Rat colonic tissue transcriptome with dietary intervention by freeze-dried baby spinach (10% w/w in AIN-93 diet)
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PROVIDER: PRJNA746797 | ENA |
REPOSITORIES: ENA
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Project description:Polyposis in rat colon (Pirc) model harbors an Apc mutation and mimics human Familial Adenomatous Polyposis (FAP), allowing for intervention studies (e.g., PMID: 27706811, PMID: 30643017). RNA-sequencing of adenomatous polyps and normal colon identified genes altered by dietary spinach consumption.
2021-09-22 | GSE180160 | GEO
Project description:To demonstrate the tolerance of mammalian sperm nucleus against extreme environments, mouse spermatozoa were freeze-dried and treated with 95 °C for 1 h or irradiated at over 5 Gy. Although all sperm were ostensibly dead after rehydration, healthy offspring were obtained from recovered sperm nuclei. The normality of those offspring were examined by microarray, and no difference were detected compare to fresh control offspring.
2021-06-16 | GSE117740 | GEO
Project description:The zebrafish embryo has repeatedly proved to be a useful model for the analysis of effects by environmental toxicants. This study was performed to investigate if an approach combining mechanism-specific bioassays with microarray techniques can obtain more in-depth insights into the ecotoxicity of complex pollutant mixtures as present, e.g., in freeze-dried whole sediment samples and their corresponding organic extracts in parallel. To this end, altered gene expression was compared to data from established bioassays as well as to results from chemical analysis. Microarray analysis revealed several classes of significantly regulated genes which could to a considerable extent be related to the hazard potential. Results indicate that potential classes of contaminants can be assigned to sediment extracts by both classical biomarker genes and corresponding expression profile analyses of known substances. However, it is difficult to distinguish between specific responses and more universal detoxification of the organism. Additionally, different gene expression was shown to be less influenced by the sampling site than by the method of exposure, which could be attributed to differential bioavailability of contaminants. Microarray analyses were performed with early life stages of zebrafish exposed to sediment extracts or freeze-dried sediment from three sampling sites (Ehingen, Lauchert, Sigmaringen) along the Upper part of the Danube River, Germany. The expression profiles were compared within the sampling sites, between the exposure scheme and to the expression pattern of model toxicants, such as 4-chloroaniline, Cadmium, DDT, TCDD, and Valproic acid (Gene Expression Omnibus Series GSE9357). Additionally, mechanism-specific bioassays and chemical analysis of the sediments have been combined and compared to the present gene expression data.
2012-12-31 | E-GEOD-31400 | biostudies-arrayexpress
Project description:Freeze-dried mouse sperm nucleus has tolerance against extreme environments
| PRJNA483053 | ENA
Project description:The zebrafish embryo has repeatedly proved to be a useful model for the analysis of effects by environmental toxicants. This study was performed to investigate if an approach combining mechanism-specific bioassays with microarray techniques can obtain more in-depth insights into the ecotoxicity of complex pollutant mixtures as present, e.g., in freeze-dried whole sediment samples and their corresponding organic extracts in parallel. To this end, altered gene expression was compared to data from established bioassays as well as to results from chemical analysis. Microarray analysis revealed several classes of significantly regulated genes which could to a considerable extent be related to the hazard potential. Results indicate that potential classes of contaminants can be assigned to sediment extracts by both classical biomarker genes and corresponding expression profile analyses of known substances. However, it is difficult to distinguish between specific responses and more universal detoxification of the organism. Additionally, different gene expression was shown to be less influenced by the sampling site than by the method of exposure, which could be attributed to differential bioavailability of contaminants.
2012-12-31 | GSE31400 | GEO
Project description:Clostridium tyrobutyricum strain:Cirm BIA 2237 | isolate:Freeze-dried stock Genome sequencing
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Project description:We report the human homologous microRNA profiles in food-grade, bovine-sourced sirloin, heart and adrenal tissue (raw, cooked, and laboratory-prepared pasteurized, freeze-dried extracts) Deep miRNA sequencing of sirloin (raw and cooked), heart tissue (raw, cooked, and pastuerized, freeze-dried extracts) and adrenal tissue (raw, cooked, and laboratory-prepared pasteurized, freeze-dried extracts), 3 replicates each process group
2015-09-02 | E-GEOD-69874 | biostudies-arrayexpress
Project description:We report the human homologous microRNA profiles in food-grade, bovine-sourced sirloin, heart and adrenal tissue (raw, cooked, and laboratory-prepared pasteurized, freeze-dried extracts)
2015-09-02 | GSE69874 | GEO
Project description:Purpose: The goal of this study was to determine the microRNA (miRNA) content of extracellular vesicles (EVs) derived from murine mesenchymal stem cells (mMSC), and evaluate reproducibility among distinct EV productions. We also aimed at assessing the effect of freeze-drying on EV miRNA content, by performing sequencing on freeze-dried EVs and calculating statistical difference between unmodified and freeze-dried EVs. Methods: mMSC-derived EVs were obtained from mMSC in culture in reduced serum medium Opti-MEM by differential centrifugation, with a final step at 100,000 g for 110 min at 4°C. EV pellets (freeze-dried (n=3) or not (n=2)) were resuspended in Qiazol lysis buffer and RNA was extracted following RNeasy Micro kit. cDNA libraries for sequencing were prepared using the TruSeq Small RNA Sample Preparation Kit. Amplified cDNA constructs were purified on 6 % PAGE gel and DNA molecules corresponding to 15–50 nucleotide transcripts were excised, eluted from gel, and concentrated. Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component (Illumina). Before statistical analysis, genes with less than 15 reads (cumulating all the analysed samples) were filtered out. Differentially expressed miRNA were identified using three Bioconductor packages: edgeR, DESeq and DESeq2. Results: Considering miRNAs detected with at least 5 counts (in terms of normalised counts), 339 miRNAs were identified and miRNA content was highly conserved among the two batches tested, with 237 miRNAs out of the 339 present in both batches (70%). Statistical analysis did not evidence statistical difference between unmodified EVs (n=2) and freeze-dried EVs (n=3) (DESeq2, p<0.05). No statistical difference was found using other Bioconductor packages DESeq and edgeR. These results indicated conservation of miRNA content following freeze-drying. Conclusion: mMSC-EV miRNA content was comparable between the two EV productions analysed, indicating reproducibility. Some of the miRNAs identified were consistent with previously published results on MSC-derived EVs. Freeze-drying conserved miRNA content.
2019-12-09 | GSE140479 | GEO
Project description:Frozen dough baking is useful method in the modern bread-making industry. However, the fermentation activity of baker’s yeast dramatically decreased after thawing due to freeze injuries, because baker’s yeast cells contained in dough experience freeze injuries during freeze-thaw processes. Here, we performed genome-wide expression analysis to determine genetic response in baker’s yeasts under freeze-thaw condition using a DNA microarray analysis. Functional and clustering analyses in gene expression reveal that genes could be characterized by the term of freeze-thaw stress. Under short-term freeze stress (freeze treatment for 3 day), genes involved in ribosomal protein were up-regulated. Under long-term freeze stress (freeze treatment for longer than 7 day), genes involved in energy synthesis were up-regulated. In each phase, genes involved in protein damage, several stresses and trehalose and glycogen metabolism were also up-regulated. Through these freeze stress, yeast cells may improve reduced efficiency of translation and enhanced cell protection mechanism to survive under freeze stress condition. These regulations of these genes would be controlled by the cAMP-protein kinase A pathway. Keywords: baker’s yeast, freeze-thaw stress, gene expression, freezing period
2009-07-31 | GSE8673 | GEO