|
| Status |
Public on Jul 25, 2018 |
| Title |
24 Hr after 13Gy WT |
| Sample type |
RNA |
| |
|
| Source name |
BAMC from mouse BM
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
gender: male
age: 3 months
tissue: bone marrow (BM)
|
| Treatment protocol |
BAMC were isolated from WT and p53-null irradiated (13 GY, 24h) and non-irradiated mice as described in (Hsiao FS et al, 2010).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol reagent, followed by clean-up and DNAseI treatment with QIAGEN Rneasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
|
| Label |
biotin
|
| Label protocol |
Expression profiling is accomplished using the Mouse WG-6 whole-genome gene expression array and direct hybridization assay (Illumina, Inc). Initially, 500ng total RNA is converted to cDNA, followed by in vitro transcription to generate biotin labeled cRNA using the Ambion Illumina TotalPrep RNA Amplification Kit (Ambion, Inc.) as per manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
1500ng of the labeled probes are then mixed with hybridization reagents and hybridized overnight at 58°C to the WG-6 BeadChips (Illumina, Inc).
|
| Scan protocol |
Following washing and staining with Cy3-streptavidin conjugate, the BeadChips are imaged using the Illumina iScan Reader to measure fluorescence intensity at each probe. The intensity of the signal corresponds to the quantity of the respective mRNA in the original sample.
|
| Description |
replicate 1
|
| Data processing |
BeadChip data files are analyzed with Illumina’s GenomeStudio (v2011.1) gene expression module (v1.9.0) to report both un-normalized and quantile normalized, background corrected gene expression signal levels.
|
| |
|
| Submission date |
Jul 24, 2018 |
| Last update date |
Jul 25, 2018 |
| Contact name |
Amanda Perez |
| E-mail(s) |
amanda.perez@roswellpark.org
|
| Organization name |
Roswell Park Cancer Institute
|
| Street address |
Elm and Carlton Streets
|
| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14263 |
| Country |
USA |
| |
|
| Platform ID |
GPL21278 |
| Series (1) |
| GSE117625 |
Comparison of irradiation-induced genes from freshly isolated bone-adherent mesenchymal cells of p53-WT and p53-null mice |
|
