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Sample GSM686626 Query DataSets for GSM686626
Status Public on Mar 15, 2011
Title NIH3T3_DMSO_18hr_rep3
Sample type RNA
Source name NIH3T3, DMSO, 18hr, replicate 3
Organism Mus musculus
Characteristics cell line: NIH3T3
treatment: DMSO
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 DMSO
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 5.409390936
A_52_P580582 8.540596756
A_52_P403405 6.01402047
A_52_P819156 6.205385996
A_51_P331831 9.6295843
A_51_P430630 5.611024797
A_52_P502357 5.611024797
A_52_P299964 8.099566982
A_51_P356389 6.709083813
A_52_P684402 9.562123149
A_51_P414208 5.908892949
A_51_P280918 10.7096044
A_52_P613688 5.409390936
A_52_P258194 5.409390936
A_52_P229271 9.187300518
A_52_P214630 11.0164207
A_52_P579519 9.684602532
A_52_P979997 5.220781371
A_52_P453864 5.409390936
A_52_P655842 5.611024797

Total number of rows: 41174

Table truncated, full table size 998 Kbytes.

Supplementary file Size Download File type/resource
GSM686626_251486829328_S01_GE1_105_Jan09_1_3.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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