NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM433222 Query DataSets for GSM433222
Status Public on Mar 07, 2012
Title miRNA expression analysis in LNCaP, biological replicate 1
Sample type RNA
 
Source name Early prostate cancer cell line LNCaP
Organism Homo sapiens
Characteristics cell line: LNCaP
tumor: prostate cancer
tumor stage: early
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label Cy5
Label protocol 1µg microRNA was Cy-5-labeled using the Mirus Bio Label IT miRNA Labeling Kit according to the manufacturer`s protocol
 
Hybridization protocol according to CombiMatrix miRNA microarray hybridization protocol
Scan protocol Arrays were scanned using a GenePix 4200 Scanner and the GenePix Pro 6.1 Software (Molecular Devices) with following settings: laser power: 40%, PMT: 500, resolution: 5µm, Focus: 85µm.
Description miRNA expression analysis in early prostate cancer cell line LNCaP.
Data processing The data were analyzed with R (version 2.9.0) and BioConductor (version 2.4). Expression levels were normalized (quantile normalization) and a linear model was fitted using the R package limma in order to identify differentially expressed miRNAs. Reliable variance estimations were obtained by empirical Bayes moderated t-statistics. False discovery rate was controlled by Benjamini-Hochberg adjustment.
 
Submission date Jul 24, 2009
Last update date Mar 07, 2012
Contact name Kristin Reiche
E-mail(s) kristin.reiche@izi.fraunhofer.de
Organization name Fraunhofer Institute for Cell Therapy and Immunology
Department Diagnostics
Street address Perlickstr. 1
City Leipzig
ZIP/Postal code 04103
Country Germany
 
Platform ID GPL8899
Series (2)
GSE17317 miRNA expression in LNCaP, PC3, Du-145 and RWPE-1 cell lines
GSE17362 miRNA expression, mRNA expression upon miRNA reconstitution, and direct mRNA target identification in prostate cancer cell lines

Data table header descriptions
ID_REF
VALUE Quantile-normalized value

Data table
ID_REF VALUE
hsa|let-7a|2mut|as|_ArraySector1 10.8850085523134
hsa|let-7a|nat|as|_ArraySector1 15.9463075894578
hsa|let-7b|2mut|as|_ArraySector1 11.3738115872316
hsa|let-7b|nat|as|_ArraySector1 15.9393351938398
hsa|let-7c|2mut|as|_ArraySector1 10.8381761851656
hsa|let-7c|nat|as|_ArraySector1 15.9756538064959
hsa|let-7d|2mut|as|_ArraySector1 10.2857588733409
hsa|let-7d|nat|as|_ArraySector1 15.9136165736534
hsa|let-7e|2mut|as|_ArraySector1 9.77016574955783
hsa|let-7e|nat|as|_ArraySector1 14.3799559192339
hsa|let-7f|2mut|as|_ArraySector1 9.27166108887747
hsa|let-7f|nat|as|_ArraySector1 13.6166396068793
hsa|let-7g|2mut|as|_ArraySector1 9.0972061262494
hsa|let-7g|nat|as|_ArraySector1 12.288382420626
hsa|let-7i|2mut|as|_ArraySector1 9.37589998615323
hsa|let-7i|nat|as|_ArraySector1 11.6778873750260
hsa|miR-100|2mut|as|_ArraySector1 9.44753944703355
hsa|miR-100|nat|as|_ArraySector1 15.379140959724
hsa|miR-101|2mut|as|_ArraySector1 10.4426551532726
hsa|miR-101|nat|as|_ArraySector1 10.9855837373119

Total number of rows: 3760

Table truncated, full table size 186 Kbytes.




Supplementary file Size Download File type/resource
GSM433222.gpr.gz 913.6 Kb (ftp)(http) GPR
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap