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Sample GSM324888 Query DataSets for GSM324888
Status Public on May 28, 2009
Title MCF-7 Luciferase Replicate 1
Sample type RNA
Source name MCF-7 Cells Luciferase Knockdown (control)
Organism Homo sapiens
Characteristics MCF-7 Cells Luciferase Knockdown (control)
Extracted molecule total RNA
Extraction protocol Total RNA was prepared using Trizol Reagent according to the manufacturer’s instructions (Invitrogen) and was further purified using RNeasy columns (Qiagen).
Label Biotin
Label protocol Seven μg of total RNA were subjected to One-Cycle Target Labeling Assay (Affymetrix) to generate biotinylated cRNA targets for hybridization to Affymetrix U133A 2.0 microarray.
Hybridization protocol Standard hybridization to Affymetrix U133A 2.0 microarray.
Scan protocol Standard scanning protocol using GeneChip Scanner.
Description N/A
Data processing The raw data were processed by Affymetrix GCOS software to obtain detection calls and signal values, and then normalized by scaling. Signals were then used in further analysis, namely batch effect adjusted and log2 median-normalized using COMBAT R.
Submission date Sep 28, 2008
Last update date May 28, 2009
Contact name W. Lee Kraus
Organization name UT Southwestern Medical Center
Street address 5323 Harry Hines Blvd.
City Dallas
State/province TX
ZIP/Postal code 75390-8511
Country USA
Platform ID GPL571
Series (4)
GSE12952 Expression Analysis Upon PARP-1 or PARG Knockdown in MCF-7 Cells
GSE12971 MCF-7 Luciferase, PARP-1, PARG, SIRT1, and macroH2A Knockdown
GSE13459 Expression analysis upon SIRT1 knockdown in MCF-7 cells

Data table header descriptions
ABS_CALL Detection Call (Present, Marginal, or Absent)
DETECTION P-VALUE P-value indicating significance level of the detection call
VALUE_2 GCOS-calculated signal intensity
VALUE Batch effect adjusted, log2 median-normalized signal intensity generated through COMBAT R

Data table
AFFX-BioB-5_at P 0.00034 435.7 0.427659
AFFX-BioB-M_at P 0.000044 467.3 0.072852
AFFX-BioB-3_at P 0.00007 265.2 0.316162
AFFX-BioC-5_at P 0.000044 907.2 0.124353
AFFX-BioC-3_at P 0.000052 1156.8 0.14191
AFFX-BioDn-5_at P 0.000044 2475 0.100259
AFFX-BioDn-3_at P 0.000052 4828.8 0.0739
AFFX-CreX-5_at P 0.000044 11451.1 0.126993
AFFX-CreX-3_at P 0.000044 14684.8 0.148549
AFFX-DapX-5_at P 0.000044 1697.7 -0.123235
AFFX-DapX-M_at P 0.000081 2870.8 -0.16223
AFFX-DapX-3_at P 0.000044 3623.6 -0.153224
AFFX-LysX-5_at P 0.00011 202.7 0.002564
AFFX-LysX-M_at P 0.000147 305.8 -0.249618
AFFX-LysX-3_at P 0.000044 587.4 -0.05798
AFFX-PheX-5_at P 0.000044 350.2 -0.20075
AFFX-PheX-M_at P 0.00007 558.9 -0.161302
AFFX-PheX-3_at P 0.000044 395.7 -0.003936
AFFX-ThrX-5_at P 0.000052 470.8 -0.020094
AFFX-ThrX-M_at P 0.000044 738.5 -0.229511

Total number of rows: 22277

Table truncated, full table size 783 Kbytes.

Supplementary file Size Download File type/resource
GSM324888.CEL.gz 2.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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