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Sample GSM779123 Query DataSets for GSM779123
Status Public on Aug 17, 2011
Title WT_Hras_SV40LT
Sample type RNA
Source name vector-transfected, wild-type, MEFs
Organism Mus musculus
Characteristics genotype/variation: wild-type
cell type: MEFs
Growth protocol Cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% FBS, 20 microM beta-mercaptoethanol, and 1x nonessential amino acid mix
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the TRIzol.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Submission date Aug 16, 2011
Last update date Aug 17, 2011
Contact name Satoru Koyanagi
Organization name Kyushu University
Department Pharmaceutics
Street address 3-1-1 Maidashi, Higashi-ku
City Fukuoka
State/province Fukuoka
ZIP/Postal code 812-8582
Country Japan
Platform ID GPL11202
Series (1)
GSE31405 Differentially expressed genes between oncogene-introduced wild-type and Atf4-/- cells

Data table header descriptions
VALUE quantile normalized signal (non-log scaled)

Data table
A_55_P2116608 7.533195 A
A_55_P2073489 1117.0601 P
A_52_P229709 3231.126 P
A_55_P2092526 6092.284 P
A_55_P2048358 8.576548 A
A_55_P2109122 9186.0715 P
A_55_P2032147 455.15535 P
A_55_P1985351 95.988275 P
A_55_P2145838 13.586435 P
A_51_P163444 5812.238928 P
A_55_P2166688 2454.155 P
A_55_P2230663 6.7683925 A
A_55_P2195172 2.8643895 A
A_55_P1953663 2.9226935 A
A_55_P2135730 11.662818 P
A_51_P174143 3.5679185 A
A_51_P419971 3426.178 P
A_55_P1967880 19167.21 P
A_55_P2364315 506.2533 P
A_51_P154780 13.239055 P

Total number of rows: 39429

Table truncated, full table size 972 Kbytes.

Supplementary file Size Download File type/resource
GSM779123.txt.gz 8.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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