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Sample GSM1571204 Query DataSets for GSM1571204
Status Public on Feb 27, 2015
Title CSA19 treatment replicate 1
Sample type RNA
Source name MCF-7 cells, 72hr, CSA19 treated, replicate 1
Organism Homo sapiens
Characteristics breast cancer cell line: MCF-7 cells
gender: female
age: 69y
treatment: 72hr in CSA19
Treatment protocol MCF-7 cells (in the logarithmic growth phase) were treated with the compounds (IC50 concentrations) or DMSO for 72 hours. Cells were maintained in a humidified environment at 37°C with 5% CO2.
Growth protocol MCF-7 cells were grown in DMEM medium supplemented with 10% fetal bovine serum and 1% penicillin (100 U/mL), streptomycin (100 μg/mL) mixture. Cells were maintained in a humidified environment at 37°C with 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the RNeasy Kit from Qiagen (Hilden, Germany) according to the manufacture's instruction. RNA concentration was measured using a NanoDrop-1000 spectrophotometer and the quality of total RNA was checked by gel analysis using the total RNA Nano chip assay on an Agilent 2100 Bioanalyzer (Agilent Technologies GmbH, Germany)
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Kit, One-Color (Agilent) according to the manufacturer's instructions followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the ND-1000 UV-VIS Spectrophotometer version 3.2.1.
Hybridization protocol 1.65 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 30 µL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 30 µL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Whole Human Genome RNA chips (8 × 60K, Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately for 2 minutes at 30°C.
Scan protocol Slides were scanned immediately after washing on the Agilent Technologies Scanner G2505C using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10µm, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression after 72hr in CSA19 treated MCF-7 cells
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol: GE1_1010_Sep10 and Grid: 028004_D_F_20120411) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Submission date Dec 22, 2014
Last update date Feb 27, 2015
Contact name Onat Kadioglu
Organization name Johannes Gutenberg University
Department Institute of Pharmacy and Biochemistry
Street address Staudinger Weg 5
City Mainz
ZIP/Postal code 55099
Country Germany
Platform ID GPL13607
Series (1)
GSE64430 Effect of cajanin stilbene acid and its synthetic derivatives on MCF-7 breast cancer cells

Data table header descriptions
VALUE processed Cy3 signal intensity (Agilent gProcessedSignal)

Data table
1 7.122637e+004
2 2.008362e+000
3 2.008362e+000
4 3.950380e+002
5 3.048513e+003
6 1.093591e+002
7 2.640338e+004
8 3.118829e+003
9 5.074463e+001
10 5.400420e+001
11 2.008362e+000
12 2.082857e+003
13 7.567535e+002
14 9.816943e+002
15 2.401829e+004
16 7.209063e+000
17 2.872950e+002
18 8.890717e+000
19 5.400252e+001
20 1.844736e+003

Total number of rows: 62976

Table truncated, full table size 1219 Kbytes.

Supplementary file Size Download File type/resource
GSM1571204_CSA19_rep1.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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