|
| Status |
Public on Oct 06, 2016 |
| Title |
VCaP siERG Replicate 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Prostate Cancer Cell Line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: VCaP
treatment: siERG
|
| Growth protocol |
VCaP cells were grown in DMEM-Glutmax (Invitrogen) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin.
|
| 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 Cy5/Cy3-label
|
| |
|
| Channel 2 |
| Source name |
Prostate Cancer Cell Line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: VCaP
treatment: siControl
|
| Growth protocol |
VCaP cells were grown in DMEM-Glutmax (Invitrogen) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin.
|
| 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 Cy5/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 G2505B scanner.Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
|
| Description |
Biological replicate 1 of 2. VCaP cells were transfected by siERG or siControl individually.
|
| Data processing |
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Control Features were omitted. The LogRatio columns from each feature file was extracted and converted to log2 ratios then merged into a single processed data matrix.
|
| |
|
| Submission date |
Oct 05, 2016 |
| Last update date |
Oct 06, 2016 |
| Contact name |
Xiaoju Wang |
| E-mail(s) |
xiaojuw@umich.edu
|
| Phone |
734-763-6056
|
| Organization name |
University of Michigan
|
| Street address |
1500 E. Medical Center Drive
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL4133 |
| Series (2) |
| GSE58940 |
Development of peptidomimetic inhibitors of the ERG gene fusion product in prostate cancer (expression) |
| GSE58975 |
Development of peptidomimetic inhibitors of the ERG gene fusion product in prostate cancer |
|
