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Sample GSM1121601 Query DataSets for GSM1121601
Status Public on Apr 12, 2013
Title Bmi1Ink4a_3
Sample type RNA
Source name colony derivied from dental epithelia
Organism Mus musculus
Characteristics genotype: Bmi1-;Ink4a/Arf-
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
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
VALUE log2 normalized signal intensity

Data table
A_52_P616356 4.908092341
A_52_P580582 7.276965615
A_52_P403405 5.503030646
A_52_P819156 4.908092341
A_51_P331831 5.230741003
A_51_P430630 6.750539513
A_52_P502357 4.716990894
A_52_P299964 8.180655119
A_51_P356389 5.62935662
A_52_P684402 10.44072645
A_51_P414208 4.908092341
A_51_P280918 7.286442249
A_52_P613688 6.923327485
A_52_P258194 7.084011098
A_52_P229271 8.281466436
A_52_P214630 9.547304258
A_52_P579519 7.232660757
A_52_P979997 5.055282436
A_52_P453864 4.908092341
A_52_P655842 6.602513297

Total number of rows: 41174

Table truncated, full table size 999 Kbytes.

Supplementary file Size Download File type/resource
GSM1121601_Bmi1Ink4a_3.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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