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Sample GSM1309445 Query DataSets for GSM1309445
Status Public on Jul 31, 2014
Title Patient 8 in group SynSa2 [transcriptome]
Sample type RNA
Source name tumor sample
Organism Homo sapiens
Characteristics histosubtype: synovial sarcoma
age at diagnosis [years]: 63
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 -2.1381464
DarkCorner -0.11381054
A_23_P146146 -0.2319231
A_23_P42935 -0.37696028
A_23_P117082 -0.5576315
A_23_P2683 -0.13736057
A_24_P358131 -0.15892649
A_33_P3367647 -0.23764896
A_23_P157316 -0.8319025
A_32_P14850 -0.41422558
A_23_P158596 0.64371777
A_23_P350107 0.17064953
A_23_P388190 -0.03146887
A_23_P106544 -0.8531656
A_33_P3219745 0.8512058
A_32_P85539 0.60315514
A_23_P94998 -0.5292039
A_33_P3235677 0.053055286
A_23_P417014 -0.4436226
A_23_P103905 -0.14258718

Total number of rows: 34183

Table truncated, full table size 802 Kbytes.

Supplementary file Size Download File type/resource
GSM1309445_SynSa2_8.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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