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Sample GSM241534 Query DataSets for GSM241534
Status Public on Jun 25, 2009
Title Cu_600uM_8h_Rep 3
Sample type RNA
 
Channel 1
Source name Control 8h
Organism Homo sapiens
Characteristics Control
Treatment protocol HepG2 cells were plated and allowed to grow until they were 50 % confluent. Cells were then treated with 100, 200, 400 and 600 mM of copper sulfate for 4, 8, 12 and 24 h.
Extracted molecule total RNA
Extraction protocol Total RNAs were isolated from untreated and treated cells using RNeasy mini kits (Qiagen, Inc.) following manufacturer's instructions. The quality of the purified RNA was determined using a BioAnalyzer (Agilent Technologies, Palo Alto, CA).
Label CY3
Label protocol Total RNA (100 ng) from control or metal-treated cells was amplified and labeled with Cy3 or Cy5 fluorescent dye using Agilent Technologies Low RNA Input Linear Amplification labeling kit following the manufacture's protocol.
 
Channel 2
Source name Cu_600uM_8h
Organism Homo sapiens
Characteristics Treated
Treatment protocol HepG2 cells were plated and allowed to grow until they were 50 % confluent. Cells were then treated with 100, 200, 400 and 600 mM of copper sulfate for 4, 8, 12 and 24 h.
Extracted molecule total RNA
Extraction protocol Total RNAs were isolated from untreated and treated cells using RNeasy mini kits (Qiagen, Inc.) following manufacturer's instructions. The quality of the purified RNA was determined using a BioAnalyzer (Agilent Technologies, Palo Alto, CA).
Label CY5
Label protocol Total RNA (100 ng) from control or metal-treated cells was amplified and labeled with Cy3 or Cy5 fluorescent dye using Agilent Technologies Low RNA Input Linear Amplification labeling kit following the manufacture's protocol.
 
 
Hybridization protocol The quantity and purity of the resulting fluorescently-labeled cRNA was evaluated using a Nanodrop ND-100 spectrophotometer (Nanodrop Technologies), and the size distribution using an Agilent Bioanalyzer. Equal amounts of Cy3- and Cy5-lableled cRNA were then hybridized to an Agilent Human Microarray (~22,000 k features) for 17 h at 65°C.
Scan protocol The hybridized microarrays were washed and scanned using an Agilent G2565BA scanner. Data were extracted from the scanned images using Agilent Feature Extraction software.
Description Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 100ng of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol. For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol. Chips were scanned with an Agilent Scanner and processed with the Agilent Feature Extraction Software.
Data processing GeneSpring GX 7.3 (Agilent Technologies) was used to identify genes that showed significant changes in gene expression with any treatment. For global normalization of raw microarray data, per spot and per chip: intensity dependent (Lowess) normalization was applied.
 
Submission date Nov 06, 2007
Last update date Aug 14, 2011
Contact name Min Ok Song
E-mail(s) songm2@niehs.nih.gov
Phone 919-541-2679
Fax 919-541-5737
Organization name NIEHS
Department DIR ETP
Lab LTEG
Street address 111 T.W. Alexander Dr
City RTP
State/province NC
ZIP/Postal code 27709
Country USA
 
Platform ID GPL6087
Series (1)
GSE9539 Global transcriptome changes in HepG2 cells exposed to copper

Data table header descriptions
ID_REF Agilent Feature Number
VALUE Natural Logarithm of Normalized Ratio (treated/control) Exported from GeneSpring

Data table
ID_REF VALUE
A_23_P107801 0.19596714
A_23_P170713 -0.111018494
A_23_P7033 -0.6143246
A_23_P363418 -0.11000963
A_23_P35796 0.18044746
A_23_P110005 -0.44261625
A_23_P374129 1.416662
A_23_P210158 0.30153966
A_23_P80718 -0.06577531
A_23_P334182 0.2743243
A_23_P35854 -0.26602665
A_23_P119178 0.07530701
A_23_P101443 -0.41312584
A_23_P320858 0.70623225
A_23_P429950 -2.5124595
A_23_P166353 -0.07365788
A_23_P48581 0.16308786
A_23_P218793 0.30668446
A_23_P131354 0.14242627
A_23_P103897 0.26613376

Total number of rows: 20185

Table truncated, full table size 464 Kbytes.




Supplementary file Size Download File type/resource
GSM241534.tif.gz 19.9 Mb (ftp)(http) TIFF
GSM241534.txt.gz 6.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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