Project description:Next-generation sequencing (RNAseq) analysis of gene expression changes during the long-term in vitro culture and osteogenic and chondrogenic differentiation of ADSCs remains to be important, as the analysis provides important clues toward employing stem cells as a therapeutic intervention. In this study, the cells were isolated from adipose tissue obtained during routine surgical procedures and subjected to 14-day in vitro culture and differentiation. The mRNA transcript levels were evaluated using the Illumina platform, resulting in the detection of 19,856 gene transcripts. The most differentially expressed genes (fold change >|2|, adjusted p value < 0.05), between day 1, day 14 and differentiated cell cultures were extracted and subjected to bioinformatical analysis based on the R programming language. The results of this study provide molecular insight into the processes that occur during long-term in vitro culture, osteogenic and chondrogenic differentiation of ADSCs, allowing the re-evaluation of the roles of some genes in MSC progression towards a range of lineages. The results improve the knowledge of the molecular mechanisms associated with long-term in vitro culture and differentiation of ADSCs, as well as providing a point of reference for potential in vivo and clinical studies regarding these cells' application in regenerative medicine.
Project description:We analyzed the difference of gene expression between the isolates havested from long-term cultures (Ma et.al. 2020). In this study, the paradaux cell line were cultured for over 40 days under different population control conditions (uncontrolled, negative feedback and paradoxical feedback. Isolates of each culture were harvested at the end of the long-term culture and preped for whole genomic RNA sequencing.
Project description:Extracellular vesicles isolated from the conditioned media of short, long-term, and rapamycin treated long-term cultured astrocytes were subjected to proteomic analysis to determine the how the EV proteome changes following long-term culture.
2020-05-27 | PXD017058 | Pride
Project description:Whole genome re-sequencing for diatom under long-term ocean warming
Project description:Naïve mouse ESCs exhibit full term developmental competence thus hold great potential in regenerative medicine. Maintaining genome stability is essential for potential application of ESCs in stem cell therapy. While ESC potency fluctuate with retrovirus activity, it is unclear whether long-term cultures affect retrotransposition and genomic stability. We compared retrotransposons in naïve ESCs using various approaches. We show that feeder-serum based culture conditions and small molecule LCDM maintain appropriate expression of retrovirus activity following long-term cultures, whereas cultures under 2iLif and a2i result in aberrant upregulation of retrotransposons. This leads to high frequent retrotransposition. Moreover, naïve ESCs on feeder-serum based culture conditions and small molecule LCDM still generate complete ESC pups by TEC assay, functional test of pluripotency, following long-term cultures, despite that all culture conditions maintain high expression levels of pluripotent genes such as Oct4, Nanog, Klf4 and Sox2. Meanwhile, long telomeres are maintained in ESCs under cultures in Feeder-serum and LCDM conditions but telomeres shortened in other conditions with increasing passages. These data provide insights into retrotransposition, genomic stability and pluripotency of naïve ESCs.
Project description:In this study, we have analyzed DNA methylation changes upon long-term culture and aging of MSC by using the HumanMethylation27 BeadChip assessing 27,578 unique CpG sites. Cells were taken from bone marrow aspirates from iliac crest (BM) of healthy donors or from the caput femoris (HIP) of elderly patients that received femoral head prosthesis.Overall, the methylation pattern was maintained throughout both long-term culture and aging but highly significant differences were observed at specific CpG sites. Notably, methylation changes in MSC were related in long-term culture and aging in vivo.
Project description:The faecal indicator bacterium Escherichia coli K12 was used to study the cellular events that take place at the transcription level using the microarray technology during short-term (physiological) and long-term (genetic) adaptation to slow growth under limited nutrient supply. Short-term and long-term adaptation were assessed by comparing the mRNA levels isolated after 40 or 500 hours of glucose-limited continuous culture at a dilution rate of 0.3 h-1 with those from batch culture with glucose excess. Keywords: glucose-limited continuous culture, adaptation, microarray, high affinity transport systems, transcriptome, Escherichia coli