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Sample GSM301305 Query DataSets for GSM301305
Status Public on Oct 03, 2008
Title 25 hours NIH3T3_Forskolin_25
Sample type RNA
 
Source name NIH3T3 fibroblasts
Organism Mus musculus
Characteristics synchronized with forskolin
Treatment protocol Cells were synchronized with forskolin 20 hours before samples were collected.
Growth protocol NIH3T3 cells (ATCC) were grown to confluence in DMEM supplimented with 10% FCS and P/S/G on 35mm dishes.
Extracted molecule total RNA
Extraction protocol Cells were washed briefly with 1X PBS. 1 mL Trizol (Invitrogen) was used to homogenize cells, and samples were frozen at -80 until total RNA was purified.
Label biotin
Label protocol Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
 
Hybridization protocol The cRNA products were fragmented to 200 nucleotides or less, heated at 99 degrees C for 5 min and hybridized for 16 h at 45 degrees C. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.
Scan protocol A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.
Description n/a
Data processing Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features.
 
Submission date Jun 27, 2008
Last update date Aug 28, 2018
Contact name Michael Hughes
E-mail(s) michael.evan.hughes@gmail.com
Organization name UPenn
Street address 421 Curie Bvd, Brb 835
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL1261
Series (1)
GSE11922 High temporal resolution profiling of NIH3T3 cells
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE signal calculated by gcRMA implemented in 'R'

Data table
ID_REF VALUE
1415670_at 75948.7
1415671_at 64868.9
1415672_at 70252.3
1415673_at 23280.7
1415674_a_at 27930.2
1415675_at 40956.8
1415676_a_at 120120.1
1415677_at 31425.8
1415678_at 145928.1
1415679_at 71938.4
1415680_at 18514.3
1415681_at 28686.1
1415682_at 13043.1
1415683_at 41440.9
1415684_at 17553.5
1415685_at 11711.4
1415686_at 89921.6
1415687_a_at 209855.2
1415688_at 60994.5
1415689_s_at 9679.2

Total number of rows: 45101

Table truncated, full table size 766 Kbytes.




Supplementary file Size Download File type/resource
GSM301305.CEL.gz 4.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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