|
| Status |
Public on Nov 10, 2012 |
| Title |
WB muscle, biological replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
Gastrocnemius and plantaris from a 7-wk-old C57BL/6J mouse with hind limbs in full weight bearing
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Healthy weight bearing muscle
strain: C57BL/6J
age: 7 wk old
muscles: Gastrocnemius and plantaris
|
| Treatment protocol |
Mice in the HU group had their hind limbs elevated off the cage floor for 5 days to induce unloading induced muscle atrophy, as described previously [Wu et al. 2011]. The use of animals in this study was approved by the Institutional Animal Care and Use Committee of Boston University (protocol number 12-012)
|
| Growth protocol |
7-week-old female wild type mice (C57BL/6J) were purchased from the Jackson Laboratory (Bar Harbor, ME). Animals were provided with chow and water ad libitum and housed individually in Boston University Animal Care Facility. After 3 days of acclimation, mice were randomly assigned to weight-bearing (WB) or hind limb unloaded (HU) groups.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Gastrocnemius and plantaris muscles harvested from anesthetized mice from both groups were snap frozen in liquid nitrogen and stored at -80ºC before use. Total RNA was isolated using the Qiagen miRNeasy Mini kit (Valencia, CA) according to manufacturer’s instructions. Extracted total RNA was treated with RNase-Free DNase I (Qiagen, Valencia, CA), quantitated by UV spectrophotometry, and quality checked by a 1% denaturing agarose gel as previously described. Each group (WB and HU) included 4 independent total RNA samples with a minimal RIN number 8.0 verified by Bioanalyzer 2100 (Agilent Technology, Palo Alto, CA).
|
| Label |
Biotin
|
| Label protocol |
Whole-transcript expression profiling experiments were carried out by the Boston University Microarray Core Facility. The Affy standard WT Sense Target Labeling assay protocol was followed to synthesize biotinylated DNA.
|
| |
|
| Hybridization protocol |
Fragmented, biotinylated DNA samples were hybridized on a mouse Gene 1.0 ST array according to manufacture's recommendation.
|
| Scan protocol |
A total of 8 array images were acquired by GeneChip Scanner 3000 7G and quality assessed by Affymetrix Expression Console (Santa Clara, CA).
|
| Description |
Whole transcript expression profiling
|
| Data processing |
Gene expression signals were generated by robust multi-array analysis (RMA) using Brainarray MoGene 1.0ST custom CDF files v.13. Differential gene expression was computed using the Comparative Marker Selection module in Genepattern database (Broad Institute, Cambridge, MA) which compares mean differences between control and unloaded groups by two-way parametric t-test. P-value ≤ 0.05 and q-value ≤ 0.05 were used to identify genes that were significantly differentially expressed with hindlimb unloading.
|
| |
|
| Submission date |
Sep 04, 2012 |
| Last update date |
Nov 10, 2012 |
| Contact name |
Susan Kandarian |
| E-mail(s) |
[email protected]
|
| Organization name |
Boston University
|
| Department |
Health Sciences
|
| Lab |
Kandarianlab
|
| Street address |
635commonwealth ave, Rm444
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL11078 |
| Series (1) |
| GSE40578 |
Differentially expressed genes during disuse atrophy. |
|
