GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM177589 Query DataSets for GSM177589
Status Public on Apr 01, 2007
Title MCF7 DN-CLIM low Replicate1
Sample type RNA
Source name MCF7-DN-CLIM-TetOff cells
Organism Homo sapiens
Characteristics Treatment with doxycycline results in low DN-CLIM level.
Extracted molecule total RNA
Extraction protocol Isolated total RNA samples were processed as recommended by Affymetrix, Inc. (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetric, Inc., Santa Clara, CA). In brief, total RNA was initially isolated using TRIzol Reagent (Gibco BRL Life Technologies, Rockville, MD), and passed through an RNeasy spin column (Qiagen, Chatsworth, CA) for further clean up. Eluted total RNAs were quantified with a portion of the recovered total RNA adjusted to a final concentration of 1 ug/ul. All starting total RNA samples were quality assessed prior to beginning target preparation/processing steps by running out a small amount of each sample (typically 25-250 ng/well) onto a RNA Lab-On-A-Chip (Caliper Technologies Corp., Mountain View, CA) that was evaluated on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).
Label biotin
Label protocol Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+ mRNA present in the isolated total RNA (10 ug total RNA starting material each sample reaction) using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Corp., Carlsbad, CA ) and poly (T)-nucleotide primers that contained a sequence recognized by T7 RNA polymerase. A portion of the resulting ds cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction (IVT), using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics, Inc., Farmingdale, NY). 15ug of the resulting biotin-tagged cRNA was fragmented to strands of 35-200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).
Hybridization protocol Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix HG-U133A array.
Scan protocol The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450, followed by scanning on a GeneChip Scanner 3000. The results were quantified and analyzed using GCOS 1.1.1 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity = 500; Normalization, All Probe Sets; Parameters, all set at default values).
Description LMO4 - LIM-only protein 4
Data processing MAS 5.0
Submission date Mar 27, 2007
Last update date Aug 28, 2018
Contact name Kevin K Lin
Organization name University of California, Irvine
Department Biological Chemistry & Medicine
Lab Bogi Andersen
Street address 250 Sprague Hall
City Irvine
State/province CA
ZIP/Postal code 92697-4030
Country USA
Platform ID GPL570
Series (1)
GSE7382 Expression profiling of MCF-7 cells with inducible LMO4 and DN-Clim expression
Reanalyzed by GSE64985
Reanalyzed by GSE119087

Data table header descriptions

Data table
AFFX-BioB-5_at 411.2 P 0.013811
AFFX-BioB-M_at 458.3 P 0.000581
AFFX-BioB-3_at 238.4 P 0.015175
AFFX-BioC-5_at 883.6 P 0.000095
AFFX-BioC-3_at 657.6 P 0.00039
AFFX-BioDn-5_at 873.2 P 0.000147
AFFX-BioDn-3_at 5998.1 P 0.000258
AFFX-CreX-5_at 11397.4 P 0.000044
AFFX-CreX-3_at 14112.1 P 0.000044
AFFX-DapX-5_at 43.6 A 0.067678
AFFX-DapX-M_at 71 A 0.195266
AFFX-DapX-3_at 4.5 A 0.891021
AFFX-LysX-5_at 10.7 A 0.724854
AFFX-LysX-M_at 10.4 A 0.672921
AFFX-LysX-3_at 5.4 A 0.455413
AFFX-PheX-5_at 8.8 A 0.843268
AFFX-PheX-M_at 5.4 A 0.760937
AFFX-PheX-3_at 58.2 A 0.617401
AFFX-ThrX-5_at 8.1 A 0.876428
AFFX-ThrX-M_at 15.6 A 0.559354

Total number of rows: 54675

Table truncated, full table size 1443 Kbytes.

Supplementary file Size Download File type/resource
GSM177589.CEL.gz 7.9 Mb (ftp)(http) CEL

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