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Sample GSM408711 Query DataSets for GSM408711
Status Public on Jun 08, 2009
Title 1984902_635
Sample type genomic
 
Source name histologically normal human colon tissue obtained from surgery for adenocarcinoma of the colon
Organism Homo sapiens
Characteristics individual: 1984902
tissue: colon
Extracted molecule genomic DNA
Extraction protocol From the frozen tissue, 5 micron thick cryosections were cut, mounted on glass slides, and stained with Hematoxylin and Eosin. Sections were reviewed by a pathologist to confirm the diagnoses of prostatic adenocarcinoma and benign tissue. Areas of tumor were selected where >60% of cells consisted of tumor cells. Areas of benign tissue were selected where >50% of cells consisted of non-neoplastic epithelium. From these areas, two 2 mm punch biopsy cores of frozen tissue were removed from the frozen block and processed for DNA and RNA extraction using a modified Qiagen Allprep DNA/RNA protocol. Briefly, tissue was homogenized in Qiagen buffer RLT with b-mercaptoethanol. Lysates were passed through Allprep DNA columns for purification of DNA. All washes and elution of DNA from the Allprep column were performed per manufacturer’s protocol. Initial flow through from the column was mixed with 3 volumes of Trizol LS reagent (Invitrogen) and processed per manufacturer’s protocol to yield total RNA.
Label Cy5
Label protocol RNA was converted to double-stranded cDNA (SuperScript Double Strand cDNA Synthesis Kit, Invitrogen USA, Carlsbad, CA) with oligo-dT primer (Promega USA) according to the manufacturer’s protocol. Resultant ds-cDNA was labeled using cy3-tagged random 9mers and Klenow fragment for 2h at 37°C, prior to denaturation and hybridization to a microarray. Genomic DNA was labeled using cy5-tagged random 9mers.
 
Hybridization protocol The Cy3- and Cy5-labeled samples were combined (5 ug each) in hybridization buffer, denatured, and hybridized to the custom 8q24 385K feature array using standard hybridization conditions for gene expression (NimbleGen Expression User Guide, Roche NimbleGen, Madison, WI). Slides were then washed and dried using standard conditions per the Roche NimbleGen protocol.
Scan protocol Slides were scanned with a GenePix 4000B Scanner. Initial pre-scannig was performed at PMT Gain = 500 and Power (%) = 100. After the pre-scan, the PMT was adjusted to avoid saturated spots.
Description RNA-normalized signal intensity; a probe was considered positive in the cDNA array when its intensity was higher (> 1) than its genomic DNA probe value.
Data processing Initially, data generated from each group of microarray scans (cDNA and genomic DNA) were normalized separately. Quantile normalization of probe intensities was carried out using the Multi-Array quantile normalization module, part of the NMPP 1.01 package with the two-step normalization option as described by Wang and colleagues (Wang, X. et al. NMPP: a user-customized NimbleGen microarray data processing pipeline. Bioinformatics 2006 22, 2955-7). First, replicate slides within each set were normalized, followed by a global normalization to adjust both sets to an average baseline.
 
Submission date May 26, 2009
Last update date Jun 07, 2009
Contact name Mark Pomerantz
E-mail(s) mark_pomerantz@dfci.harvard.edu
Phone 617-632-1914
Fax 617-632-2165
Organization name Dana-Farber Cancer Institute
Department Medical Oncology
Street address 44 Binney St.
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL8592
Series (1)
GSE16228 RNA expression at chromosome 8q24 in human colon

Data table header descriptions
ID_REF
VALUE Qnormalized signal intensity
SIGNAL_RAW raw signal

Data table
ID_REF VALUE SIGNAL_RAW
CHR08FS125080002 1160.26 912.22
CHR08FS125080009 1219.2 956.33
CHR08FS125080021 1192.74 936.56
CHR08FS125080029 1270.48 994.78
CHR08FS125080036 975.25 775.67
CHR08FS125080050 1057.13 836.56
CHR08FS125080060 1568.5 1212.67
CHR08FS125080063 2576.44 1923.44
CHR08FS125080077 620.25 508.56
CHR08FS125080087 757.07 612.89
CHR08FS125080096 891.2 713.56
CHR08FS125080100 2081.07 1579.11
CHR08FS125080110 999.32 793.44
CHR08FS125080123 1272.42 996.33
CHR08FS125080131 1162.9 914.22
CHR08FS125080145 1165.47 916.22
CHR08FS125080155 2563.68 1914.78
CHR08FS125080162 2916.9 2148.67
CHR08FS125080173 2249.95 1698
CHR08FS125080222 2356.65 1773.22

Total number of rows: 389307

Table truncated, full table size 12202 Kbytes.




Supplementary file Size Download File type/resource
GSM408711.pair.gz 5.9 Mb (ftp)(http) PAIR
Processed data included within Sample table

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