|
| Status |
Public on Mar 07, 2012 |
| Title |
miRNA scramble expression in LNCaP, biological replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
Prostate cancer cell line LNCaP transfected with miRNA scramble
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
tumor: prostate cancer
tumor stage: early
mirna: scramble
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
2µg RNA were analyzed according to the manufacturer's protocol.
|
| |
|
| Hybridization protocol |
Affymetrix GeneChip Human Genome U133A 2.0 Arrays were processed according to the manufacturer`s protocol.
|
| Scan protocol |
GeneChips were processed using the Affymetrix GCS3000 7G system according to manufacturer`s protocol.
|
| Description |
Gene expression data from LNCaP cells transfected with miRNA scramble.
|
| Data processing |
The data were analyzed with R (version 2.9.0) and BioConductor (version 2.4). Quality assessment of arrays included exploration of distributions of probe intensities across all arrays, of average background values, and RNA quality was examined by RNA degradation plots. Diagnostic plots based on a probe level model (PLM) have been used to rule out chips with spatial artifacts (Chip pseudo-images, normalized unscaled standard error (NUSE) plot and relative log expression (RLE) plot). Background adjusted normalized data was retrieved by the RMA (robust multi-array average) procedure. Loss of mRNA expression was conducted by fitting a linear model using the R package limma. Reliable variance estimations were obtained by empirical Bayes moderated t-statistics. False discovery rate was controlled by Benjamini-Hochberg adjustment.
|
| |
|
| Submission date |
Jul 24, 2009 |
| Last update date |
Mar 07, 2012 |
| Contact name |
Kristin Reiche |
| E-mail(s) |
kristin.reiche@izi.fraunhofer.de
|
| Organization name |
Fraunhofer Institute for Cell Therapy and Immunology
|
| Department |
Diagnostics
|
| Street address |
Perlickstr. 1
|
| City |
Leipzig |
| ZIP/Postal code |
04103 |
| Country |
Germany |
| |
|
| Platform ID |
GPL571 |
| Series (2) |
| GSE17315 |
mRNA expression upon reconstitution of miR-130a, miR-203 and miR-205 in prostate cancer cell line LNCaP |
| GSE17362 |
miRNA expression, mRNA expression upon miRNA reconstitution, and direct mRNA target identification in prostate cancer cell lines |
|
