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Sample GSM177585 Query DataSets for GSM177585
Status Public on Apr 01, 2007
Title MCF7 LMO4 low Replicate3B
Sample type RNA
Source name MCF7-LMO4-TetOff cells
Organism Homo sapiens
Characteristics Treatment with doxycycline results in low LMO4 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 Mar 31, 2007
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 GPL97
Series (1)
GSE7382 Expression profiling of MCF-7 cells with inducible LMO4 and DN-Clim expression

Data table header descriptions

Data table
AFFX-BioB-5_at 645.2 P 0.00762
AFFX-BioB-M_at 1219.2 P 0.000258
AFFX-BioB-3_at 637.8 P 0.004998
AFFX-BioC-5_at 1866.6 P 0.000147
AFFX-BioC-3_at 1422.8 P 0.000297
AFFX-BioDn-5_at 1684.3 P 0.000297
AFFX-BioDn-3_at 9917.4 P 0.000225
AFFX-CreX-5_at 17881.5 P 0.000044
AFFX-CreX-3_at 31982.8 P 0.000044
AFFX-DapX-5_at 61.8 A 0.216524
AFFX-DapX-M_at 97.4 A 0.340661
AFFX-DapX-3_at 33.6 A 0.659339
AFFX-LysX-5_at 55.1 A 0.39692
AFFX-LysX-M_at 73.4 A 0.574038
AFFX-LysX-3_at 37.5 A 0.340661
AFFX-PheX-5_at 5.8 A 0.945787
AFFX-PheX-M_at 12.5 A 0.9273
AFFX-PheX-3_at 80.1 A 0.544587
AFFX-ThrX-5_at 33.9 A 0.824672
AFFX-ThrX-M_at 74.2 A 0.440646

Total number of rows: 22645

Table truncated, full table size 592 Kbytes.

Supplementary file Size Download File type/resource
GSM177585.CEL.gz 3.5 Mb (ftp)(http) CEL

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