E-GEOD-7221 - Comparison of rat thoracic duct to vena cava

Status
Submitted on 7 March 2007, released on 15 May 2010, last updated on 2 May 2014
Organism
Rattus norvegicus
Samples (8)
Array (1)
Protocols (16)
Description
While blood vessels have muscular walls that undergo tonic contractions to alter vascular resistance and, thus, control blood flow, lymphatics at the level of the collecting vessels and higher have muscular walls capable of rapid phasic contractions that generate lymph flow in addition to tonic contractions that regulate lymph flow resistance. While the ability of lymphatics to undergo rapid phasic contractions has been known for several centuries, the biological elements governing this phenomenon remain unknown. In an attempt to gain insight into the structural and regulatory elements that give lymphatic vessels their unique contractile capabilities, we utilized two-color microarray analysis to compare the thoracic duct of the rat to the vena cava of the same donor animal. Total cellular RNA was isolated immediately following vessel isolation and amplified in the presence of amino allyl dUTP. The resulting modified aRNA was conjugated to either Cy3 or Cy5 dye prior to hybridization to a rat 5.7K oligonucleotide array. Analysis and filtering of the data obtained from the microarray image yielded several contractile and regulatory genes with altered expression in the thoracic duct relative to the vena cava. Further evaluation of the data obtained in this study may aid in illustrating the unique properties of the lymphatic vessel and its muscular wall. Keywords: Thoracic duct, lymphatics, microarray Four unique thoracic duct/vena cava sample pairs were individually analyzed via two-color microarray analysis yielding 4 biological replicates. To minimize dye bias, a dye balance design was utilized in which the orientation of dye assignment was alternated between vessel pairs (i.e. two thoracic duct samples were labeled with Cy3 and two were labeled with Cy5). Prior to analysis, the data from 2 of the replicates was transformed to accomodate the dye balance such that all thoracic duct data is interpreted as Cy5 and all vena cava data is interpreted as Cy3.
Experiment type
transcription profiling by array 
Contacts
David C. Zawieja <dcz@tamu.edu>, David C Zawieja, Eric A Bridenbaugh
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-7221.idf.txt
Sample and data relationshipE-GEOD-7221.sdrf.txt
Raw data (1)E-GEOD-7221.raw.1.zip
Processed data (1)E-GEOD-7221.processed.1.zip
Array designA-GEOD-4886.adf.txt
R ExpressionSetE-GEOD-7221.eSet.r
Links