|
| Status |
Public on Oct 03, 2012 |
| Title |
Erb1 vs. GFP 388829 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
PC3 cells, prostate adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
transfection: GFP
cell line: PC3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed with TRIzol reagent (Invitrogen Carlsbad, CA) and chloroform extraction according to the manufacturer’s protocol.
|
| Label |
Cy3
|
| Label protocol |
Labeling was carried out with aminoallyl-modified dUTP incorporated during cDNA synthesis using Superscript III (Invitrogen). Incubation with Cy3 or Cy5 monoreactive NHS-ester dured 30 min.
|
| |
|
| Channel 2 |
| Source name |
PC3 cells, prostate adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
transfection: ERb1
cell line: PC3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed with TRIzol reagent (Invitrogen Carlsbad, CA) and chloroform extraction according to the manufacturer’s protocol.
|
| Label |
Cy5
|
| Label protocol |
Labeling was carried out with aminoallyl-modified dUTP incorporated during cDNA synthesis using Superscript III (Invitrogen). Incubation with Cy3 or Cy5 monoreactive NHS-ester dured 30 min.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed at 42 °C for at least 40 hours after pooling of samples for each array. Subsequent to hybridization the slides were washed in three SDS/SSC wash buffers of stepwise lower stringency.
|
| Scan protocol |
Slides were scanned using an Axon GenePix 4400A (MDS Analytical Technologies) to obtain TIFF files.
|
| Data processing |
Manual processing of data was carried out in GenePix Pro 6.1 to identify possible major issues. Subsequent analysis was carried out in the R environment using the following packages: Bioconductor bundle, Limma, Aroma, KTH. Print-tip lowess was used for normalization and empirical Bayes t-test for statistical analysis. Cut-offs set as described in article.
|
| |
|
| Submission date |
Jan 13, 2012 |
| Last update date |
Oct 04, 2012 |
| Contact name |
Philip Jonsson |
| E-mail(s) |
pkjonsson@uh.edu
|
| Organization name |
University of Houston
|
| Street address |
Department of Biology and Biochemistry – NSM Center for Nuclear Receptors and Cell Signaling 3605 Cullen Blvd, Science & Engineering Research Center Bldg 545
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77204-5056 |
| Country |
USA |
| |
|
| Platform ID |
GPL15127 |
| Series (1) |
| GSE35095 |
Gene expression profiling of PC3 cells stably expressing ERbeta1 and ERbeta2 |
|
