Affymetrix GeneChip™ Canine Gene 1.1ST Array of Quiescent and activated canine valvular interstitial cell under TGFB1 and SB431542 treatment
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ABSTRACT: Quiescent canine valvular interstitial cells (n=3) and activated valvular interstitial cells (n=3) were grown in 2% FBS. Quiescent cells were treated with either TGFB1 or vehicle for 3 days and activated cells were treated with SB431542 for 4 days. mRNA was extracted using the qiagen RNeasy minikit and assessed by the agilent 2200 bioanalsyser. all samples passed quality control and transcriptomic analysis was performed by edinburgh genomics using the Affymetrix GeneChip™ Canine Gene 1.1ST Array. Results were reported as CEL files and then analysed in Affymetrix expression console (version 1.4.1.46) using the canine 1.1ST library files from Affymetrix. Robust Multi-array Average (RMA) was used to perform gene level normalisation and signal level summarisation.Following this, quality control assessment was performed on the data set. This included assessment of hybridisation (spike in) controls, labelling (poly-A) controls and area under the curve (AUC) control, probe cell intensity boxplots, a signal histogram graph and principle component analysis (PCA) plot. Following this assessment, the datasets were exported with annotation as a text file or as a CHT file. Affymetrix transcriptome analysis console (version 3.1.0.5) was used to perform paired or unpaired one-way analysis of variance (ANOVA).
INSTRUMENT(S): GeneTitan® multi-channel instrument, RNeasy minikit
ORGANISM(S): Canis lupus familiaris
SUBMITTER: Greg Markby
PROVIDER: E-MTAB-8096 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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