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Sample GSM466406 Query DataSets for GSM466406
Status Public on Apr 30, 2012
Title diploidy (FW_2)
Sample type RNA
 
Source name embryonic fibroblast, diploid
Organism Mus musculus
Characteristics genotype/variation: normal control
Growth protocol Cells were grow in DMEM containing 10% FBS to 80% confluence
Extracted molecule total RNA
Extraction protocol Total RNA was purified with RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. ). After ribosomal RNA reduction (Invitrogen, Carlsbad, CA) to remove most of the 18S and 28S rRNAs, the GeneChip WT (whole transcript) cDNA Synthesis Kit, WT cDNA Amplification Kit, and WT Terminal Labeling Kit (Affymetrix, Inc., Santa Clara, CA) were used for target preparation. Ten µg of cRNA (antisense RNA) were added to the second-cycle cDNA reaction followed by fragmentation and Terminal Labeling process.
Label Biotin
Label protocol One µg of each sample was processed using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay (https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf
 
Hybridization protocol The hybridization cocktails containing 2.5 ug of the fragmented, end-labeled cDNA were applied to the GeneChip® Human Gene 1.0 ST arrays. Hybridization was performed for 16 hours, and the arrays were washed and stained with the GeneChip Fluidics Station 450 using FS450_0007 script.
Scan protocol Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.4 to produce CEL intensity files.
Description control group
Data processing Data were background corrected with GC bin, quantile normalized and summarized by interPLIER algorithm with Affymetrix Expression Console.
 
Submission date Oct 29, 2009
Last update date Apr 30, 2012
Contact name Xiwei Wu
E-mail(s) xwu@coh.org
Organization name City of Hope National Medical Center
Department Computational and Quantitative Medicine
Street address 1500 E. Duarte Rd.
City Duarte
State/province CA
ZIP/Postal code 91010
Country USA
 
Platform ID GPL6246
Series (2)
GSE18802 Comparison of gene expression profiles in diploid and transformed tetraploid MEF cells
GSE18815 Comparison of diploid and transformed tetraploid MEF cells: gene expression and DNA methylation profiling

Data table header descriptions
ID_REF
VALUE Log2 transformed Expression Console processed signal intensity with offset of 1

Data table
ID_REF VALUE
10608634 9.128613039
10608635 9.817015612
10608636 6.762481703
10608637 7.260496187
10608638 3.428946345
10608639 4.789207575
10608640 7.324540613
10608641 6.455656002
10608642 8.315693018
10608643 12.00738124
10608644 6.430117975
10608645 8.90014226
10608646 5.358607249
10608647 12.3356639
10608648 9.442134863
10608649 5.893362211
10608650 8.882398504
10608651 6.336461928
10608652 4.441616269
10608653 7.901711654

Total number of rows: 28944

Table truncated, full table size 589 Kbytes.




Supplementary file Size Download File type/resource
GSM466406.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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