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Sample GSM242230 Query DataSets for GSM242230
Status Public on May 08, 2008
Title US-1078955 vs. Human Liver 119
Sample type RNA
 
Channel 1
Source name Liver
Organism Homo sapiens
Characteristics US-1078955
Treatment protocol No treatment
Extracted molecule total RNA
Extraction protocol Trizol Lysis + RNeasy Column
Label Cy3
Label protocol One round of RT-IVT to cRNA
 
Channel 2
Source name Liver
Organism Homo sapiens
Characteristics pool
Treatment protocol No treatment
Extracted molecule total RNA
Extraction protocol Trizol Lysis + RNeasy Column
Label Cy5
Label protocol One round of RT-IVT to cRNA
 
 
Hybridization protocol Labeled cRNAs were fragmented to an average size of approximately 50 to 100 nucleotides in the presence of 10 mM zinc chloride and adding a hybridization buffer containing 1 M sodium chloride, 0.5 percent sodium sarcosine, 50 mM morpholino-ethane sulfonic acid (pH 6.5), and formamide (final concentration, 30 percent at 40°C); After hybridization, the slides were washed
Scan protocol slides were scanned using a confocal laser scanner (Agilent Technologies, Palo Alto, CA). Fluorescence intensities of the scanned images were quantified, normalized, and balanced
Description Liver samples (1-2 g) were acquired from Caucasian individuals from three independent liver collections at tissue resource centers at Vanderbilt University, University of Pittsburg, and Merck Research Laboratories. All individuals were compared to a common pool created from equal portions of RNA from 191 (111 from Vanderbilt University and 80 from University of Pittsburg) samples.
Data processing Rosetta Resolver Ratio Experiment using Rosetta Resolver Agilent Error Model
 
Submission date Nov 12, 2007
Last update date May 08, 2008
Contact name eric e schadt
E-mail(s) eric_schadt@merck.com
Organization name Merck
Department Genetics
Street address 401 Terry Ave N
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL4372
Series (1)
GSE9588 Mapping the Genetic Architecture of Gene Expression in Human Liver

Data table header descriptions
ID_REF Rosetta generated unique probe identifier
VALUE same as UNF_VALUE but with flagged values removed
LOGINTENSITY Corrected average log intensity of channels
PVALUE P-value of LogRatio
QUALITY 1 - if good and non control, 0 - otherwise
UNF_VALUE Corrected Log10 Ratio of channels (CH2/CH1)

Data table
ID_REF VALUE LOGINTENSITY PVALUE QUALITY UNF_VALUE
10019475365 -0.1670 -0.6640 2.2790e-001 1 -0.1670
10019481149 -0.3584 -0.0324 1.0412e-002 1 -0.3584
10019495284 0.0067 -0.8313 9.6365e-001 1 0.0067
10019687586 0.0136 -1.1170 9.4337e-001 1 0.0136
10019713746 -0.0638 -0.5099 6.2290e-001 1 -0.0638
10019799479 -0.0344 -0.7179 8.0385e-001 1 -0.0344
10019809115 0.0053 -0.4384 9.6699e-001 1 0.0053
10019874890 -0.0670 -0.8468 6.5353e-001 1 -0.0670
10019903058 0.1567 -1.4951 6.2715e-001 1 0.1567
10019909307 -0.1057 -0.6791 4.4139e-001 1 -0.1057
10019911222 0.1855 -0.4507 1.5993e-001 1 0.1855
10019924807 -0.0755 -1.3529 7.7735e-001 1 -0.0755
10019927856 0.3116 -0.2376 2.3039e-002 1 0.3116
10019932383 -0.2161 -0.5051 1.0917e-001 1 -0.2161
10019948931 0.0008 -1.2432 9.9724e-001 1 0.0008
10019975533 0.0648 -1.1584 7.4614e-001 1 0.0648
10019977224 0.2505 -0.5934 7.1929e-002 1 0.2505
10019977227 0.0180 -0.0045 8.8438e-001 1 0.0180
10019987588 -0.0571 -0.8460 7.0151e-001 1 -0.0571
10020008603 -0.1458 -0.4916 2.6718e-001 1 -0.1458

Total number of rows: 39302

Table truncated, full table size 1873 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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