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Sample GSM363989 Query DataSets for GSM363989
Status Public on May 25, 2010
Title Podoplanin 14
Sample type RNA
Source name MCF7 breast carcinoma xenograft, human podoplanin transfected, cell clone 14
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 14.
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 41988.39357
297907 358.7237887
297912 4884.264765
297935 315.5875848
297990 299.015691
297993 463.0909127
298000 16558.09951
298038 316.6194257
298121 879.8568836
298130 888.7008535
298143 2758.676424
298150 298.9329244
298151 535.8606874
298155 764.1555855
298165 703.5570567
298174 681.849013
298188 617.1961158
298200 62257.20922
298246 1015.678554
298248 546.2943094

Total number of rows: 33012

Table truncated, full table size 608 Kbytes.

Supplementary file Size Download File type/resource
GSM363989.txt.gz 436.7 Kb (ftp)(http) TXT
Processed data included within Sample table

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