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Sample GSM226851 Query DataSets for GSM226851
Status Public on Sep 11, 2007
Title CMix Self-Self 3
Sample type RNA
 
Channel 1
Source name CMix Ref3
Organism Rattus norvegicus
Characteristics Total RNA was isolated from each of three rat livers and brains, and equal mass amounts of each of these six samples were combined to create a mixed RNA population. One 20 microgram aliquot of the total RNA mixture was used to generate the labeled probe.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.
Label Cy3
Label protocol indirect labeling protocol
 
Channel 2
Source name CMix Test3
Organism Rattus norvegicus
Characteristics Total RNA was isolated from each of three rat livers and brains, and equal mass amounts of each of these six samples were combined to create a mixed RNA population. One 20 microgram aliquot of the total RNA mixture was used to generate the labeled probe.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.
Label Cy5
Label protocol indirect labeling protocol
 
 
Hybridization protocol Cy3 and Cy5 labeled probes were combined and competitively hybridized to microarrays for 18 hours at 37C.
Scan protocol Slides were scanned using ScanArray 5000 fluorescent scanner (GSI Lumonics, Billerica, MA). The resulting images were quantified using QuantArray v3.0 image analysis software with the Fixed Circle spot finding algorithm software (GSI Lumonics, Billerica, MA) with a spot diameter of 150µm, an inner background diameter of 234µm, and an outer background diameter of 313µm. Minimum and maximum intensity limits for signal classification were the 55th and 90th percentile, and those for background classification were the 5th and 20th percentile.
Description This experiment was conducted to study dye-byes effects. Channel 1 and Channel 2 have identical biological sample labeled with two different dyes.

Data processing Raw quantitated array data was normalized using subaray-based quadratic correction algorithm.
 
Submission date Sep 04, 2007
Last update date Aug 14, 2011
Contact name Egle Juskeviciute
Organization name Thomas Jefferson University
Department Pathology
Street address 1020 Locust st. JAH 527
City Philadelphia
State/province PA
ZIP/Postal code 19107
Country USA
 
Platform ID GPL5803
Series (1)
GSE8950 Rat Brain-Heart-Liver Control Mix Self-Self Hybridization

Data table header descriptions
ID_REF
VALUE Log2(Test (Cy5)/Ref(Cy3)) normalized using quadratic correction algorithm

Data table
ID_REF VALUE
3 -0.098314904
4 -0.071875693
5 0.060655652
6 -0.024982366
7 -0.009283972
8 -0.020278243
9 0.005154269
10 0.033116836
11 -0.081159694
12 0.007770168
13 0.035729317
14 -0.000499363
21 -0.089031322
22 -0.160133711
23 -0.063618877
24 -0.181761548
25 -0.044104144
26 -0.171101066
27 0.013357671
28 -0.129981498

Total number of rows: 17596

Table truncated, full table size 305 Kbytes.




Supplementary file Size Download File type/resource
GSM226851.txt.gz 1.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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