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Sample GSM67209 Query DataSets for GSM67209
Status Public on Jan 19, 2006
Title colon.3
Sample type RNA
Source name colon
Organism Mus musculus
Characteristics Adult C57/BLJ6 Female Mouse
Extracted molecule total RNA
Extraction protocol Extracted using the Invitrogen Micro-to-Midi Total RNA Purification System (Catalog # 12183-018). RNA samples were treated with DNAseI for 30 minutes at 37, extracted twice with phenol/chloroform, once with chloroform and ethanol precipitated.
Label biotin
Label protocol RNA was primed with random hexamers and reverse transcribed. After the reaction was completed, RNA was removed from the reaction by alkaline hydrolysis and the cDNA was purified using Qiagen PCR Quick Purification Kit. A typical reaction started with 5-6ug of total RNA usually yielded ~3ug of cDNA. The cDNA was then fragmented using DNAseI in an empirically controlled reaction that yields DNA fragments of 50-200 bases. This fragmented cDNA was then end labeled using terminal deoxynucleotidyl transferase and "DNA-Labeling-Reagent-1a (DLR-1a)", which is a biotinylated dideoxynucleoside triphosphate.
Hybridization protocol Targets were hybridized to chips in 7% DMSO solution for 16 hrs overnight at 50. Microarrays were washed, processed with anti-biotin antibodies and streptavidin-phycoerythrin according to the standard Affymetrix protocol.
Scan protocol standard Affymetrix procedures
Description Tissue
Data processing Intensity values from the DNA arrays were normalized using a quantile normalization (Bolstad et al., 2003), and probe set summaries were derived using the Robust Multi-chip Analysis (RMA) procedure (Irizarry et al., 2003a; Irizarry et al., 2003b) with two modifications. The first modification was to remove all probes with 17 or more continuous bases that match to any other mouse transcript in order to minimize cross-hybridization issues. The second modification was to use the mode of the probe intensity values of similar GC content probes for the background estimate of a particular probe. For example, if a probe has a GC count of 16, then the mode of the intensity of all the probes with a GC count of 16 was used as a background estimate as opposed to RMA in which the mode of all the probes is used as a background estimate for all the probes.
Submission date Aug 04, 2005
Last update date Jan 19, 2006
Contact name Charles Sugnet
Organization name UC Santa Cruz
Department MCD
Lab Ares
Street address Sinsheimer Labs
City Santa Cruz
State/province CA
ZIP/Postal code 95064
Country USA
Platform ID GPL2720
Series (1)
GSE3063 Mouse Alt-Splice Tissue Panel (Brain vs Non-Brain)

Data table header descriptions
VALUE Probe Set Summary Estimate

Data table
AFFX-18SRNAMur/X00686_3_at 21049.54
AFFX-18SRNAMur/X00686_5_at 22146.77
AFFX-18SRNAMur/X00686_M_at 22517.06
AFFX-b-ActinMur/M12481_3_at 1531.59
AFFX-b-ActinMur/M12481_5_at 1909.05
AFFX-b-ActinMur/M12481_M_at 1547.23
AFFX-BioB-3_at 1059.93
AFFX-BioB-5_at 605.86
AFFX-BioB-M_at 931.15
AFFX-BioC-3_at 1131.41
AFFX-BioC-5_at 1265.25
AFFX-BioDn-3_at 6366.03
AFFX-BioDn-5_at 1703.34
AFFX-CreX-3_at 9303.12
AFFX-CreX-5_at 7548.60
AFFX-DapX-3_at 8.74
AFFX-DapX-5_at 8.27
AFFX-DapX-M_at 12.57
AFFX-GapdhMur/M32599_3_at 624.51
AFFX-GapdhMur/M32599_5_at 663.26

Total number of rows: 59198

Table truncated, full table size 1634 Kbytes.

Supplementary data files not provided

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