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Sample GSM686628 Query DataSets for GSM686628
Status Public on Mar 15, 2011
Title NIH3T3_Rapamycin_18hr_rep1
Sample type RNA
Source name NIH3T3, Rapamycin, 18hr, replicate 1
Organism Mus musculus
Characteristics cell line: NIH3T3
treatment: 50 nM Rapamycin
Treatment protocol NIH3T3 cells were treated with DMSO, 50 nM rapamycin, or 2 mM PP242 for 18 hours
Growth protocol NIH3T3 cells were cultured in DMEM supplemented with 10% BCS and penicillin/streptomycin.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using QIAshredder and RNeasy Mini kits (Qiagen). RNA was quantified by Nanodrop and integrity was assessed on an Agilent 2100 Bioanalyzer.
Label Cy3
Label protocol RNA was amplified using the whole transcriptome amplification kits (Sigma) following the manufacturer’s protocol, and subsequent Cy3-CTP labeling was performed using one-color labeling kits (NimbleGen). The size distribution and quantity of the amplified product was assessed by Nanodrop and Bioanalyzer.
Hybridization protocol Equal amounts of Cy3 labeled target were hybridized to Agilent mouse whole genome 4x44K Ink-jet arrays. Hybridizations were performed for 14 hrs, according to the manufacturers protocol.
Scan protocol Arrays were scanned using the Agilent microarray scanner.
Description Gene expression in NIH3T3 cells after 18hr treatment with 50 nM Rapamycin
Data processing Raw signal intensities were extracted with Feature Extraction v10.1 software. The dataset was normalized using the quantile normalization method. No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization.
Submission date Mar 07, 2011
Last update date Mar 15, 2011
Contact name Beatrice Wang
Organization name Univeristy of California, San Francisco
Street address 600 16th Street MC 2280
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
Platform ID GPL7202
Series (1)
GSE27784 Transcriptional profiling of ATP-competitive mTOR inhibitors reveals mTORC1 and mTORC2 specific regulatory networks

Data table header descriptions
VALUE quantile normalized signal intensity

Data table
A_52_P616356 5.383704292
A_52_P580582 8.79820176
A_52_P403405 5.805206455
A_52_P819156 6.606713646
A_51_P331831 9.709658248
A_51_P430630 5.69464808
A_52_P502357 5.182394353
A_52_P299964 8.307770032
A_51_P356389 6.606713646
A_52_P684402 9.797661526
A_51_P414208 5.603626345
A_51_P280918 10.86935286
A_52_P613688 6.026984441
A_52_P258194 6.425565605
A_52_P229271 9.116235647
A_52_P214630 10.96697998
A_52_P579519 9.76113565
A_52_P979997 5.076815597
A_52_P453864 5.182394353
A_52_P655842 5.603626345

Total number of rows: 41174

Table truncated, full table size 1000 Kbytes.

Supplementary file Size Download File type/resource
GSM686628_251486829200_S01_GE1_105_Jan09_1_4.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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