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Sample GSM423118 Query DataSets for GSM423118
Status Public on Oct 01, 2015
Title 1970
Sample type RNA
 
Channel 1
Source name Genist.1.1.12.1.48
Organism Homo sapiens
Characteristics cell line: MCF-7 human breast carcinoma cell line (ECACC No. 86012803)
compound: Genistein
concentration: 1µM
exposure: 48h
Treatment protocol MCF-7 cells were seeded in T-25 Nunc culture flasks at a density of 300,000 cells per flask. After 72h steroid-deprivation, cells were exposed for 1h, 4h, or 48h at a high or low concentration. The highest concentration represents the highest non-cytotoxic or highest soluble concentration. Non-cytotoxic concentrations were derived from AlamarBlue viability assays (Nociari et al. 1998).
Extracted molecule total RNA
Extraction protocol RNA was extracted using the RNeasy mini kit from Qiagen, according to the manufacturer's protocol.
Label Cy5
Label protocol From 1 µg of cellular RNA, poly-A RNA was reversed transcribed using a poly dT-T7 primer. The resulting cDNA was immediately used for one round of amplification by T7 in vitro transcription reaction in the presence of Cyanine 5-CTP (LRILAK, Agilent). The amplified and labeled RNA probes were purified separately with RNeasy purification columns (Qiagen, Belgium). Probes were verified for amplification yield and incorporation efficiency by measuring the RNA concentration at 280 nm and Cy5 incorporation at 650 nm using a Nanodrop spectrophotometer.
 
Channel 2
Source name PCB.2.1.12.1.48
Organism Homo sapiens
Characteristics cell line: MCF-7 human breast carcinoma cell line (ECACC No. 86012803)
compound: PCB126
concentration: 2µM
exposure: 48h
Treatment protocol MCF-7 cells were seeded in T-25 Nunc culture flasks at a density of 300,000 cells per flask. After 72h steroid-deprivation, cells were exposed for 1h, 4h, or 48h at a high or low concentration. The highest concentration represents the highest non-cytotoxic or highest soluble concentration. Non-cytotoxic concentrations were derived from AlamarBlue viability assays (Nociari et al. 1998).
Extracted molecule total RNA
Extraction protocol RNA was extracted using the RNeasy mini kit from Qiagen, according to the manufacturer's protocol.
Label Cy3
Label protocol From 1 µg of cellular RNA, poly-A RNA was reversed transcribed using a poly dT-T7 primer. The resulting cDNA was immediately used for one round of amplification by T7 in vitro transcription reaction in the presence of Cyanine 3-CTP (LRILAK, Agilent) The amplified and labeled RNA probes were purified separately with RNeasy purification columns (Qiagen, Belgium). Probes were verified for amplification yield and incorporation efficiency by measuring the RNA concentration at 280 nm and Cy3 incorporation at 550 nm using a Nanodrop spectrophotometer.
 
 
Hybridization protocol Samples were hybridized on dual color Agilent's custom MCF-7 Microarray (Agilent, Diegem, Belgium; GEO accession number GPL8637).
Scan protocol After washing, the slides were scanned with a microarray scanner (Agilent) and images were processed using Feature Extraction Software version 8.5 (Agilent).
Description 1970
Data processing The Agilent processed signal values (i.e., feature gProcessedSignal from Agilent Feature Extraction v8.5.1.1) were used for the data analysis. Base 2 log-ratios (Cy5/Cy3) were computed and averaged over the duplicate spots. Control probes were removed prior to analysis.
 
Submission date Jun 29, 2009
Last update date Oct 01, 2015
Contact name Rekin's Janky
E-mail(s) Nucleomics.Bioinformatics@vib.be
Organization name VIB
Department Nucleomics Core
Street address Herestraat 49 Box 816
City Leuven
ZIP/Postal code B-3000
Country Belgium
 
Platform ID GPL8637
Series (1)
GSE16881 Use of toxicogenomics for screening of estrogenic activity

Data table header descriptions
ID_REF
VALUE log 2 normalized signal intensity ratio (Cy5/Cy3)

Data table
ID_REF VALUE
A_23_P100022 0.4
A_23_P100074 0.16
A_23_P100088 0.21
A_23_P100111 -0.03
A_23_P100141 -0.41
A_23_P100203 -0.62
A_23_P100220 0
A_23_P100278 -0.87
A_23_P100315 -0.07
A_23_P100341 -0.42
A_23_P100344 0.84
A_23_P100362 0.18
A_23_P100453 -0.03
A_23_P100455 -0.05
A_23_P100501 -0.03
A_23_P100529 -0.25
A_23_P100576 0.24
A_23_P100583 0.14
A_23_P100642 -0.29
A_23_P100653 -0.42

Total number of rows: 5114

Table truncated, full table size 89 Kbytes.




Supplementary file Size Download File type/resource
GSM423118.txt.gz 3.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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