Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

DeepCAGE and DeepSAGE with proliferating and differentiated C2C12 mouse myoblasts

ABSTRACT: We use tag-based next generation sequencing analysis to quantify gene expression levels during myogenic differentiation and focused on the identifcation of novel 3' ends with DeepSAGE and novel 5' ends with DeepCAGE. Illumina DeepCAGE and DeepSAGE with C2C12 cells at time points T0 (proliferating) and T9 (differentiated) days of differentiation.

ORGANISM(S): Mus musculus

SUBMITTER: Peter 't Hoen

PROVIDER: E-GEOD-21580 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies.

Hestand Matthew S MS Klingenhoff Andreas A Scherf Matthias M Ariyurek Yavuz Y Ramos Yolande Y van Workum Wilbert W Suzuki Makoto M Werner Thomas T van Ommen Gert-Jan B GJ den Dunnen Johan T JT Harbers Matthias M 't Hoen Peter A C PA

Nucleic acids research 20100707 16

Next-generation sequencing is excellently suited to evaluate the abundance of mRNAs to study gene expression. Here we compare two alternative technologies, cap analysis of gene expression (CAGE) and serial analysis of gene expression (SAGE), for the same RNA samples. Along with quantifying gene expression levels, CAGE can be used to identify tissue-specific transcription start sites, while SAGE monitors 3'-end usage. We used both methods to get more insight into the transcriptional control of my ...[more]

PMID: 20615900

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Project description:High-fat diet or exposure to saturated fatty acids affects skeletal muscle growth and function. The aim of the present study was to investigate the effect of palmitate on the transcriptomic profile of mouse C2C12 myoblasts. Global gene expression was evaluated using whole mouse genome oligonucleotide microarrays, and the results were validated through real-time PCR. A total of 4047genes were identified as differentially expressed, including 3492 down-regulated and 555 up-regulated genes during 48-h-exposure to palmitate (0.1 mmol/l). Functional classification showed the involvement of PA-regulated genes in several processes which regulate cell growth. In conclusion, palmitate modifies the expression of genes associated with: i) myoblast responsiveness to hormones and growth factors, ii) cytokine and growth factor expression, and iii) regulation of cell-cell cell-matrix communication. Such alterations can affect myoblast growth and differentiation, however further studies in this field are required. To whom the correspondence should be addressed: Dr K. Grzelkowska-Kowalczyk; e-mail: k_grzel_kow@poczta.fm, tel/fax: (48 22) 847 24 52 After scanning of hybridized microarrays, quantitation of slide images was performed using Feature Extraction Software (Agilent) using default parameters and the raw data were exported to GeneSpring GX 12 (Agilent, Santa Clara, CA) and log2 transformed. For identification of genes significantly altered in cell compared with the control normal gene set. Total detected entities were filtered by flags (detected, non detected) and error (coefficient of variation: CV < 50.0 percent) to remove very low signal entities and to select reproducible signal values of entities among the replicated experiments, respectively. In statistical analysis, separated for experiment with myoblasts treated with palmitate acid was used t-test unpaired (p < 0.05) with multiple testing correction: Benjamini-Hochberg <0.05, all significant changes over fold change 1.6 were selected.

Dataset Information

DeepCAGE and DeepSAGE with proliferating and differentiated C2C12 mouse myoblasts

Publications

Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies.

Similar Datasets

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