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Sample GSM1309469 Query DataSets for GSM1309469
Status Public on Jul 31, 2014
Title Patient 9 in group SynSa3 [transcriptome]
Sample type RNA
Source name tumor sample
Organism Homo sapiens
Characteristics histosubtype: synovial sarcoma
age at diagnosis [years]: 56
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 0.7155781
DarkCorner -0.4952612
A_23_P146146 -0.6109824
A_23_P42935 -0.016880512
A_23_P117082 -0.6740649
A_23_P2683 1.4617054
A_24_P358131 -2.331388
A_33_P3367647 -0.6192374
A_23_P157316 -2.827179
A_32_P14850 0.3485713
A_23_P158596 0.45672727
A_23_P350107 -2.6619737
A_23_P388190 -0.33653474
A_23_P106544 1.2443938
A_33_P3219745 -0.17414618
A_32_P85539 0.23341179
A_23_P94998 -1.1036799
A_33_P3235677 -0.05138302
A_23_P417014 -0.8514199
A_23_P103905 0.2883339

Total number of rows: 34183

Table truncated, full table size 812 Kbytes.

Supplementary file Size Download File type/resource
GSM1309469_SynSa3_9.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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