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Sample GSM2255410 Query DataSets for GSM2255410
Status Public on Jul 30, 2016
Title MCF7_Ag-60_6h_rep2
Sample type RNA
 
Source name MCF-7, 60nm AgNP exposure, 6h
Organism Homo sapiens
Characteristics cell type: MCF-7 (ATCC)
exposure duration: 6h
exposure material: 60nm AgNPs
exposure dose: 25 µg/ml
Treatment protocol Cells were exposed for 6h or 24h at 37°C (95% RH, 5% CO2) to Ag-20, Ag-30, Ag-60, or Ag-110 AgNPs at a concentration of 25 µg/ml, or to AgNO3 at a concentration of 1.5 µg/ml (n=3)
Growth protocol Both cell types were seeded at a density of ~40,000 ells/cm2 in a 6-well plate, and grown towards a confluency of ~60%.
Extracted molecule total RNA
Extraction protocol cells were washed to remove remaining nanoparticles, resuspended in 600 µl RLT buffer (RNeasy, Qiagen, Venlo, the Netherlands) containing 1% β-mercapto ethanol (Sigma). The lysate was further purified using the Qiashredder, followed by the RNeasy Mini Kit, including DNase treatment (Qiagen, Venlo, The Netherlands). RNA concentration and purity was determined using the Nanodrop ND1000 spectrophotometer (Isogen, De Meern, The Netherlands) and the Shimadzu MultiNA (Tokyo, Japan) and Agilent Bioanalyzer was used to analyze the quality and integrity of the RNA samples.
Label biotin
Label protocol Biotin (biotin-16-UTP) labeled cRNA was amplified from the total RNA using the Illumina TotalPrep-96 RNA Amplification Kit (Ambion, Life Technologies, Bleiswijk, the Netherlands).
 
Hybridization protocol 750 ng of each labeled cRNA sample was hybridized overnight at 58 °C onto the Illumina HumanHT-12 v4 Expression BeadChip.
Scan protocol the BeadChip was washed and incubated with Streptavidin-Cy3 and the chips were scanned using the Illumina iScan array scanner (Illumina, San Diego, USA). Primary gene expression of the scanned BeadChip arrays was performed using Illumina’s Genomestudio v 2011.1 software with the default settings advised by Illumina.
Description NA
Data processing Normalization and analysis of the datasets was performed using MadMax. A variance Stabilization and Normalization (VSN) method was used to obtain expression values. After background subtraction the spot intensities were floored to 40, followed by 2 log mean centering and calculation of 2 log rations of treatments versus the average of the control samples.
 
Submission date Jul 29, 2016
Last update date Jul 30, 2016
Contact name Meike van der Zande
E-mail(s) meike.vanderzande@wur.nl
Organization name Wageningen University & Research
Street address Akkermaalsbos 2
City Wageningen
ZIP/Postal code 6708AK
Country Netherlands
 
Platform ID GPL10558
Series (1)
GSE84982 Different responses of Caco-2 and MCF-7 cells to silver nanoparticles are based on highly similar mechanisms of action

Data table header descriptions
ID_REF
VALUE A VSN normalization method was used

Data table
ID_REF VALUE
ILMN_1762337 134.145058
ILMN_2055271 156.903997
ILMN_1736007 136.546598
ILMN_2383229 148.134492
ILMN_1806310 133.423773
ILMN_1779670 137.669812
ILMN_1653355 126.751114
ILMN_1717783 111.517696
ILMN_1705025 115.548944
ILMN_1814316 155.156862
ILMN_2359168 101.524476
ILMN_1731507 115.207851
ILMN_1787689 133.634191
ILMN_3241953 189.381380
ILMN_1745607 118.491833
ILMN_2136495 105.981498
ILMN_1668111 149.391339
ILMN_2295559 116.405920
ILMN_1735045 324.866214
ILMN_1680754 139.232125

Total number of rows: 47323

Table truncated, full table size 1113 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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