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Sample GSM1959242 Query DataSets for GSM1959242
Status Public on Dec 15, 2016
Title MCF-7_Rg1 ginsenoside (2ug/ml) rep.1
Sample type RNA
 
Source name MCF-7 treated with Rg1 ginsenoside (2ug/ml)
Organism Homo sapiens
Characteristics cell line: MCF-7
cell type: breast cancer
gender: female
Treatment protocol No special treatments before harvesting were carried out.
Growth protocol Cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal calf serum, 2% glutamine, 1% penicillin and 1% streptomycin stock solutions. Cells were incubated at 37°C/ 95% air/ 5% CO2 and the media was changed every two days.
Extracted molecule total RNA
Extraction protocol Cells were washed 3 times using PBS and total RNA was collected from adherent tissue culture cells using Trizol (Invitrogen) according to the manufacturer’s instructions. RNA was quantified (A260) using a Nanodrop-1000 spectrophotometer (Nanodrop Technologies).
Label biotin
Label protocol Complimentary RNA (cRNA) was produced according to Affymetrix geneChip® 3' IVT Express kit Technical Manual (http://media.affymetrix.com/support/downloads/manuals/3_ivt_express_kit_manual.pdf)
 
Hybridization protocol Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® PrimeView™ Human . GeneChips were washed and stained in the Affymetrix Fluidics Station 400. Hybridization reactions to Affymetrix Maize GeneChip expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).
Scan protocol Scanning of the Affymetrix GeneChip® PrimeView™ Human expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).
Description Gene expression data from MCF_7 breast cancer cells (24 day incubation)
Data processing Data extraction was also performed by Expression Analysis Inc. Expression values were calculated using the Affymetrix GeneChip Operating System (GCOS) and were based on the difference of the PM (Perfect Match) signal and MM (Mismatch) signal at each of the probe pairs. The fluorescent signal values from each array were normalized to achieve similar overall intensity between arrays. The fluorescent signal values of any hybridization reaction were then multiplied by a scaling factor to make their (trimmed) mean intensity equal to 500. The scaling factor is unique to each hybridization reaction and is in general below 10
 
Submission date Dec 01, 2015
Last update date Dec 15, 2016
Contact name Mariya Khodakovskaya
E-mail(s) m_khod@yahoo.com
Organization name University of Arkansas at Little Rock
Department Biology
Street address 2801 S. University Avenue
City Little Rock
State/province AR
ZIP/Postal code 72204
Country USA
 
Platform ID GPL15207
Series (1)
GSE75570 Expression data from MCF-7 breast cancer cells treated with CNTs, ginsenosides (Rb1 and Rg1) and conjugates (Rb-CNTs and Rg-CNTs)

Data table header descriptions
ID_REF
VALUE GCOS signal
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 650.4 P 0.0000
AFFX-BioB-M_at 862.4 P 0.0000
AFFX-BioB-3_at 631.1 P 0.0000
AFFX-BioC-5_at 1272.3 P 0.0000
AFFX-BioC-3_at 1829.1 P 0.0000
AFFX-BioDn-5_at 3388.6 P 0.0000
AFFX-BioDn-3_at 5374.1 P 0.0000
AFFX-CreX-5_at 14739.0 P 0.0000
AFFX-CreX-3_at 17240.9 P 0.0000
AFFX-DapX-5_at 184.6 P 0.0000
AFFX-DapX-M_at 1018.0 P 0.0000
AFFX-DapX-3_at 2093.0 P 0.0000
AFFX-LysX-5_at 43.6 P 0.0000
AFFX-LysX-M_at 108.5 P 0.0000
AFFX-LysX-3_at 168.2 P 0.0000
AFFX-PheX-5_at 69.0 P 0.0000
AFFX-PheX-M_at 136.2 P 0.0000
AFFX-PheX-3_at 187.7 P 0.0000
AFFX-ThrX-5_at 55.9 P 0.0000
AFFX-ThrX-M_at 162.8 P 0.0000

Total number of rows: 49395

Table truncated, full table size 1343 Kbytes.




Supplementary file Size Download File type/resource
GSM1959242_EA09092_313332_PRIMEVIEW_RGG1.CEL.gz 1.9 Mb (ftp)(http) CEL
GSM1959242_EA09092_313332_PRIMEVIEW_RGG1.CHP.gz 345.6 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data are available on Series record
Processed data provided as supplementary file

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