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Sample GSM712476 Query DataSets for GSM712476
Status Public on Apr 21, 2011
Title LN443/control vs LN443/PDGF-A
Sample type RNA
 
Channel 1
Source name Control LN443/GFP
Organism Homo sapiens
Characteristics cell line: LN443
cell type: glioma cells
transfection: GFP
Treatment protocol Glioma cells were grown to ~ 80% confluence in DMEM media containg 10% FBS, then subjected t serum starvation for 24 hr before total RNA preparation.
Growth protocol Standard gene expression techniques were used to express human PDGF-A gene encoded by a retroviral pMXI-gfp vector in glioma cells. Stable expressing cell lines were selected by FACS sorting for GFP=positive cell popultions.
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions
Label Cy3
Label protocol 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label
 
Channel 2
Source name transfected cells: LN444/PDGF-A
Organism Homo sapiens
Characteristics cell line: LN443
cell type: glioma cells
transfection: PDGF-A
Treatment protocol Glioma cells were grown to ~ 80% confluence in DMEM media containg 10% FBS, then subjected t serum starvation for 24 hr before total RNA preparation.
Growth protocol Standard gene expression techniques were used to express human PDGF-A gene encoded by a retroviral pMXI-gfp vector in glioma cells. Stable expressing cell lines were selected by FACS sorting for GFP=positive cell popultions.
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions
Label Cy5
Label protocol 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label
 
 
Hybridization protocol Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
Scan protocol Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
Data processing Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.
 
Submission date Apr 20, 2011
Last update date Apr 21, 2011
Contact name HAIZHONG FENG
E-mail(s) FENGH@upmc.edu
Phone 4126233219
Organization name UNIVERSITY OF PITTSBURGH
Street address 5117 CENTRE AVE
City PITTSBURGH
State/province PA
ZIP/Postal code 15213
Country USA
 
Platform ID GPL4133
Series (1)
GSE28748 Human glioma cells: Control (GFP) vs PDGF-A expressing

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 -1.714872372e-001
2 0.000000000e+000
3 0.000000000e+000
4 0.000000000e+000
5 0.000000000e+000
6 0.000000000e+000
7 0.000000000e+000
8 0.000000000e+000
9 0.000000000e+000
10 0.000000000e+000
11 0.000000000e+000
12 9.015860695e-002
13 3.727278254e-002
14 -1.149882378e-001
15 3.101983480e-001
16 1.580906192e-001
17 6.851452017e-002
18 -6.322900871e-002
19 9.361554970e-002
20 1.540394461e-001

Total number of rows: 45015

Table truncated, full table size 1017 Kbytes.




Supplementary file Size Download File type/resource
GSM712476_US23502362_251485040305_S01_GE2-v5_95_Feb07_1_3.txt.gz 15.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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