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Sample GSM889220 Query DataSets for GSM889220
Status Public on Mar 08, 2012
Title Sporadic Colorectal Cancer MMR deficient tumors_89
Sample type RNA
 
Source name Colorectal cancer, sporadic
Organism Homo sapiens
Characteristics tissue: colorectal cancer
disease state: sporadic colorectal cancer
age: 83
gender: male
Extracted molecule total RNA
Extraction protocol Three to five 5 μm sections per FFPE block were used for RNA isolation. RNA deparaffinization, extraction and purification were performed using the High Pure RNA Paraffin Kit (Roche, Castle Hill, Australia) according to the manufacturer's instructions. RNA concentration was determined using a NanoDrop Spectrophotometer (NanoDrop Technologies, Wilmington, DE), and samples yielding sufficient RNA (200 ng) with 260/280 ratios >1.8 were selected.
Label Cy3
Label protocol Ligated products were PCR-amplified and labeled with a universal Cy3-coupled primer, after which single-stranded labeled products were precipitated and then hybridized to WG gene expression BeadChips as previously described (Kuhn et al. 2004).
 
Hybridization protocol Standard Illumina hybridization protocol.
Scan protocol Standard Illumina iScan N240 scanning protocol.
Description AM89
Data processing Illumina gene expression data were loaded and interpreted in GenomeStudio software (Illumina, San Diego, CA). Data were normalized using background correction, the cubic spline method and plate scaling. Normalized gene expression data were then exported, and only RefSeq features with a detection P value of ≤0.01 in at least 80% of the samples (n=122) were used in further analyses. Technical replicates within samples were average combined to create one signature per tumor. Next, data were loaded into MeV v4 (Saeed et al. 2003), where they were log2 transformed and median centered across assays. Significance analysis of microarrays (SAM) was used to identify significantly differentially expressed genes (false-discovery rate, FDR ≤ 5%). Hierarchical clustering and SAM were done in MeV (Saeed et al. 2003).
 
Submission date Mar 07, 2012
Last update date Mar 08, 2012
Contact name Mev Dominguez
E-mail(s) mev_dv@yahoo.com
Phone +46 705792722
Organization name Lund University
Department Oncology
Lab BioMedical Center
Street address Klinikgatan 28
City Lund
State/province N/A
ZIP/Postal code SE-221 84, Lund
Country Sweden
 
Platform ID GPL14951
Series (1)
GSE36335 Distinct tumorigenic pathways within hereditary nonpolyposis colorectal cancer

Data table header descriptions
ID_REF
VALUE Cubic-normalized signal
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1762337 1661.177 0
ILMN_2055271 147.7512 0.1827586
ILMN_2383229 731.4047 0
ILMN_1806310 1942.776 0
ILMN_1779670 133.4211 0.6275862
ILMN_1717783 136.7865 0.4931034
ILMN_1814316 136.9151 0.4862069
ILMN_2359168 139.6115 0.3896552
ILMN_1731507 137.2752 0.4655173
ILMN_1787689 140.5296 0.3655172
ILMN_3241953 722.6469 0
ILMN_1745607 13235.83 0
ILMN_2136495 124.7863 0.9827586
ILMN_1668111 126.7074 0.9379311
ILMN_2295559 143.4065 0.2758621
ILMN_1735045 3025.316 0
ILMN_1680754 152.9751 0.1103448
ILMN_2375184 132.8899 0.6689655
ILMN_1659452 153.1714 0.1103448
ILMN_1767388 136.5637 0.5034482

Total number of rows: 29377

Table truncated, full table size 802 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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