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Sample GSM189852 Query DataSets for GSM189852
Status Public on Feb 12, 2008
Title Colon adenocarcinoma (11692T)
Sample type RNA
 
Source name 11692T
Organism Homo sapiens
Characteristics Tissue: Colon
Disease state: colon adenocarcinoma
Individual: 11692
Clinical info: Follow up status: Alive or censored
Extracted molecule total RNA
Extraction protocol OSU - Tri-Reagent Protocol
Other: RNA isolation was performed using TRIZOL Reagent (Invitrogen, Carlsbad) according to manufacturer's instructions. Briefly, colon tissue was homogenized in TRIZOL reagent and chloroform was added and liquid phases were separated with centrifugation. The supernatant was collected and RNA was precipitated with isopropanol washed with 75% ethanol. RNA was resuspended in DEPC treated water and 5 micrograms were used for each microarray experiment.
Label alexa 647
Label protocol OSU - Labeling Protocol
Other: Processed by using a method of direct detection of the biotin-containing transcripts by streptavidin-Alexa647 conjugate.
 
Hybridization protocol OSU - Sample Hybridization Protocol
Qty. of labeled target: 5 ug of total RNA
Other: Labeled targets from 5ug of total RNA were used for hybridization on each miRNA microarray chip containing human and mouse miRNA genes. All probes on these microarrays are 40-mer oligonucleotides spotted by contacting technologies and covalently attached to a polymeric matrix. The microarrays were hybridized in 6x SSPE (0.9 M NaCl / 60 mM NaH2PO4 H20 / 8 mM EDTA, pH 7.4) / 30% formamide at 25C for 18 hr, washed in 0.75x TNT (Tris HCL/NaCl/Tween 20) at 37C for 40 min.
Scan protocol OSU - Scanning Protocol
Other: Processed slides were scanned by using a PerkinElmer ScanArray XL5K Scanner, with the laser set to 635 nm, at Power 80 and PMT 70 setting, and a scan resolution of 10 um.
Description No additional information.
Data processing Data Processing Protocol
Calculation Method: The microarrays used for this analysis were pin-spotted microRNA microarrays (from the Ohio State University Comprehensive Cancer Center, version 2.0). Intensities of each spot were the median intensities of foreground. Each of 170 microarrays used for this study contained 11520 spots. All spots where foreground intensity was less than background were reassigned as NA (NA marks missing data spots). All spots flagged as deficient by the scanner were also reassigned as NA. All blank (no oligo) spots with high foreground intensity were reassigned as NA. Each microRNA oligo is represented by quadruplicate spots on these arrays as two distant pairs of two adjacent spots. If there were 0 or 1 NA for an oligo quadruple, and the means of the distant oligo pairs differed by > 1 on the log2 scale, all of the quadruplicate spots were reassigned as NA. If there were 2 NAs for an oligo quadruple and the two non-NA spot intensities differed by > 1 on the log2 scale, all of the quadruplicate spots were reassigned NA. If there were 3 NA spots for a quadruple, the final spot was reassigned as NA. In total, 1,082,689 of 1,958,400 spots were reassigned as NA using these methods. LOESS (Locally Weighted Scatterplot Smoothing) normalization was performed using the R software package. All data was then imported into BRB array tools version 3.5.0 for analysis and all replicate spots were averaged. There were originally 85 pairs (tumor and paired nontumorous tissue) of arrays used. One case that was originally identified as an incident colon carcinoma patient was later found to have been diagnosed as carcinoma in situ and was removed from the analysis leaving the study population of 84 subjects.
 
Submission date May 17, 2007
Last update date Feb 12, 2008
Contact name Curtis C Harris
E-mail(s) Curtis_Harris@nih.gov
Phone (301) 496-2048
Fax (301) 496-0497
Organization name National Cancer Institute
Department Center for Cancer Research
Lab Laboratory of Human Carcinogenesis
Street address Building 37, Room 3068A
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL4700
Series (1)
GSE7828 MicroRNA profiles of 84 colon adenocarcinomas and paired nontumorous

Data table header descriptions
ID_REF unique spot id
VALUE same as UNF_VALUE but with flagged values removed
Slide_block Array block location
Slide_column Array column location
Slide_row Array row location
Sample_median Sample median Intensity
Sample_mean Sample mean Intensity
Sample_SD Sample Standard Deviation
Sample_BKD_median Sample median Background Level
Sample_BKD_mean Sample mean Background Level
Sample_BKD_SD Sample Background Standard Deviation
Flag Quality flag measure
UNF_VALUE Sample median Intensity

Data table
ID_REF VALUE Slide_block Slide_column Slide_row Sample_median Sample_mean Sample_SD Sample_BKD_median Sample_BKD_mean Sample_BKD_SD Flag UNF_VALUE
1-1-1 282 1 1 1 282 299 147 143 156 84 0 282
1-1-2 1 1 2 167 178 89 136 149 80 -50 167
1-1-3 1 1 3 162 173 90 132 149 80 -50 162
1-1-4 1 1 4 158 162 85 138 150 81 -50 158
1-1-5 1 1 5 185 189 105 134 143 80 -50 185
1-1-6 1 1 6 148 162 78 136 146 83 -50 148
1-1-7 1 1 7 141 149 83 134 147 82 -50 141
1-1-8 653 1 1 8 653 701 280 140 149 82 0 653
1-1-9 1 1 9 160 163 83 139 151 82 -50 160
1-1-10 288 1 1 10 288 347 222 141 158 95 0 288
1-1-11 335 1 1 11 335 373 160 145 158 88 0 335
1-1-12 1 1 12 168 171 98 134 148 82 -50 168
1-1-13 1 1 13 150 154 74 141 153 86 -50 150
1-1-14 5288 1 1 14 5288 7224 5059 141 150 87 0 5288
1-1-15 1 1 15 146 158 88 139 152 82 -50 146
1-1-16 1 1 16 144 159 92 137 152 86 -50 144
1-1-17 1 1 17 146 158 82 140 149 80 -50 146
1-1-18 1 1 18 123 146 88 138 148 81 -50 123
1-2-1 301 1 2 1 301 319 150 141 153 84 0 301
1-2-2 1 2 2 178 182 99 132 146 83 -50 178

Total number of rows: 11520

Table truncated, full table size 536 Kbytes.




Supplementary file Size Download File type/resource
GSM189852.txt.gz 418.0 Kb (ftp)(http) TXT
Processed data provided as supplementary file
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