|
| Status |
Public on Nov 15, 2010 |
| Title |
5'Aza-treated LNCaP at 48 hr v2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Human LNCaP Prostate Cancer Cell Line, control treatment
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCAP
treatment: DMSO control
time point: 48 hour
|
| Treatment protocol |
LNCaP cells maintained in 100 mm dishes were serum starved for 24 hours. After 24 hours the cells were treated with either 1uM 5'Aza-cytidine (Sigma) or the vehicle Di methyl Sulphoxide for control cells (Used to dissolve 5-Aza) for 24 and 48 hours.
|
| Growth protocol |
LNCaP cells are cultured in RPMI media containing 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At the indicated time points cells were lysed with Trizol reagent (Invitrogen) and total RNA isolated for array experiment according to 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 |
Human LNCaP Prostate Cancer Cell Line, 5’Azacytidine-treated
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCAP
treatment: 5’Azacytidine
time point: 48 hour
|
| Treatment protocol |
LNCaP cells maintained in 100 mm dishes were serum starved for 24 hours. After 24 hours the cells were treated with either 1uM 5'Aza-cytidine (Sigma) or the vehicle Di methyl Sulphoxide for control cells (Used to dissolve 5-Aza) for 24 and 48 hours.
|
| Growth protocol |
LNCaP cells are cultured in RPMI media containing 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At the indicated time points cells were lysed with Trizol reagent (Invitrogen) and total RNA isolated for array experiment according to 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).
|
| Description |
Replicate 2 of 2, @48hr with 5'Aza treatment
raw data file: 09282007_251485019555_S01_GE2-v5_95_Feb07_1_4.txt
|
| Data processing |
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.
|
| |
|
| Submission date |
Nov 15, 2010 |
| Last update date |
Nov 15, 2010 |
| Contact name |
Jung Kim |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Michigan
|
| Street address |
1400 E. Medical Center Drive
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL4133 |
| Series (2) |
| GSE25346 |
Agilent expression analysis of LNCaP cells following 5'aza-treatment |
| GSE27619 |
Deep sequencing reveals distinct patterns of DNA methylation and transcript isoform regulation in prostate cancer |
|
