NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1394598 Query DataSets for GSM1394598
Status Public on Apr 21, 2015
Title LNCaP_miR-135b_36h_B1
Sample type RNA
 
Source name LNCaP_miR-135b_36h
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: 36h
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 36h
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 6.55999991530024
ILMN_2055271 6.99366593507317
ILMN_1736007 6.74405349203296
ILMN_2383229 6.59863592205232
ILMN_1806310 6.54938407128597
ILMN_1779670 6.46541568199743
ILMN_1653355 6.71030366834892
ILMN_1717783 6.10258322276924
ILMN_1705025 6.80736536339474
ILMN_1814316 6.67301053814913
ILMN_2359168 6.51707507112712
ILMN_1731507 6.41148008485599
ILMN_1787689 6.28592100166344
ILMN_3241953 7.8009236300269
ILMN_1745607 6.16729448291367
ILMN_2136495 6.39211439110833
ILMN_1668111 6.40898600860723
ILMN_2295559 6.53801925114642
ILMN_1735045 6.76218224421684
ILMN_1680754 6.82176152012306

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap