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Sample GSM433202 Query DataSets for GSM433202
Status Public on Mar 07, 2012
Title miRNA scramble expression in LNCaP, biological replicate 3
Sample type RNA
Source name Prostate cancer cell line LNCaP transfected with miRNA scramble
Organism Homo sapiens
Characteristics cell line: LNCaP
tumor: prostate cancer
tumor stage: early
mirna: scramble
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol 2µg RNA were analyzed according to the manufacturer's protocol.
Hybridization protocol Affymetrix GeneChip Human Genome U133A 2.0 Arrays were processed according to the manufacturer`s protocol.
Scan protocol GeneChips were processed using the Affymetrix GCS3000 7G system according to manufacturer`s protocol.
Description Gene expression data from LNCaP cells transfected with miRNA scramble.
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 RMA (robust multi-array average) procedure. Loss of mRNA expression was conducted by fitting a linear model using the R package limma. 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
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)
GSE17315 mRNA expression upon reconstitution of miR-130a, miR-203 and miR-205 in prostate cancer cell line LNCaP
GSE17362 miRNA expression, mRNA expression upon miRNA reconstitution, and direct mRNA target identification in prostate cancer cell lines

Data table header descriptions

Data table
1007_s_at 7.02338142589275
1053_at 5.44598696681148
117_at 2.36093727254010
121_at 2.38711533011513
1255_g_at 2.35939022713168
1294_at 2.56029197554362
1316_at 2.35939022713168
1320_at 2.35956509717133
1405_i_at 2.38504911450209
1431_at 2.35939022713168
1438_at 2.6001642406954
1487_at 5.92029308326465
1494_f_at 2.36009223958174
1598_g_at 2.39811209485749
160020_at 2.37433475378630
1729_at 4.91834372641066
1773_at 2.98030238668410
177_at 2.35939022713168
179_at 2.38044130127871
1861_at 3.81222277822527

Total number of rows: 22277

Table truncated, full table size 606 Kbytes.

Supplementary file Size Download File type/resource
GSM433202.CEL.gz 1.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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