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Epithelium transition profile

ABSTRACT: Transcriptional Profiling of the Transition from Normal Intestinal Epithelia to Adenomas and Carcinomas in the APC(Min/+) Mouse. Samples used in analysis: * GSM6191-GSM6196 (WT): Ilea epithelial cells from C57/BL6 wild-type samples * GSM6197-GSM6201 (Adenoma): Epithelial cells from crypts of adenomas of APC(Min/+) mice * GSM6202-GSM6206 (Carcinoma): Epithelial cells from crypts of carcinomas of APC(Min/+) mice Using a PixCell IIe instrument (Arcturus), ~30,000 laser firings per sample were used to collect cells of interest. RNA was extracted from captured cells by PicoPure (Arcturus) technique, followed by 2 rounds of RiboAmp amplification (Arcturus), with incorporation of biotinylated nucleotides (Enzo) in the IVT of round 2. All protocols were as per manufacturers instructions. 15ug of labeled cRNA from individual samples were hybridized to respective MG_U74Av2 chips (Affymetrix) and washed/stained using the standard EukGEWS2v4 protocol (Affymetrix). Chips were scanned and analyzed using MAS 5 (Affymetrix) and data scaled to TI=500. Pairwise comparisons using the Mann-Whitney test were performed in DMT 3 (Affymetrix), comparing: * WT vs Adenoma (n=6 x n=5; 83.3% concordance) * WT vs Carcinoma (n=5 x n=5; 84% concordance) * Adenoma vs Carcinoma (n=5 x n=5; 84% concordance) This resulted in the identification of differentially expressed transcripts. Fold changes were calculated from signal-log-ratios. Identified transcripts were clustered based on functional information which was publicly available at time of analysis, obtained through the NetAffx web portal (Affymetrix). Keywords = colon cancer Keywords = gene expression Keywords = DNA microarrays Keywords = beta-catenin Keywords = familial adenomatous polyposis Keywords: ordered

ORGANISM(S): Mus musculus

PROVIDER: GSE422 | GEO | 2003/09/12

SECONDARY ACCESSION(S): PRJNA84985

REPOSITORIES: GEO

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Project description:Transcriptional Profiling of the Transition from Normal Intestine to Adenoma in the APC(Min/+) Mouse. Tissue was from male 91-days old APC(Min/+) mouse (an animal model for human colon cancer). RNA was purified using Trizol and labeled for hybridization to high density oligonucleotide Affymetrix MG_U74Av2 arrays, using manufacturer protocol. We measured the relative expression level of >12000 genes and ESTs. ----------------------------------------- Samples used in analysis: * GSM12501: Normal intestine diet #1 sample C1_0112 Dnmt+/- Min/+ * GSM12502: Tumor diet #1 sample T1_0112 Dnmt+/- Min/+ * GSM12503: Normal intestine diet #1 sample C2_0112 Dnmt+/+ Min/+ * GSM12504: Tumor diet #1 sample T2_0112 Dnmt+/+ Min/+ * GSM12505: Normal intestine diet #2 sample C1_003 Dnmt+/- Min/+ * GSM12506: Tumor diet #2 sample T1_003 Dnmt+/- Min/+ * GSM12507: Normal intestine diet #2 sample C2_003 Dnmt+/+ Min/+ * GSM12508: Tumor diet #2 sample T2_003 Dnmt+/+ Min/+ * GSM12509: Normal intestine diet #3 sample C1_005 Dnmt+/- Min/+ * GSM12510: Tumor diet #3 sample T1_005 Dnmt+/- Min/+ * GSM12511: Normal intestine diet #3 sample C2_005 Dnmt+/+ Min/+ * GSM12512: Tumor diet #3 sample T2_005 Dnmt+/+ Min/+ - - - - - - - - - - - - - - - - - - - - - Comparisons were performed as described in Chen Z, Ge B, Hudson TJ and Rozen R. Gene Expression Patterns 1, 89-93, 2002. Comparing Normal intestine vs Adenoma. - - - - - - - - - - - - - - - - - - - - - This resulted in the identification of differentially expressed transcripts. Identified transcripts were clustered based on functional information which was publicly available at time of analysis, obtained through the NetAffx WEB portal (www.Affymetrix.com) and literature. Keywords = Mouse Keywords = Min Keywords = normal Keywords = intestine Keywords = tumor Keywords = tumour Keywords = colon cancer Keywords = gene expression Keywords = beta-catenin Keywords = high density oligonucleotide microarrays Keywords = familial adenomatous polyposis Keywords = FAP Keywords = colorectal cancer Keywords = Affymetrix MGU74Av2 GeneChip probe array Keywords = mouse model Keywords = APC Keywords = adenomatous polyposis coli Keywords: ordered

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Epithelium transition profile

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