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Sample GSM1309465 Query DataSets for GSM1309465
Status Public on Jul 31, 2014
Title Patient 5 in group SynSa3 [transcriptome]
Sample type RNA
Source name tumor sample
Organism Homo sapiens
Characteristics histosubtype: synovial sarcoma
age at diagnosis [years]: 47
gender: Male
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 0.030136585
DarkCorner 0.4813962
A_23_P146146 0.40500355
A_23_P42935 2.318056
A_23_P117082 -0.029325247
A_23_P2683 -0.05888915
A_24_P358131 0.06331396
A_33_P3367647 1.0891061
A_23_P157316 0.09619331
A_32_P14850 0.19878006
A_23_P158596 -2.317558
A_23_P350107 -0.03791356
A_23_P388190 -0.25974774
A_23_P106544 -1.7435746
A_33_P3219745 0.66815615
A_32_P85539 -0.6208644
A_23_P94998 0.029876947
A_33_P3235677 3.0911942
A_23_P417014 0.17307854
A_23_P103905 -1.0963054

Total number of rows: 34183

Table truncated, full table size 801 Kbytes.

Supplementary file Size Download File type/resource
GSM1309465_SynSa3_5.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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