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Sample GSM567173 Query DataSets for GSM567173
Status Public on Mar 07, 2012
Title AGO2-RNA upon miR-205 reconstitution in LNCaP, biological replicate 3
Sample type RNA
 
Source name AGO2 bound RNA in prostate cancer cell line LNCaP upon miR-205 reconstitution
Organism Homo sapiens
Characteristics cell line: LNCaP
tissue: prostate cancer
tumor stage: early
Treatment protocol Cells were transfected using the Nucleofector 2 Technology (Amaxa) according to the instructions. For miRNA reconstitution 2.5ug plasmid DNA for each miRNA was used. AGO2 RNA co-immunoprecipitation (AGO2 co-IP) was performed using AG02-1 11A antibody (Ascenion).
Growth protocol Cells were grown in medium to confluency (LNCaP cells: RPMI 1640 medium with L-glutamine (PAA) (10%FCS (Biochrom), 100Units/ml penicillin, 100 µg/ml streptomycin (PAA) and 10mM HEPES buffer (Biochrom), PC-3 and Du-145 cells: DMEM/F-12 medium with L-glutamine (PAA) (10\%FCS (Biochrom), 100Units/ml penicillin, 100 µg/ml streptomycin (PAA)), and RWPE-1 cells: Keratinocyte-Serum free medium (Gibco-BRL) (5ng/ml human recombinant EGF and 0.05mg/ml bovine pituary extract (Gibco-BRL))).
Extracted molecule total RNA
Extraction protocol Trizol extraction of AGO2 bound RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol 2µg RNA were analyzed on Affymetrix GeneChip Human Genome U133A 2.0 Arrays according to the manufacturer`s protocol.
 
Hybridization protocol GeneChips were proceed using the Affymetrix GCS3000 7G system according to manufacturer`s protocol.
Scan protocol GeneChips were proceed using the Affymetrix GCS3000 7G system according to manufacturer`s protocol.
Description AGO2 bound RNA
For identifying direct targets of miR-205 a AGO2-RNA co-immunoprecipitation as described by (Beitzinger et al. 2007) was performed. AGO2-bound mRNAs were identified by using Affymetrix Genechips.
Data processing The data were analyzed with R (version 2.9.0) and BioConductor (version 2.4). Quality assessment of arrays included exploration of distributions of probe intensities across all arrays, of average background values, and RNA quality was examined by RNA degradation plots. Diagnostic plots based on a probe level model (PLM) have been used to rule out chips with spatial artifacts (Chip pseudo-images, normalized unscaled standard error (NUSE) plot and relative log expression (RLE) plot). Background adjusted normalized data was retrieved by the GCRMA (robust multi-array average) procedure.
 
Submission date Jul 16, 2010
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 GPL571
Series (2)
GSE17362 miRNA expression, mRNA expression upon miRNA reconstitution, and direct mRNA target identification in prostate cancer cell lines
GSE22979 Profiling of direct mRNA targets of miR-130a, miR-203 and miR-205 in prostate cancer cell line LNCaP

Data table header descriptions
ID_REF
VALUE GCRMA normalized signal intensity

Data table
ID_REF VALUE
1007_s_at 6.86738938772703
1053_at 3.66506017307294
117_at 2.36465406742836
121_at 2.39436083782272
1255_g_at 2.34732728554919
1294_at 2.50928475428101
1316_at 3.11385032429501
1320_at 2.40217673342029
1405_i_at 2.35409212686491
1431_at 2.3481420180511
1438_at 2.80818228067287
1487_at 6.22936450921182
1494_f_at 2.34732728554919
1598_g_at 2.36353808986667
160020_at 2.38491005367853
1729_at 3.99791708294769
1773_at 2.71885586515756
177_at 2.34732728554919
179_at 2.39295772936225
1861_at 3.62385818977168

Total number of rows: 22277

Table truncated, full table size 606 Kbytes.




Supplementary file Size Download File type/resource
GSM567173.CEL.gz 1.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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