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Sample GSM372686 Query DataSets for GSM372686
Status Public on Jul 01, 2009
Title Normal adrenal cortex replicate3
Sample type RNA
 
Channel 1
Source name adrenal cortex, normal cortex tissue
Organism Homo sapiens
Characteristics tissue: adrenal cortex
gender: female
age at the time of surgery: 58.29 years
hormonal status: normal hormonal status
Treatment protocol After surgical removal tissue samples were immediately snap frozen in liquid nitrogen and stored at -80○ until RNA isolation. Histological diagnoses were confirmed in each cases.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from homogenized tissue samples using Rneasy Lipid Tissue Mini Kit (Qiagen GmbH, Hilden, Germany) following the manufacturer's instructions.
Label Cy5
Label protocol 1 µg of total RNA mixed with RNA Spike-In-Kit (Agilent Tech. Inc., Santa Clara, CA) was reverse transcribed and Cyanine 5 or Cyanine 3-CTP-labeled (Perkin-Elmer, Waltham, Massachusetts, MA, USA) complementary RNA (cRNA) was synthetized using the Low RNA Input Linear Amplification Kit (Agilent Tech. Inc., Santa Clara, CA) according to the manufacturer’s Dual Color Expression Microarray Protocol version 5.5. Successful labeling, cRNA yield and purity were controlled on a Nanodrop ND-1000 Spectrophotometer (Thermo Scientific, Wilmington, DE).
 
Channel 2
Source name Uniform reference RNA pooled from total RNA of all 16 tissues examined.
Organism Homo sapiens
Characteristics tissue: adrenal cortex
Treatment protocol After surgical removal tissue samples were immediately snap frozen in liquid nitrogen and stored at -80○ until RNA isolation. Histological diagnoses were confirmed in each cases.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from homogenized tissue samples using Rneasy Lipid Tissue Mini Kit (Qiagen GmbH, Hilden, Germany) following the manufacturer's instructions.
Label Cy3
Label protocol 1 µg of total RNA mixed with RNA Spike-In-Kit (Agilent Tech. Inc., Santa Clara, CA) was reverse transcribed and Cyanine 5 or Cyanine 3-CTP-labeled (Perkin-Elmer, Waltham, Massachusetts, MA, USA) complementary RNA (cRNA) was synthetized using the Low RNA Input Linear Amplification Kit (Agilent Tech. Inc., Santa Clara, CA) according to the manufacturer’s Dual Color Expression Microarray Protocol version 5.5. Successful labeling, cRNA yield and purity were controlled on a Nanodrop ND-1000 Spectrophotometer (Thermo Scientific, Wilmington, DE).
 
 
Hybridization protocol 825 ng of cyanine 5-CTP-labeled cRNA per sample was mixed with an equal amount of cyanine 3-CTP-labeled uniform reference cRNA, and hybridized to 4x44 K Whole Human Genome Microarrays (Agilent Tech. Inc., Santa Clara, CA) according to the manufacturer’s protocol.
Scan protocol Array scan was performed with Agilent DNA Microarray Scanner G2565BA.
Description N/A
Data processing Agilent Feature Extraction Software 8.5 was used for feature extraction and array normalization with default normalization scenario for Agilent 4x44 K two-colour array platforms.
 
Submission date Feb 20, 2009
Last update date Jul 01, 2009
Contact name Zsófia Tömböl
Organization name Semmelweis University
Department 2nd Department of Medicine
Street address Szentkirályi u. 46.
City Budapest
ZIP/Postal code H-1088
Country Hungary
 
Platform ID GPL6480
Series (1)
GSE14922 Human Adrenocortical Tumors: normal cortex vs inactive adenoma vs cortisol secreting adenoma vs adrenocortical cancer

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
GE_BrightCorner 0.31445628
DarkCorner -0.06437783
A_24_P66027 0.053528666
A_32_P77178 -0.06779149
A_23_P212522 -0.6165446
A_24_P934473 0.15263653
A_24_P9671 -0.58474845
A_32_P29551 0.12997651
A_24_P801451 0.1911481
A_32_P30710 -0.09024435
A_32_P89523 1.7446873
A_24_P704878 -0.30312836
A_32_P86028 0.15376762
A_24_P470079 1.9665279
A_23_P65830 0.5438887
A_23_P109143 -1.04535
A_24_P595567 0.027855933
A_24_P391591 -1.6190268
A_24_P799245 0.02574674
A_24_P932757 0.02597215

Total number of rows: 41078

Table truncated, full table size 948 Kbytes.




Supplementary file Size Download File type/resource
GSM372686.txt.gz 835.1 Kb (ftp)(http) TXT
Processed data included within Sample table

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