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Sample GSM1394600 Query DataSets for GSM1394600
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.
 
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 6.78699111349721
ILMN_2055271 6.90446800341575
ILMN_1736007 6.6372437159577
ILMN_2383229 6.56523805006788
ILMN_1806310 6.43981238805751
ILMN_1779670 6.66812916844883
ILMN_1653355 6.69674972973586
ILMN_1717783 6.15760885155541
ILMN_1705025 6.49165100333303
ILMN_1814316 6.50991077287327
ILMN_2359168 6.42306911043638
ILMN_1731507 6.07091504229883
ILMN_1787689 6.47075172741086
ILMN_3241953 7.1271429087747
ILMN_1745607 6.1229593130338
ILMN_2136495 6.39513488652193
ILMN_1668111 6.52846483402858
ILMN_2295559 6.60181676688133
ILMN_1735045 6.57088707939616
ILMN_1680754 6.59230308466447

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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