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Sample GSM1309439 Query DataSets for GSM1309439
Status Public on Jul 31, 2014
Title Patient 16 in group SynSa1 [transcriptome]
Sample type RNA
 
Source name tumor sample
Organism Homo sapiens
Characteristics histosubtype: synovial sarcoma
age at diagnosis [years]: 5
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
E-mail(s) jprzybyl@stanford.edu
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
ID_REF
VALUE Normalized signal intensity (Quantile normalization)

Data table
ID_REF VALUE
GE_BrightCorner 2.7262478
DarkCorner 0.70251656
A_23_P146146 0.61675215
A_23_P42935 -0.011548042
A_23_P117082 -0.04221487
A_23_P2683 0.44356346
A_24_P358131 1.9456625
A_33_P3367647 0.5863962
A_23_P157316 0.7675636
A_32_P14850 -2.056682
A_23_P158596 -0.19139719
A_23_P350107 0.24054956
A_23_P388190 -0.12217474
A_23_P106544 -0.32170916
A_33_P3219745 0.23332739
A_32_P85539 -1.2452703
A_23_P94998 0.0
A_33_P3235677 1.7099714
A_23_P417014 1.0755658
A_23_P103905 -0.030470371

Total number of rows: 34183

Table truncated, full table size 789 Kbytes.




Supplementary file Size Download File type/resource
GSM1309439_SynSa1_16.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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