|
| Status |
Public on Apr 21, 2015 |
| Title |
LNCaP_Scr_12h_B1 |
| Sample type |
RNA |
| |
|
| Source name |
LNCaP_Scr_12h
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
dsmz cat. #: ACC 256
cell type: Prostate carcinoma
cell line origin: Left supraclavicular lymph node metastasis from a 50-year-old man with prostate carcinoma in 1977
cell morphology: Adherent fibroblastoid cells growing in aggregates and as single cells
transfected with: Ambion pre-miR negative control #1 (scrambled pre-miR, Scr) at 20 nM
incubation time: 12h
|
| Biomaterial provider |
DSMZ (http://www.dsmz.de/home.html)
|
| Treatment protocol |
LNCaP cells were transfected with Ambion pre-miR™ construct for miR-135b or with pre-miR negative control #1 (scrambled pre-miR) at 20 nM, and incubated for 12h, 24h or 36h
|
| Growth protocol |
Normal growth conditions, according to instructions by provider
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total cellular RNAs were isolated with MiRVana total RNA isolation kit (Ambion).
|
| Label |
biotin
|
| Label protocol |
Illumina Total Prep RNA Amplification kit (Ambion). In vitro transcription reaction overnight (14h) and during it cRNA was biotinylated. The cRNA concentrations where checked with Nanodrop ND-1000 and cRNA quality was controlled by BioRad™s Experion electrophoresis station.
|
| |
|
| Hybridization protocol |
750 ng of each cRNA sample were hybridized into Illumina’s Sentrix HumanHT-12 v4 Expression Bead Chips at 58 °C overnight according to Illuminaâ Whole-Genome Gene Expression Direct Hybridization Assay Guide (part # 11322355, rev.A)
|
| Scan protocol |
Chips were scanned with Illumina Bead Array Reader (Factor=1.5, PMT=552, Filter=100%).
|
| Description |
LNCaP cells transfected with Ambion pre-miR negative control #1 (scrambled pre-miR, Scr) at 20 nM, and incubated for 12h
|
| Data processing |
The numerical results were extracted with GenomeStudio v. 2010.2; Gene Expression Module v. 1.7.0 without any normalization or background subtraction. The data was preprocessed by Bioconductor lumi package (version 1.8.3). It was vst transformed and quantile normalized.
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| |
|
| Submission date |
May 20, 2014 |
| Last update date |
Apr 21, 2015 |
| Contact name |
Anna Aakula |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute for Molecular Medicine Finland, FIMM
|
| Street address |
Tukholmankatu 8
|
| City |
HELSINKI |
| ZIP/Postal code |
00290 |
| Country |
Finland |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE57820 |
The effect of miRNA-135b overexpression on the gene expression profile of LNCaP cells |
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