|
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 |
|