|
Status |
Public on Aug 07, 2007 |
Title |
RWPE-ETV1_dye_rep2 |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
RWPE-ETV1
|
Organism |
Homo sapiens |
Characteristics |
benign prostate cell line RWPE stably expressing ETV1
|
Treatment protocol |
Cells were not treated prior to RNA extraction.
|
Growth protocol |
RWPE-GUS or RWPE-ETV1 cells were maintained in Keratinocyte-SFM supplemented with bovine pituitary extract (25 mg/ 500 ml) human recomninant EGF (2.5 ug/500 ml medium) and 3ug/ml blasticidin
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated with Trizol (Invitrogen Cat. No. 15596-026, Carlsbad, CA), according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNAeasy Mini Kit (Cat. No. 74104) according to the manufacturer's instructions.
|
Label |
Cy3
|
Label protocol |
One ug of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).
|
|
|
Channel 2 |
Source name |
RWPE-GUS
|
Organism |
Homo sapiens |
Characteristics |
benign prostate cell line RWPE stably expressing the GUS control gene
|
Treatment protocol |
Cells were not treated prior to RNA extraction.
|
Growth protocol |
RWPE-GUS or RWPE-ETV1 cells were maintained in Keratinocyte-SFM supplemented with bovine pituitary extract (25 mg/ 500 ml) human recomninant EGF (2.5 ug/500 ml medium) and 3ug/ml blasticidin
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated with Trizol (Invitrogen Cat. No. 15596-026, Carlsbad, CA), according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNAeasy Mini Kit (Cat. No. 74104) according to the manufacturer's instructions.
|
Label |
Cy5
|
Label protocol |
One ug of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).
|
|
|
|
Hybridization protocol |
825ng of Cy3 and Cy5 labelled aRNA were hybridized competitively for 17 hrs in a 65 C hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to the manufacturer's recommnded protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent). Arrays were washed according to the manufacturer's recommended protocol including the Stabilization and Drying Solution step (Two-Color Microarray-Based Gene Expression Analysis, Agilent).
|
Scan protocol |
Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B, Agilent) using the default settings for 4x44k format two-color arrays.
|
Description |
na
|
Data processing |
Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (Version 9.1.3.1). Spot values were normalized using the default linear-lowess normalization. To identify differentially expressed features, we filtered the data to only include features showing significant differential expression in (PValueLogRatio < 0.01) in all four hybridizations with at least 2 fold average over- or under-expression (LogRatio) after dye flip correction.
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|
|
Submission date |
May 03, 2007 |
Last update date |
Aug 07, 2007 |
Contact name |
Scott Tomlins |
E-mail(s) |
tomlinss@med.umich.edu
|
Phone |
734-615-1417
|
Organization name |
University of Michigan
|
Department |
Pathology
|
Lab |
Chinnaiyan Lab
|
Street address |
1400 E. Medical Center Dr., 5410 CCGC
|
City |
Ann Arbor |
State/province |
MI |
ZIP/Postal code |
48109 |
Country |
USA |
|
|
Platform ID |
GPL4133 |
Series (1) |
GSE7701 |
Profiling of RWPE cells stably over-expressing ETV1 |
|