|
| Status |
Public on Feb 04, 2011 |
| Title |
quadriceps, control mouse, experiment2, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
control mouse, independent second experiment
|
| Organism |
Mus musculus |
| Characteristics |
tissue: quadriceps muscle
gender: female
age: 2 months
treatment: control
experiment: independent second experiment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Quadriceps muscles were dissected and immediately snap frozen in liquid nitrogen. Total RNA was isolated from the frozen muscle tissues using TRIzol reagent (Invitrogen).
|
| Label |
biotin
|
| Label protocol |
Total RNA was labeled with biotin using the GeneChip Whole Transcript (WT) Sense Target Labeling Assay following the manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
Affymetrix GeneChip Mouse Gene 1.0 ST arrays were hybridized with the labeled cDNA overnight.
|
| Scan protocol |
Arrays were processed and scanned using Fluidics Station 450 and GeneChip Scanner 3000 7G (Affymetrix).
|
| Description |
Gene expression data from control mouse.
|
| Data processing |
Array data were preprocessed using RMA (apt-1.12.0 and MoGene-1_0-st-v1.r4.analysis-lib-files) and analyzed using the limma package (version 3.4.4, R version 2.11.1, and mogene10sttranscriptcluster.db version 5.0.1) . When multiple probesets mapped to the same gene, the probeset with the highest inter-quantile range across all arrays was retained. Note that in the manuscript, the original and validation studies were analyzed independently, including separate RMA preprocessing; the RMA scores in the Sample tables are also computed separately for the two studies. If analyzing fold-changes from both studies together, explicitly including a factor to correct for the batch variation between the two experiments is advised.
|
| |
|
| Submission date |
Dec 22, 2010 |
| Last update date |
Feb 04, 2011 |
| Contact name |
Fedik Rahimov |
| E-mail(s) |
[email protected]
|
| Phone |
617-355-4042
|
| Fax |
617-730-0253
|
| Organization name |
Boston Children's Hospital
|
| Department |
Genetics
|
| Lab |
Kunkel
|
| Street address |
3 Blackfan Circle, CLS 15030.4
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE25306 |
Gene expression profiling of skeletal muscles treated with a soluble activin type IIB receptor |
|
