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Sample GSM324889 Query DataSets for GSM324889
Status Public on May 28, 2009
Title MCF-7 Luciferase Replicate 2
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 0.00039 479.8 0.11388
AFFX-BioB-M_at P 0.000052 443.4 0.096697
AFFX-BioB-3_at P 0.000258 266.2 0.012647
AFFX-BioC-5_at P 0.000044 919.9 0
AFFX-BioC-3_at P 0.000044 1161.6 0.038606
AFFX-BioDn-5_at P 0.000044 2083.3 0
AFFX-BioDn-3_at P 0.00007 4580.5 0.03593
AFFX-CreX-5_at P 0.000044 10546.9 0
AFFX-CreX-3_at P 0.000044 13987.8 0.007596
AFFX-DapX-5_at P 0.00006 1005.9 -0.142123
AFFX-DapX-M_at P 0.000127 1869.1 -0.158421
AFFX-DapX-3_at P 0.000052 2323.5 -0.158116
AFFX-LysX-5_at P 0.000856 161.4 0.036205
AFFX-LysX-M_at P 0.004017 168.4 0.125866
AFFX-LysX-3_at P 0.00011 325.8 0.091693
AFFX-PheX-5_at P 0.00007 194.3 -0.122876
AFFX-PheX-M_at P 0.00006 260.1 0.047613
AFFX-PheX-3_at P 0.000052 287.6 -0.085509
AFFX-ThrX-5_at P 0.000095 281.3 -0.026131
AFFX-ThrX-M_at P 0.000081 373 -0.204685

Total number of rows: 22277

Table truncated, full table size 784 Kbytes.

Supplementary file Size Download File type/resource
GSM324889.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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