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Sample GSM1309475 Query DataSets for GSM1309475
Status Public on Jul 31, 2014
Title Patient 15 in group SynSa3 [transcriptome]
Sample type RNA
Source name tumor sample
Organism Homo sapiens
Characteristics histosubtype: synovial sarcoma
age at diagnosis [years]: 23
gender: Female
Treatment protocol not applicable
Growth protocol not applicable
Extracted molecule total RNA
Extraction protocol Total RNA of sufficient integrity and purity was obtained from 57 tumor specimens using the miRNeasy Mini Kit (Qiagen) with optional DNase treatment using RNase-free DNase Set (Qiagen). RNA quality was checked using Bio-Rad Experion system (Bio-Rad Laboratories).
Label Cy3
Label protocol Total RNA (25ng) was reverse transcribed into cDNA by incorporating a T7 oligo-dT promoter primer prior to the generation of fluorescent cRNA using an Agilent LowInput Quick Amp Labeling Kit (Agilent Technologies, SantaClara, CA, USA).
Hybridization protocol Gene expression analysis was performed using Human Gene Expression 4x44K v2 microarrays (G4845A) according to the one-color microarray-based expression analysis protocol (Agilent Technologies).
Scan protocol The microarray slides were scanned using the Agilent G2565A DNA Microarray Scanner (Agilent Technologies, SantaClara, CA, USA).
Description Gene expression in metastatic/recurrent tumor sample
Data processing Image analysis was done using the Feature Extraction V10.10.1.1 software (Agilent Technologies, SantaClara, CA, USA). Microarray data were analyzed using Gene Spring GX default workflow parameters for Agilent one-color expression experiments (Agilent Technologies, SantaClara, CA, USA).
Submission date Jan 17, 2014
Last update date Jul 31, 2014
Contact name Joanna Przybyl
Organization name Stanford University
Department Department of Pathology
Street address 300 Pasteur Drive
City Stanford
ZIP/Postal code 94305
Country USA
Platform ID GPL13497
Series (2)
GSE54187 Metastatic potential is determined early in synovial sarcoma development and reflected by tumor molecular features [transcriptome]
GSE54188 Metastatic potential is determined early in synovial sarcoma development and reflected by tumor molecular features

Data table header descriptions
VALUE Normalized signal intensity (Quantile normalization)

Data table
GE_BrightCorner 0.99556684
DarkCorner 5.531352
A_23_P146146 5.491362
A_23_P42935 0.5674095
A_23_P117082 -1.5159903
A_23_P2683 -0.37372983
A_24_P358131 2.656418
A_33_P3367647 5.5171795
A_23_P157316 5.9680557
A_32_P14850 -1.1065416
A_23_P158596 6.0674267
A_23_P350107 -0.6836715
A_23_P388190 -2.029835
A_23_P106544 -2.4433472
A_33_P3219745 3.8878508
A_32_P85539 -2.480276
A_23_P94998 -0.77360547
A_33_P3235677 2.44657
A_23_P417014 5.311876
A_23_P103905 -1.3146536

Total number of rows: 34183

Table truncated, full table size 783 Kbytes.

Supplementary file Size Download File type/resource
GSM1309475_SynSa3_15.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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