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Sample GSM1309479 Query DataSets for GSM1309479
Status Public on Jul 31, 2014
Title Patient 20 in group SynSa3 [transcriptome]
Sample type RNA
Source name tumor sample
Organism Homo sapiens
Characteristics histosubtype: synovial sarcoma
age at diagnosis [years]: 15
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 0.01665783
DarkCorner -0.5649829
A_23_P146146 -0.63711834
A_23_P42935 -0.8970561
A_23_P117082 0.26359916
A_23_P2683 0.16623282
A_24_P358131 1.9039421
A_33_P3367647 -0.6387882
A_23_P157316 -1.5924702
A_32_P14850 -0.8356166
A_23_P158596 0.6260488
A_23_P350107 0.046230555
A_23_P388190 0.1816032
A_23_P106544 0.32349348
A_33_P3219745 -0.54811
A_32_P85539 0.1834755
A_23_P94998 -0.32272458
A_33_P3235677 0.20765448
A_23_P417014 -0.8625784
A_23_P103905 1.1052818

Total number of rows: 34183

Table truncated, full table size 815 Kbytes.

Supplementary file Size Download File type/resource
GSM1309479_SynSa3_20.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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