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Sample GSM1502868 Query DataSets for GSM1502868
Status Public on Jan 01, 2015
Title Adrenocortical carcinoma clincal sample 5
Sample type RNA
 
Source name ACC patient sample 5
Organism Homo sapiens
Characteristics tissue: Adrenocortical carcinoma
source: Anonymous patient sample
Treatment protocol Samples were obtained during surgery and snap frozen in liquid nitrogen and stored at -80 C.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from approximately 30 mg of fresh frozen tissue using a Qiazol protocol (RNeasy Mini Kit, Qiagen, Hilden, Germany) in accordance with the manufacturer’s instructions. RNA quality was assessed using the Agilent 2100 Bioanalyser (Agilent Technologies, Englewood, CO, USA) with a minimum RNA integrity number (RIN) of seven required.
Label Cy3
Label protocol Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.
 
Hybridization protocol 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.
Scan protocol The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).
Data processing Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 15 out of 23 samples. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 12.0). GO analysis and Pathway analysis were performed in the standard enrichment computation method.
 
Submission date Sep 11, 2014
Last update date Jan 01, 2015
Contact name Anthony R Glover
E-mail(s) anthony.glover@sydney.edu.au
Organization name University of Sydney
Lab Cancer Genetics
Street address Level 9, Kolling Institute of Medical Research, Royal North Shore Hospital
City NSW
State/province St Leonards, Sydney
ZIP/Postal code 2065
Country Australia
 
Platform ID GPL16956
Series (1)
GSE61359 Long noncoding RNAs profiles of adrenocortical carcinomas, adrenocortical adenomas and normal adrenal cortex

Data table header descriptions
ID_REF
VALUE Quantile normalized signal intensity

Data table
ID_REF VALUE
ASHGA5P007773 3.962689
ASHGA5P006930 8.262194
ASHGA5P050699 10.460895
ASHGA5P008172 4.741246
ASHGA5P012016 7.9830823
ASHGA5P007747 6.675192
ASHGA5P001180 4.541786
ASHGA5P003003 6.348557
ASHGA5P006671 8.936782
ASHGA5P036194 5.9045196
ASHGA5P013870 5.5338044
ASHGA5P016060 2.429219
ASHGA5P050222 7.035046
ASHGA5P005374 3.7568436
ASHGA5P009847 2.429219
ASHGA5P053556 10.492282
ASHGA5P013963 4.668528
ASHGA5P032406 4.9412556
ASHGA5P034316 8.789877
ASHGA5P011047 4.918831

Total number of rows: 35549

Table truncated, full table size 814 Kbytes.




Supplementary file Size Download File type/resource
GSM1502868_C5.txt.gz 2.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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