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Sample GSM1121592 Query DataSets for GSM1121592
Status Public on Apr 12, 2013
Title WT_3
Sample type RNA
 
Source name colony derivied from dental epithelia
Organism Mus musculus
Characteristics genotype: WT
cell type: dental stem cell colony derivied from dental epithelia
genetic background: mixed
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy mini kit
Label Cy3
Label protocol RNA was amplified using the Sigma whole transcriptome amplification kits following the manufacturer’s protocol (Sigma-Aldrich, St Louis, MO), and subsequent Cy3-CTP labeling was performed using NimbleGen one-color labeling kits (Roche-NimbleGen Inc, Madison, WI). Labeled Cy3-cDNA was assessed using the Nandrop ND-8000 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome.
 
Hybridization protocol Hybridizations were performed for 17 hrs, according to the manufacturers protocol.
Scan protocol Arrays were scanned using the Agilent microarray scanner and raw signal intensities were extracted with Feature Extraction v10.6 software.
Data processing This dataset was normalized using the quantile normalization method that is proposed by Bolstad et al (2003). No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization.
 
Submission date Apr 11, 2013
Last update date Apr 18, 2013
Contact name Brian Biehs
E-mail(s) brianbiehs@gmail.com
Organization name UCSF
Street address 505 Parnassus Ave
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
 
Platform ID GPL7202
Series (2)
GSE46000 Transcriptional profiling of 2D colonies derived from WT, Bmi1-/-, and Bmi1-/-;Ink4a/Arf Labial cervical loops
GSE46001 Bmi1

Data table header descriptions
ID_REF
VALUE log2 normalized signal intensity

Data table
ID_REF VALUE
A_52_P616356 4.738767837
A_52_P580582 8.134098259
A_52_P403405 7.395534135
A_52_P819156 5.310158318
A_51_P331831 5.686500527
A_51_P430630 9.804393232
A_52_P502357 4.923624611
A_52_P299964 10.41005379
A_51_P356389 5.668884984
A_52_P684402 11.82194335
A_51_P414208 6.131856961
A_51_P280918 5.833838844
A_52_P613688 6.846744023
A_52_P258194 9.892277172
A_52_P229271 7.106170317
A_52_P214630 6.741946927
A_52_P579519 6.002252452
A_52_P979997 5.726558779
A_52_P453864 5.270528942
A_52_P655842 7.786923022

Total number of rows: 41174

Table truncated, full table size 999 Kbytes.




Supplementary file Size Download File type/resource
GSM1121592_WT_3.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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