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Sample GSM200182 Query DataSets for GSM200182
Status Public on Jan 05, 2008
Title Pancreatic cancer sample, Sample_ID = 1b, DNA
Sample type genomic
 
Channel 1
Source name genomic DNA from ASO1
Organism Homo sapiens
Characteristics Pancreatic cancer sample, Sample_ID = 1b, DNA
Extracted molecule genomic DNA
Extraction protocol RNA was extracted from four to five 5-um sections using an RNA extraction kit (Roche High Pure RNA Paraffin kit), yielding 0.5 - 3 ug of total RNA.
Label Cy3
Label protocol GoldenGateĀ® assay was done as described previously (Fan JB et al, Illumina Universal bead arrays, 2006)
 
Channel 2
Source name genomic DNA from ASO2
Organism Homo sapiens
Characteristics Pancreatic cancer sample, Sample_ID = 1b, DNA
Extracted molecule genomic DNA
Extraction protocol RNA was extracted from four to five 5-um sections using an RNA extraction kit (Roche High Pure RNA Paraffin kit), yielding 0.5 - 3 ug of total RNA.
Label Cy5
Label protocol GoldenGateĀ® assay was done as described previously (Fan JB et al, Illumina Universal bead arrays, 2006)
 
 
Hybridization protocol Array image processing and signal extraction were done as described previously (Fan JB et al, Illumina Universal bead arrays, 2006)
Scan protocol Arrays were imaged using Illumina BeadArray Reader scanner (Illumina).
Description none
Data processing Image analysis and data extraction software were as described previously (Oliphant, A., Barker, D.L., Stuelpnagel, J.R., and Chee, M.S. 2002. BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. Biotechniques 32: S56-S61.; Galinsky, V.L. 2003. Automatic registration of microarray images II: Hexagonal grid. Bioinformatics 19: 1832-1836.). Each sequence type is represented by an average of thirty beads on the array. Bead signals are computed with weighted averages of pixel intensities, and local background is subtracted. Sequence-type signal is calculated by averaging corresponding bead signals with outliers removed (using median absolute deviation).
 
Submission date Jun 11, 2007
Last update date Nov 13, 2007
Contact name Aik Choon Tan
E-mail(s) actan@jhu.edu
Phone 410-502-8743
Fax 410-614-9006
Organization name Johns Hopkins University
Department The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins
Street address 1650 Orleans Street, RM 1M86
City Baltimore
State/province MD
ZIP/Postal code 21231
Country USA
 
Platform ID GPL5359
Series (2)
GSE8055 Allele-Specific Expression 2
GSE9596 Allele-specific expression in familial pancreatic cancer

Data table header descriptions
ID_REF
VALUE genotype AA/AB/BB
Cy3 ASO1 signal
Cy5 ASO2 signal
log2ratio log2 Cy3/Cy5

Data table
ID_REF VALUE Cy3 Cy5 log2ratio
rs8073904 AB 7002 5146 0.444315604694704
rs1056169 BB 533 29474 -5.78916352276835
rs1056174 BB 547 19949 -5.18863178585114
rs1064152 AA 25592 230 6.7979152261713
rs1064156 BB 542 21633 -5.31879708602001
rs2229068 BB 551 30016 -5.76753560394422
rs2229070 BB 1158 26829 -4.53408612344424
rs7457 BB 1087 25100 -4.52926351869819
rs1318056 BB 728 24175 -5.05343362905287
rs2274230 AA 11860 207 5.84032943193404
rs10206004 AB 4608 7916 -0.7806308956052
rs1134723 AA 13936 2088 2.73862291202898
rs1146031 AA 23221 1662 3.80443781521411
rs2228947 BB 1200 20185 -4.07217727587199
rs6729964 AA 12908 209 5.94861873040606
rs11169974 AB 18291 3147 2.5390848680792
rs11831802 BB 1686 23743 -3.81582579399485
rs2641516 AA 13689 236 5.85808638980497
rs2641529 BB 1568 10711 -2.77209571465335
rs2714 BB 2253 18555 -3.04188878234946

Total number of rows: 1189

Table truncated, full table size 47 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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