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Sample GSM1309429 Query DataSets for GSM1309429
Status Public on Jul 31, 2014
Title Patient 5 in group SynSa1 [transcriptome]
Sample type RNA
Source name tumor sample
Organism Homo sapiens
Characteristics histosubtype: synovial sarcoma
age at diagnosis [years]: 28
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 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 1.1698818
DarkCorner -0.60225487
A_23_P146146 -0.654202
A_23_P42935 0.24684238
A_23_P117082 -0.10026455
A_23_P2683 0.20648623
A_24_P358131 0.0
A_33_P3367647 -0.68329144
A_23_P157316 -0.27620792
A_32_P14850 0.13981247
A_23_P158596 0.11847782
A_23_P350107 -0.43105125
A_23_P388190 0.35400295
A_23_P106544 -0.3939867
A_33_P3219745 0.102775574
A_32_P85539 0.21105194
A_23_P94998 0.050485134
A_33_P3235677 1.0990272
A_23_P417014 -1.0514092
A_23_P103905 0.13535595

Total number of rows: 34183

Table truncated, full table size 797 Kbytes.

Supplementary file Size Download File type/resource
GSM1309429_SynSa1_5.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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