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Sample GSM363987 Query DataSets for GSM363987
Status Public on May 25, 2010
Title Podoplanin 6
Sample type RNA
Source name MCF7 breast carcinoma xenograft, human podoplanin transfected, cell clone 6
Organisms Homo sapiens; Mus musculus
Characteristics MCF7 human breast carcinoma cells, stably transfected with the pTet-Off regulator plasmid and the pTRE2hyg response plasmid (Clontech) containing full-length cDNA of human podoplanin (transcript variant 1, GenBank Accession number NM_006474), xenografted into BALB/cA nude mice. Cell clone podoplanin 6.
Growth protocol 15 mio. MCF7 human breast carcinoma cells, in a 1:1 mixture of serum-free DMEM and Cultrex basement membrane extract (R&D), were injected bilaterally into the mammary fatpad of 7 to 9 weeks old female BALB/cA nude mice (Taconic). The total injection volume was 0.2 ml. At the same time mice were implanted s.c. in the interscapular region with 0.72 mg, 60-day release 17β-estradiol pellets (Innovative Research of America). Each cell clone was injected into five mice and tumors were grown for 24 days before mice were euthanized and tumors harvested.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from approximately 25 mg RNAlater (Ambion)-stabilized tumor tissue using the EZ1 RNA Universal Tissue Kit and the BioRobot EZ1 (Qiagen), according to the manufacturer’s instructions, including DNase digestion. Equal amounts of RNA of each tumor derived from the same MCF7 cell clone (10 tumors per cell clone) were pooled into one sample for labeling and hybridization.
Label Digoxigenin-UTP
Label protocol Digoxigenin-UTP labeled cRNA was generated from 1 µg of total RNA for each sample using the Applied Biosystems NanoAmp RT-IVT Labeling Kit (PN 4365715) according to the manufacturer’s protocol.
Hybridization protocol Array hybridization, array processing, chemiluminescence detection, image acquisition, and analysis were performed using the Applied Biosystems Chemiluminescence Detection Kit (PN 4342142) and the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer according to the manufacturer’s protocol. 20 µg labeled cRNA were applied per array.
Scan protocol Scanning was performed according to the Chemiluminescent Detection Kit (PN 4339627) and Chemiluminescent Microarray Analyzer User Guide (PN 4338852).
Description comparative transcriptional profiling
Data processing The Expression Array System Software suite performs the auto-gridding, feature extraction, fluorescence normalization, and signal data generation. The quantification data contain many distinct measurements for each probe, including the three basic measurements: Signal, S/N, and Flag values. The Signal value is the fully corrected, background subtracted measurement of chemiluminescent signal for gene expression values. The S/N value represents the ratio of signal above noise, or the measurement uncertainty of the probe signal, and can be used as a confidence level for the probe measurement. An S/N of 3 represents approximately a 99.95% confidence that the probe is detected above the background noise. In situations where the probe showed S/N < 1, the signal measurement is replaced with a 1 SDEV upper limit based on its probe signal SDEV. Quantile normalization of the raw signals was performed using R software version 2.3.1 (The R Foundation for Statistical Computing).
Submission date Jan 23, 2009
Last update date May 24, 2010
Contact name Leah N Cueni
Organization name ETH Zurich
Department Institute of Pharmaceutical Sciences
Street address Wolfgang Pauli-Str. 10
City Zurich
ZIP/Postal code 8093
Country Switzerland
Platform ID GPL2995
Series (2)
GSE14551 Gene expression profiling of tumor stroma of MCF7 breast cancer xenografts overexpressing podoplanin (mouse array)
GSE14552 Gene expression profiling of MCF7 breast cancer xenografts overexpressing podoplanin

Data table header descriptions
VALUE Quantile normalized signal intensity calculated using R software version 2.3.1 (The R Foundation for Statistical Computing)

Data table
297784 37427.95472
297907 2039.310116
297912 3487.767417
297935 621.228494
297990 537.3037497
297993 608.4920113
298000 8928.346871
298038 443.1048105
298121 2096.398507
298130 680.0986002
298143 643.2729111
298150 546.6457955
298151 449.1981354
298155 547.2686982
298165 1240.020794
298174 2892.273047
298188 381.1798218
298200 52793.03919
298246 693.814982
298248 466.5909685

Total number of rows: 33012

Table truncated, full table size 608 Kbytes.

Supplementary file Size Download File type/resource
GSM363987.txt.gz 434.0 Kb (ftp)(http) TXT
Processed data included within Sample table

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