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Sample GSM466405 Query DataSets for GSM466405
Status Public on Apr 30, 2012
Title diploidy (FW_1)
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 8.278031225
10608635 9.758056612
10608636 7.432124273
10608637 7.046578367
10608638 3.46727948
10608639 2.87774425
10608640 6.92552477
10608641 6.721646078
10608642 8.192292814
10608643 12.69904534
10608644 6.192785959
10608645 9.137554755
10608646 3.672425342
10608647 12.28971633
10608648 8.449437568
10608649 5.581049901
10608650 8.202515674
10608651 5.61205756
10608652 4.69543711
10608653 8.219120107

Total number of rows: 28944

Table truncated, full table size 589 Kbytes.




Supplementary file Size Download File type/resource
GSM466405.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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