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Sample GSM1196235 Query DataSets for GSM1196235
Status Public on Feb 01, 2016
Title 241102_Di
Sample type RNA
 
Channel 1
Source name tumor
Organism Mus musculus
Characteristics tissue: high-grade astrocytoma (HGA) tumor
ID: 241102
genotype: TRPnull
brain location: Di
batch: 1
subtype: 3
survival (mo): 3.25
diagnosis: GBM
Treatment protocol Tumors were harvested from bains of mice and immediately flash-frozen in liquid nitrogen.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted s with Qiagen RNeasy kit according to manufacturer's instructions
Label Cy5
Label protocol Labeling was performed according to the Low RNA Input Linear Amplification kit from Agilent. 1µg of RNA was primed with 1.2 µl of provided T7 promoter primer at 65 °C for 10 minutes. Reverse transcription was performed with provided Moloney Murine Leukemia Virus Reverse Transcriptase at 40 °C for 2 hours, 65 °C for 15 minutes, and 4 °C for 5 minutes. Laeled RNA was made by adding 1µl of 10mM Cy3 or Cy5 added to trancription cocktail and incubated at 40 °C for 2 hours, 4 °C for 1 minute.
 
Channel 2
Source name Stratagene whole mouse reference RNA
Organism Mus musculus
Characteristics sample type: Stratagene whole mouse reference RNA
Treatment protocol Tumors were harvested from bains of mice and immediately flash-frozen in liquid nitrogen.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted s with Qiagen RNeasy kit according to manufacturer's instructions
Label Cy3
Label protocol Labeling was performed according to the Low RNA Input Linear Amplification kit from Agilent. 1µg of RNA was primed with 1.2 µl of provided T7 promoter primer at 65 °C for 10 minutes. Reverse transcription was performed with provided Moloney Murine Leukemia Virus Reverse Transcriptase at 40 °C for 2 hours, 65 °C for 15 minutes, and 4 °C for 5 minutes. Laeled RNA was made by adding 1µl of 10mM Cy3 or Cy5 added to trancription cocktail and incubated at 40 °C for 2 hours, 4 °C for 1 minute.
 
 
Hybridization protocol Labeled sample RNA and Stratagen Universal Mouse Reference RNA (Agilent, #740100) as a reference were cohybridized at 65 C for 17 hours in a rotating hybridization oven.
Scan protocol Microarrays were scanned on an Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology (Part no. G2565CA)
Data processing Image analyzed using Agilent Feature Extraction Software. Data was uploaded to the UNC microarray database (UMD). Data was normalized in UMD using Lowess normalization on the Cy3 and Cy5 channels. Data extraction was performed by selecting genes with an absolute signal intensity of at least 10 units in both dye channels and data present in at least 70% of experimental samples, afterwhich replicate probe IDs were collapsed by averaging. Samples from different batches were combined using the parametric settings in combatR, a module in the R statistical programming language (R Development Core Team, 2006 http://www.R-project.org) with no covariates included. Normalized data provided is the filtered, batch combined, non-median centered data used to draw conclusions in the study.
 
Submission date Jul 26, 2013
Last update date Feb 01, 2016
Contact name Ryan Miller
E-mail(s) miller@med.unc.edu
Phone 919-966-4333
Organization name University of North Carolina
Department Pathology
Street address 6109B NRB CB 7250
City Chapel HIll
State/province North Carolina
ZIP/Postal code 27599
Country USA
 
Platform ID GPL11202
Series (2)
GSE49266 Progression from low- to high-grade astrocytoma is characterized by transcriptomal heterogeneity and genomic number copy alterations (part 2)
GSE49269 Progression from low- to high-grade astrocytoma is characterized by transcriptomal heterogeneity and genomic number copy alterations

Data table header descriptions
ID_REF
VALUE lowess normalized log2 ratio (cy5/cy3)

Data table
ID_REF VALUE
A_51_P100034 0.690969448
A_51_P100174 0.203780971
A_51_P100208 2.441301055
A_51_P100289 -0.351083462
A_51_P100298 -1.073858192
A_51_P100309 0.038247903
A_51_P100327 0.939356534
A_51_P100537 -0.140697639
A_51_P100573 0.065060642
A_51_P100625 -0.171485697
A_51_P100768 -0.56246774
A_51_P100776 0.151943964
A_51_P100787 -0.053237212
A_51_P100828 -0.721786285
A_51_P100852 -1.174394798
A_51_P100991 -0.681300918
A_51_P100997 0.092313004
A_51_P101006 0.53672072
A_51_P101075 0.006352545
A_51_P101137 1.47403767

Total number of rows: 31810

Table truncated, full table size 806 Kbytes.




Supplementary file Size Download File type/resource
GSM1196235_US82800149_252665511644_S01_GE2_105_Dec08_1_1.txt.gz 15.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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