Transcriptomics

Dataset Information

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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: Matthew S Hestand  Peter A 't Hoen   Peter A.C. 't Hoen    

PROVIDER: E-GEOD-21580 | ArrayExpress | 2010-07-06

SECONDARY ACCESSION(S): SRP002400GSE21580PRJNA127015

REPOSITORIES: GEO, ArrayExpress, ENA

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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]

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