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Sample GSM612716 Query DataSets for GSM612716
Status Public on Sep 01, 2011
Title E5_vs_pMSG_96h_rep2 (mRNA)
Sample type RNA
 
Channel 1
Source name pMSG_96h_rep2
Organism Homo sapiens
Characteristics cell type: skin keratinocytes
cell line: HaCaT
transfection: vector control
time: 96h
Treatment protocol E5 expression was induced by 1 mM dexamethasone treatment for different times.
Growth protocol HaCaT-E5 and control cells were grown in D-MEM growth medium with 10% FBS and glutamine and antibiotics, and serum-starved 24h before treatment.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from confluent cell cultures using TriPure reagent (Roche Applied Science, Indianapolis, IN, USA)
Label Cy5
Label protocol Cy5 and Cy3 indirect labelling using (Ambion, Austin, TX) amino allyl messageamp II aRNA amplification kit according to instructions.
 
Channel 2
Source name E5_96h_rep2
Organism Homo sapiens
Characteristics cell type: skin keratinocytes
cell line: HaCaT
transfection: type 16 E5 oncogene
time: 96h
Treatment protocol E5 expression was induced by 1 mM dexamethasone treatment for different times.
Growth protocol HaCaT-E5 and control cells were grown in D-MEM growth medium with 10% FBS and glutamine and antibiotics, and serum-starved 24h before treatment.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from confluent cell cultures using TriPure reagent (Roche Applied Science, Indianapolis, IN, USA)
Label Cy3
Label protocol Cy5 and Cy3 indirect labelling using (Ambion, Austin, TX) amino allyl messageamp II aRNA amplification kit according to instructions.
 
 
Hybridization protocol Hybridization was performed as described in the Agilent (Agilent Technologies, Rockville, MD) two color microarray-based gene expression analysis manual suggests. Hybridization for 16 h at +65 ºC. Washing was performed by the Agilent protocol 5 minutes in GE wash buffer 1 and one minute in GE wash buffer 2 (+37ºC). Arrays were dried with a 1 minute spin in a Spectrafuge mini (Labnet, Woodbridge, NJ).
Scan protocol Default scanning performed with Axon 4200AL for Cy3 and Cy5 using resolution of five micrometer.
Description mRNA expression in E5 vs control cells after 96h induction
Data processing quantile normalization of the log2 ratios
 
Submission date Oct 25, 2010
Last update date Sep 01, 2011
Contact name Dario Greco
E-mail(s) dario.greco@tuni.fi
Organization name Tampere University
Department Faculty of Medicine and Health Technology
Lab Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)
Street address Arvo ylpön Katu 34
City Tampere
ZIP/Postal code 33520
Country Finland
 
Platform ID GPL4133
Series (1)
GSE24908 Human Papillomavirus 16 E5 modulates the expression of host microRNAs

Data table header descriptions
ID_REF
VALUE quantile normalized log2 ratios E5 vs. control

Data table
ID_REF VALUE
23011 0.157191906
25861 0.222741949
40029 0.113813279
12389 -0.251200022
10328 0.061062874
25051 -0.070406051
28887 0.859325589
18582 0.566016627
10813 0.245634245
10308 0.29970123
29524 0.023163068
36849 0.459088302
15547 0.021699053
20551 -0.172948491
38433 0.094791787
36162 -0.325844731
27803 0.436702455
34452 1.703214026
22658 -0.904421751
19264 -0.514395668

Total number of rows: 43376

Table truncated, full table size 770 Kbytes.




Supplementary file Size Download File type/resource
GSM612716_96h_rep2.gpr.gz 10.7 Mb (ftp)(http) GPR
Processed data included within Sample table

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