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Sample GSM1023102 Query DataSets for GSM1023102
Status Public on Aug 07, 2013
Title nT 1
Sample type RNA
 
Channel 1
Source name nT 1
Organism Mus musculus
Characteristics treatment: ShcA wild type expression
cell line: NMuMG-NT2197
Growth protocol NMuMG-NT2197 cells were generated, cultured, and transfected with a pMSCV/hygro expression vector (Clontech) expressing a wildtype ShcA cDNA or a ShcA mutant harbouring an arginine to glutamine substitution at amino acid 175 (R175Q)
Extracted molecule total RNA
Extraction protocol Total RNA (1-2.5ng) from microdissected material was subjected to two rounds of linear amplification using a RiboAmp HSPlus Amplification Kit (Cat. #: KIT0525, Applied Biosystems) following the manufacturer’s protocol.
Label Cy3
Label protocol The profiles of resulting amplified RNA (aRNA) were assessed using a 2100 Bioanalyzer (Agilent Technologies). The aRNA samples (5μg) were conjugated to Cy3 dye using an Arcturus Turbo Labeling Kit (Cat. #: KIT0609, Applied Biosystems). Universal human reference RNA (Stratagene) was amplified using the same procedure and labeled with Cy5 dye (CAT # KIT0619, Applied Biosystems).
 
Channel 2
Source name Universal Mouse Reference
Organism Mus musculus
Characteristics sample type: Universal Mouse Reference
Growth protocol NMuMG-NT2197 cells were generated, cultured, and transfected with a pMSCV/hygro expression vector (Clontech) expressing a wildtype ShcA cDNA or a ShcA mutant harbouring an arginine to glutamine substitution at amino acid 175 (R175Q)
Extracted molecule total RNA
Extraction protocol Total RNA (1-2.5ng) from microdissected material was subjected to two rounds of linear amplification using a RiboAmp HSPlus Amplification Kit (Cat. #: KIT0525, Applied Biosystems) following the manufacturer’s protocol.
Label Cy5
Label protocol The profiles of resulting amplified RNA (aRNA) were assessed using a 2100 Bioanalyzer (Agilent Technologies). The aRNA samples (5μg) were conjugated to Cy3 dye using an Arcturus Turbo Labeling Kit (Cat. #: KIT0609, Applied Biosystems). Universal human reference RNA (Stratagene) was amplified using the same procedure and labeled with Cy5 dye (CAT # KIT0619, Applied Biosystems).
 
 
Hybridization protocol Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
Scan protocol Images were quantified using Agilent Feature Extraction Software
Description nT
Data processing Microarray data were extracted using Feature Extraction Software (Agilent Technologies). The arrays were normalized using normexp background correction, loess within array and quantile between array normalization.
 
Submission date Oct 19, 2012
Last update date Aug 07, 2013
Contact name Sean Cory
E-mail(s) sean.cory@mcgill.ca
Organization name McGill
Department Goodman Cancer centre
Lab Hallett
Street address 3649 Promenade Sir William Osler
City Montreal
State/province QC
ZIP/Postal code H3G 0B1
Country Canada
 
Platform ID GPL11202
Series (1)
GSE41718 The ShcA PTB Domain Functions as a Biological Sensor of Phospho-tyrosine Signaling During Breast Cancer Progression

Data table header descriptions
ID_REF
VALUE -INV_VALUE: normalized log10 ratio (Cy3/Cy5)
INV_VALUE normalized log10 ratio (Cy5/Cy3)

Data table
ID_REF VALUE INV_VALUE
(+)E1A_r60_1 -0.0250676 0.025067608
(+)E1A_r60_3 0.111717 -0.111716678
(+)E1A_r60_a104 -0.112648 0.112647806
(+)E1A_r60_a107 0.00539076 -0.005390764
(+)E1A_r60_a135 -0.17331 0.173310288
(+)E1A_r60_a20 -0.159803 0.1598032
(+)E1A_r60_a22 0.254481 -0.254480907
(+)E1A_r60_a97 0.154028 -0.154027833
(+)E1A_r60_n11 -0.203811 0.203810597
(+)E1A_r60_n9 -0.17331 0.173310288
(-)3xSLv1 0.0162165 -0.016216486
A_51_P100034 -1.14115 1.141149803
A_51_P100174 -2.2963 2.296301943
A_51_P100208 -0.66058 0.660579679
A_51_P100289 -2.26233 2.262329448
A_51_P100298 1.13135 -1.131351572
A_51_P100309 -0.164645 0.164645085
A_51_P100327 -4.19679 4.196792185
A_51_P100347 0.488129 -0.488128691
A_51_P100519 0.169974 -0.169974419

Total number of rows: 39485

Table truncated, full table size 1361 Kbytes.




Supplementary file Size Download File type/resource
GSM1023102_US22502628_252665512251_S01_GE2-v5_95_Feb07_1_4.txt.gz 15.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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