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Sample GSM1309434 Query DataSets for GSM1309434
Status Public on Jul 31, 2014
Title Patient 10 in group SynSa1 [transcriptome]
Sample type RNA
Source name tumor sample
Organism Homo sapiens
Characteristics histosubtype: synovial sarcoma
age at diagnosis [years]: 27
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 primary 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 -0.16652107
DarkCorner 0.0
A_23_P146146 -0.022559643
A_23_P42935 -0.4789939
A_23_P117082 -0.45798016
A_23_P2683 0.040368557
A_24_P358131 0.14933729
A_33_P3367647 -0.034112453
A_23_P157316 0.0
A_32_P14850 0.08849621
A_23_P158596 -0.5261879
A_23_P350107 -0.13376617
A_23_P388190 -1.1637197
A_23_P106544 0.35826683
A_33_P3219745 -0.1693654
A_32_P85539 -0.097682
A_23_P94998 0.5596061
A_33_P3235677 -0.80159235
A_23_P417014 -0.38559628
A_23_P103905 -0.17743397

Total number of rows: 34183

Table truncated, full table size 790 Kbytes.

Supplementary file Size Download File type/resource
GSM1309434_SynSa1_10.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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