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Sample GSM1394596 Query DataSets for GSM1394596
Status Public on Apr 21, 2015
Title LNCaP_miR-135b_24h_B1
Sample type RNA
 
Source name LNCaP_miR-135b_24h
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: 24h
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™ construct for miR-135b at 20 nM, and incubated for 24h
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
E-mail(s) anna.aakula@fimm.fi
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

Data table header descriptions
ID_REF
VALUE quantile normalized

Data table
ID_REF VALUE
ILMN_1762337 6.75230332230067
ILMN_2055271 6.900023546841
ILMN_1736007 6.63856819557782
ILMN_2383229 6.45101341340421
ILMN_1806310 6.48643392396893
ILMN_1779670 6.33632374378242
ILMN_1653355 6.72169536049817
ILMN_1717783 6.08265206256593
ILMN_1705025 6.77701618132595
ILMN_1814316 6.5902250085549
ILMN_2359168 6.25952157804287
ILMN_1731507 6.23060684154937
ILMN_1787689 6.40496727952791
ILMN_3241953 7.77458377692841
ILMN_1745607 6.21636625407031
ILMN_2136495 6.34415339794958
ILMN_1668111 6.58282225826463
ILMN_2295559 6.59644552964942
ILMN_1735045 6.5160582976867
ILMN_1680754 6.7085197843493

Total number of rows: 47323

Table truncated, full table size 1379 Kbytes.




Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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