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Sample GSM1428856 Query DataSets for GSM1428856
Status Public on Jan 31, 2016
Title T_240418
Sample type RNA
 
Channel 1
Source name TRP allograft tumor_untreated
Organism Mus musculus
Characteristics strain background: C57BL/6
mouse id: 240418
survival (days): 32
treatment: untreated
tissue: high-grade astrocytoma allografts
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: reference
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 07, 2014
Last update date Jan 31, 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 (1)
GSE59116 Core pathway mutations induce de-differentiation of murine astrocytes into glioblastoma stem cells that are sensitive to radiation but resistant to temozolomide.

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

Data table
ID_REF VALUE
A_51_P100034 1.306
A_51_P100174 -0.55
A_51_P100289 -0.151
A_51_P100298 -0.95
A_51_P100327 -1.11
A_51_P100537 -0.18
A_51_P100573 0.25
A_51_P100625 -0.31
A_51_P100776 0.37
A_51_P100787 0.17
A_51_P100828 -1.39
A_51_P100852 -1.93
A_51_P100991 0.041
A_51_P100997 0.24
A_51_P101006 -0.7
A_51_P101075 0.08
A_51_P101137 1.149
A_51_P101196 -1.04
A_51_P101228 0.07
A_51_P101375 0.11

Total number of rows: 27397

Table truncated, full table size 527 Kbytes.




Supplementary file Size Download File type/resource
GSM1428856_US82800149_252665511691_S01_GE2_107_Sep09_1_1.txt.gz 15.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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