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Sample GSM1394594 Query DataSets for GSM1394594
Status Public on Apr 21, 2015
Title LNCaP_miR-135b_12h_B1
Sample type RNA
Source name LNCaP_miR-135b_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™ construct for miR-135b at 20 nM
incubation time: 12h
Biomaterial provider DSMZ (
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™ construct for miR-135b 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.
Submission date May 20, 2014
Last update date Apr 21, 2015
Contact name Anna Aakula
Organization name Institute for Molecular Medicine Finland, FIMM
Street address Tukholmankatu 8
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

Data table header descriptions
VALUE quantile normalized

Data table
ILMN_1762337 6.706933011294
ILMN_2055271 6.98799578758587
ILMN_1736007 6.73562014809699
ILMN_2383229 6.60403645455993
ILMN_1806310 6.59846466293485
ILMN_1779670 6.44101201810101
ILMN_1653355 6.66205358025466
ILMN_1717783 6.34308708992951
ILMN_1705025 6.71055374026177
ILMN_1814316 6.48400747699376
ILMN_2359168 6.19997525552521
ILMN_1731507 6.24919732855095
ILMN_1787689 6.42341100995891
ILMN_3241953 7.5848515184021
ILMN_1745607 6.23041648302682
ILMN_2136495 6.36082892113242
ILMN_1668111 6.3305218506716
ILMN_2295559 6.55493620432604
ILMN_1735045 6.55837122528365
ILMN_1680754 6.99601739446263

Total number of rows: 47323

Table truncated, full table size 1379 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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