|
| Status |
Public on Jan 31, 2016 |
| Title |
vector control 1 |
| Sample type |
RNA |
| |
|
| Source name |
mouse embryonic fibroblast
|
| Organism |
Mus musculus |
| Characteristics |
strain: isogenic to C56BL/6
tissue: Fibroblast
Sex: male
|
| Treatment protocol |
Cells were in the logarithmically growing phase, and grown to semi-confluency in 60mm dishes (Corning).
|
| Growth protocol |
The cells wee cultured in DMEM supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, 1% L-glutamine at 37˚C in a 5% CO2 incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the triplicated 60mm dishes with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. The qualities of RNA samples were verified by Agilent 2100 Bioanalyzer (Agilent Technology) and then the set of nine RNA samples (3 preparations from 3 cell lines) were analyzed using GeneChip FLUIDICS station 450 and Affymetrix GeneChip Scanner 7G (Affymetrix) at the Microarray Core of the University of Kentucky. Transcriptional intensities of 41,344 genes were processed using PARTEK.
|
| Label |
biotin
|
| Label protocol |
Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
the set of nine RNA samples (3 preparations from 3 cell lines) were analyzed with Mouse GeneChip ST2.0 using GeneChip FLUIDICS station 450 at the Microarray Core of the University of Kentucky.
|
| Scan protocol |
Affymetrix GeneChip Scanner 7G (Affymetrix) at the Microarray Core of the University of Kentucky.
|
| Description |
RMA expression value derived from Expression Console software; core-exon analysis
|
| Data processing |
Raw data were processed with the Exon Array Computational Tool (PARTEK). Specifically, the entire 41,345 genes (anova_011014.xlsx) based on false discovery rate (FDR) (P < 0.05) generated 7,115 genes and recorded in the file named ANOVA_FDR005.txt.
|
| |
|
| Submission date |
Mar 11, 2014 |
| Last update date |
Jan 31, 2016 |
| Contact name |
Tadahide Izumi |
| E-mail(s) |
t.izumi@uky.edu
|
| Phone |
859-257-6472
|
| Organization name |
University of Kentucky
|
| Department |
Toxicology
|
| Lab |
HSRB 336
|
| Street address |
1095 VA Dr
|
| City |
Lexington |
| State/province |
KY |
| ZIP/Postal code |
40536 |
| Country |
USA |
| |
|
| Platform ID |
GPL16570 |
| Series (1) |
| GSE55765 |
Gene expression influenced by human APE1 and mouse Ape1 in a mouse embryonic fibroblast line. |
|
