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Sample GSM1196263 Query DataSets for GSM1196263
Status Public on Feb 01, 2016
Title 246300_BS
Sample type RNA
 
Channel 1
Source name tumor
Organism Mus musculus
Characteristics tissue: high-grade astrocytoma (HGA) tumor
ID: 246300
genotype: TRPhet
brain location: BS
batch: 3
subtype: 1
survival (mo): 4.17
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 0.695067764
A_51_P100174 1.280834419
A_51_P100208 2.203516525
A_51_P100289 -0.708154988
A_51_P100298 -1.299807375
A_51_P100309 0.05018822
A_51_P100327 2.448791775
A_51_P100537 -0.32654082
A_51_P100573 0.290601526
A_51_P100625 -0.142156284
A_51_P100768 -0.308690459
A_51_P100776 0.038569949
A_51_P100787 -0.060184897
A_51_P100828 -1.073208255
A_51_P100852 1.911325971
A_51_P100991 -0.45949231
A_51_P100997 0.114398819
A_51_P101006 0.30688287
A_51_P101075 0.136229111
A_51_P101137 1.651045068

Total number of rows: 31810

Table truncated, full table size 806 Kbytes.




Supplementary file Size Download File type/resource
GSM1196263_US82800149_252665513846_S01_GE2_107_Sep09_1_1.txt.gz 15.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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