Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of mouse stem cell differentiation

ABSTRACT: Stem cell development requires selection of specific genetic programs to direct cellular fate. Using microarray technology, we profile expression trends at selected timepoints during stem cell differentiation to characterize these changes. Experiment Overall Design: Total RNA was isolated using the Micro-to-Midi isolation kit (Invitrogen), and subjected to comparative gene expression profiling by labelled cRNA hybridization to the mouse genome 430 2.0 microarray (Affymetrix). Data acquired using the GeneChip Scanner 3000 was analyzed with the Genespring GX 7.3 microarray data software bioinformatics suite (Agilent Technologies) restricting the derived gene list to identify differentially expressed genes defined by a >1.5-fold difference and P<0.05. Data population sets were normalized to the undifferentiated phenotype, and quality filtered to eliminate background noise prior to hierarchical clustering.

ORGANISM(S): Mus musculus

SUBMITTER: Atta Behfar

PROVIDER: E-GEOD-6689 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:purose:The large-scale reproduction of Phaeocystis globosa has caused serious damage to the marine ecosystem in the coastal waters of China. The outbreak of algae blooms depends on the competitive advantage of their heteromorphic life history: colonial formation is beneficial to resist zooplankton predation, and the single isolated cells can absorb nutrients rapidly. To better understand the different types of cells characteristics of P. globosa that facilitate rapid expansion, single isolated cells (GX-S) and colonial cells (GX-C) are separated by filtration. methods:For RNA exaction, the biomass was resuspended in 2 mL RNA extraction buffer (1:1 mix of aqua-phenol and buffer L [0.5% SDS, 10 mM EDTA, 0.2 M sodium acetate (pH 5), and 1:100 β-mercaptoethanol)] and then incubated with DNase I (Takara, Japan) for 30 min at 37 °C to remove genomic DNA. RNA quality analysis, library construction, sequencing, data filtering and mapping were performed by the Novogene Bioinformatics Technology Co., Ltd. (Beijing, China). mRNA profiles of 10 days GX-C and GX-S were generated by deep sequencing, in triplicate. results:Three biological replicates from GX-S and GX-C were ensured statistical comparability and reliability of data. Raw data ranged from 25, 608,632 to 35,516,726 reads per sample. After producing more than 24 million clean reads, removing low-quality sequences and adapter sequences. Additionally, 4386 genes were differentially expressed at statistically significant levels, which included 2268 up-regulated genes and 2118 down-regulated genes. Genes with significant differential expression were involved in several pathways, including starch and sucrose, phagosome, inositol phosphate metabolism, fatty acid degradation. conclusions: In summary, we can find that colonial cells have stronger carbon fixation capacity. It is not used to synthesize fatty acids as reserves of energy, but to secrete EPS. The reduction of fatty acid makes P. globosa become “low-quality food” and the formation of colony from EPS reduces the chance of being ingestion by zooplankton.

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Transcription profiling of mouse stem cell differentiation

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