Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-Seq comparing murine intestinal smooth muscle under healthy intestinal epithelium (WT mice) and intestinal smooth muscle under a lawn of intestinal tumors (ApcMin mice)

ABSTRACT: Intestinal smooth muscle was dissected from the jejununal-ileal region of 3 WT mice and 3 ApcMin mice to see gene expression differences between smooth muscle growing directly under tumors and smooth muscle growing under healthy epithelium.

INSTRUMENT(S): Illumina NovaSeq X

ORGANISM(S): Mus musculus

SUBMITTER: Rouan Yao

PROVIDER: E-MTAB-17036 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Smooth muscle cells (SMCs) are important in a number of physiological systems and organs, including the cardiovascular system. The hallmark property of differentiated SMCs is the ability to contract, but contractile SMCs themselves show a range of phenotypes allowing prolonged tonic contraction in vascular smooth muscle or rapid phasic contraction in tissues such as bladder. Another distinctive characteristic, in contrast with terminally differentiated striated muscle cells, is that SMCs exhibit phenotypic plasticity. Vascular SMCs are able to modulate their phenotype along a continuum between a contractile phenotype, characteristic of healthy blood vessels, and a more proliferative âsyntheticâ phenotype, so-named for the enhanced synthesis and secretion of extracellular matrix components. Synthetic phenotype cells are found in a number of pathological situations such as atherosclerosis and arterial injury. We used mouse exon-junction (MJAY) arrays to gain insights into both the global contribution of alternative splicing events in re-shaping the transcriptome of dedifferentiating mouse aorta and bladder SMCs, and into the underlying regulatory mechanisms of the alternative splicing program. Affymetrix splice junction arrays (MJAY) were used to profile changes in both alternative splicing and transcript levels during the phenotypic modulation of smooth muscle cells when placed in culture. RNA extracted from intact aorta and bladder smooth muscle tissue was used for differentiated samples. For dedifferentiated, proliferative samples smooth muscle cells were enzymatically dispersed and grown in tissue culture for a week. Triplicate RNA samples were prepared from smooth muscle tissue of mouse aorta and bladder (differentiated) and from smooth muscle cells from each tissue cultured for 7 days (proliferative). The samples allowed comparison of alternative splicing (and other transcriptome) changes between differentiated and proliferative smooth muscle cell samples from two distinct types of smooth muscle cell, as well as allowing direct comparison of aorta (tonic smooth muscle) and bladder (phasic smooth muscle).

Dataset Information

RNA-Seq comparing murine intestinal smooth muscle under healthy intestinal epithelium (WT mice) and intestinal smooth muscle under a lawn of intestinal tumors (ApcMin mice)

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