|
| Status |
Public on Jul 01, 2016 |
| Title |
3_WT_Control_A3 |
| Sample type |
RNA |
| |
|
| Source name |
WT, Control, Batch A, replicate 3
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Embryo
cell type: Mouse embryonic fibroblasts (MEFs)
genotype: Wild Type
treatment: Control
batch: A
replicate: 3
|
| Treatment protocol |
Primary MEFs were treated with Fsk for 90 min, irradiated with 20 Gy IR for 120 min (20 Gy), or treated with 20 Gy IR 30 min prior to Fsk (20 Gy/Fsk) after serum starvation for 16 hours.
|
| Growth protocol |
Primary mouse embryonic fibroblasts (MEFs) were maintained in Dulbecco's modified Eagle's medium (DMEM) containing 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIzol (Invitrogen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop spectrophotometer.
|
| Label |
Cy3
|
| Label protocol |
RNA samples were labeled using the Agilent Low Input Quick Amp Labeling Kit, One-Color.
|
| |
|
| Hybridization protocol |
Hybridizations were carried out using an Agilent Technologies DNA microarray model #G2565 CA.
|
| Scan protocol |
Microarrays were carried out using Agilent SurePrint G3 Mouse Gene Expression 8x60K Microarray 8-plex slides (n=6 embryos per genotype/per condition).
|
| Description |
Gene expression from WT Control treated
|
| Data processing |
The pixel intensity data acquired from the microarrays were quantile normalized and log base 2 transformed. Since the arrays were processed at two dFskferent times (A and B), the data were corrected for this batch effect using ComBat and an empirical Bayes, non-parametric model of the data was performed with genotype and treatment as covariates. The data was then filtered by removing probes Fsk 40 of the 48 arrays had values less than the 5th percentile and missing values subsequently imputed by flooring them at the 5th percentile.
|
| |
|
| Submission date |
Jun 30, 2016 |
| Last update date |
Jul 01, 2016 |
| Contact name |
Pierre Robert Bushel |
| E-mail(s) |
bushel@niehs.nih.gov
|
| Phone |
919-316-4564
|
| Organization name |
NIEHS
|
| Department |
Biostatistics and Computational Biology Branch
|
| Lab |
Bioinformatics
|
| Street address |
P.O. Box 12233
|
| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL10787 |
| Series (1) |
| GSE83891 |
Tunable regulation of CREB DNA binding activity couples genotoxic stress response and metabolism |
|
