NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1394605 Query DataSets for GSM1394605
Status Public on Apr 21, 2015
Title LNCaP_Scr_36h_B2
Sample type RNA
 
Source name LNCaP_Scr_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 negative control #1 (scrambled pre-miR, Scr) 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 negative control #1 (scrambled pre-miR, Scr) 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 6.6155207581266
ILMN_2055271 6.9436762605691
ILMN_1736007 6.52788470104292
ILMN_2383229 6.52976272486102
ILMN_1806310 6.47243488704967
ILMN_1779670 6.73837021432146
ILMN_1653355 6.62621827522647
ILMN_1717783 6.31978941302602
ILMN_1705025 6.84856950580415
ILMN_1814316 6.59652372609402
ILMN_2359168 6.3702358157333
ILMN_1731507 6.21767589315284
ILMN_1787689 6.64990200398388
ILMN_3241953 7.26072395418323
ILMN_1745607 6.21817228638053
ILMN_2136495 6.33609117602214
ILMN_1668111 6.6434932803844
ILMN_2295559 6.92878895572667
ILMN_1735045 6.55819491165321
ILMN_1680754 6.73123420484624

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