Transcriptomics

Dataset Information

2

Scleroderma Architecture Cell Lines


ABSTRACT: The data from these cell lines is described in figure 2 of the mansucript "Systemic and cell-type specific gene expression patterns in scleroderam skin" by Whitfield et al. (2003) PNAS. Aortic smooth muscle cells and microvascular endothelial cells were obtained from Clonetics and cultured in the recommended media; Hs578T myofibroblast-like cells were grown in RPMI-1640 supplemented with phenol red, glutamine (2 mM) and 5% fetal calf serum; HeLa S3 epithelial cells were obtained from the American Type Culture Collection (ATCC) and cultured as described in Whitfield et al., MBC, (2002). Normal, morphea and scleroderma fibroblasts were derived from normal, morphea and scleroderma skin biopsies taken by Dr. Kari Connolly at UCSF. In all cases, RNA was prepared from cells 48 hrs after changing the culture media to avoid the induction of serum responsive genes. Poly(A) RNA from each cell line was reverse-transcribed into Cy5-dUTP (Amersham Pharmacia Biotech, Piscataway NJ) labeled cDNA and reference RNA reverse-transcribed into Cy3-dUTP (Amersham Pharmacia Biotech, Piscataway NJ) labeled cDNA using standard methods. Cells grown in culture were analyzed on cDNA microarrays containing 40,512 elements representing 28,384 UniGene clusters (UniGene Build No. 155, released 9-28-2002) manufactured in the Stanford Microarray Facility (http://www.microarray.org). Equal amounts of Cy5- and Cy3-labeled cDNA were hybridized to spotted cDNA microarrays and scanned using a GenePix 4000A Scanner (Axon Instruments, Union City CA). Detailed protocols are available at http://brownlab.stanford.edu/protocols.html/. Data were extracted by superimposing a grid over each array using GenePix 3.0 software (Axon Instruments, Union City CA). Spots of poor quality, determined by visual inspection, were excluded from further analysis. A cell type comparison design experiment design type compares cells of different type for example different cell lines. Computed

ORGANISM(S): Homo sapiens  

SUBMITTER: Stanford Microarray Database   Michael Whitfield  Jen-Tsan Chi 

PROVIDER: E-GEOD-3887 | ArrayExpress | 2005-12-20

SECONDARY ACCESSION(S): GSE3887PRJNA104865

REPOSITORIES: GEO, ArrayExpress

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