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Sample GSM1394601 Query DataSets for GSM1394601
Status Public on Apr 21, 2015
Title LNCaP_Scr_12h_B2
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.
 
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 6.65277091932508
ILMN_2055271 6.94015039627592
ILMN_1736007 6.84000406111891
ILMN_2383229 6.39777078236088
ILMN_1806310 6.54608785838553
ILMN_1779670 6.59339787789636
ILMN_1653355 6.70081002552529
ILMN_1717783 5.98272434774297
ILMN_1705025 6.4218346331608
ILMN_1814316 6.43601238876817
ILMN_2359168 6.31566620135466
ILMN_1731507 6.09910419970077
ILMN_1787689 6.49243389335064
ILMN_3241953 7.28361178398854
ILMN_1745607 6.30330057246304
ILMN_2136495 6.33077716008385
ILMN_1668111 6.53022947758657
ILMN_2295559 6.83558587204477
ILMN_1735045 6.60706962622594
ILMN_1680754 6.49694027314805

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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