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Sample GSM241514 Query DataSets for GSM241514
Status Public on Jun 25, 2009
Title Cu_400uM_12h_Rep 5
Sample type RNA
 
Channel 1
Source name Control 12h
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 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.
 
Channel 2
Source name Cu_400uM_12h
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 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.
 
 
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 0.08375901
A_23_P170713 0.29556224
A_23_P7033 -0.1478441
A_23_P363418
A_23_P35796 0.25386387
A_23_P110005 -0.31137833
A_23_P374129 0.04139983
A_23_P210158 -0.10684169
A_23_P80718
A_23_P334182 0.18888888
A_23_P35854
A_23_P119178 0.086707905
A_23_P101443 -0.21070954
A_23_P320858
A_23_P429950
A_23_P166353 0.15238833
A_23_P48581 -0.103344694
A_23_P218793 -0.1238234
A_23_P131354 -0.15620333
A_23_P103897 -0.16335835

Total number of rows: 20213

Table truncated, full table size 441 Kbytes.




Supplementary file Size Download File type/resource
GSM241514.tif.gz 18.2 Mb (ftp)(http) TIFF
GSM241514.txt.gz 5.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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