was to characterize the transcriptional effects induced by subcutaneous IFN-beta-1b treatment (Betaferon, 250 g every other day) in patients with relapsing-remitting form of multiple sclerosis (MS).
Long-term genome-wide blood RNA expression profiles yield novel molecular response candidates for IFN-beta-1b treatment in relapsing remitting MS.
Sex
View SamplesThis SuperSeries is composed of the SubSeries listed below.
No associated publication
Specimen part
View SamplesGene expression profile comparison from fibroblasts of Huntington individuals and normal ones
Gene expression profile in fibroblasts of Huntington's disease patients and controls.
Sex, Age, Specimen part, Disease
View SamplesComparison of the differential expression mRNA profiles from the brain cortex of hypoxia and normaixa rats by silica microarray chip
No associated publication
Specimen part
View SamplesBone mineral density and structure candidate gene analysis in alcohol-non-preferring (NP), alcohol-preferring (P), congenic NP (NP.P) and congenic P (P.NP) rats
Identification of genes influencing skeletal phenotypes in congenic P/NP rats.
No sample metadata fields
View SamplesFemoral neck bone mineral density and structure candidate gene analysis in Fischer 344 (F344) and Lewis (LEW) rats
Genomic expression analysis of rat chromosome 4 for skeletal traits at femoral neck.
No sample metadata fields
View Samples