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Sample GSM1121602 Query DataSets for GSM1121602
Status Public on Apr 12, 2013
Title Bmi1Ink4a_4
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 4.845490051
A_52_P580582 6.818459007
A_52_P403405 5.599912842
A_52_P819156 4.898450233
A_51_P331831 5.133399125
A_51_P430630 6.507398241
A_52_P502357 4.774128144
A_52_P299964 8.035898787
A_51_P356389 5.398743692
A_52_P684402 10.18633094
A_51_P414208 12.10474616
A_51_P280918 7.630722162
A_52_P613688 6.263503957
A_52_P258194 6.984133595
A_52_P229271 8.091567616
A_52_P214630 9.336404067
A_52_P579519 7.641329262
A_52_P979997 4.800252806
A_52_P453864 5.912290583
A_52_P655842 6.632995197

Total number of rows: 41174

Table truncated, full table size 997 Kbytes.

Supplementary file Size Download File type/resource
GSM1121602_Bmi1Ink4a_4.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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