|
| Status |
Public on Dec 25, 2018 |
| Title |
AJ Pi[-] d5 #1, batch A |
| Sample type |
RNA |
| |
|
| Source name |
Femur bone following experimental fracture
|
| Organism |
Mus musculus |
| Characteristics |
tissue: bone fracture callus
gender: male
batch: batch A
strain: AJ
diet: Pi[-]
timepoint: day 5
animal: 1034
|
| Treatment protocol |
Pi group: Phosphate deficiency (Pi) was initiated 2 days prior to fracture and was maintained for 15 days by supplying the mice with a low phosphate diet (Harlan Laboratories, Madison, WI). Phosphate was then replenished and bone healing was allowed to continue until 35 days. For the three strains of mice, control groups were included where the mice were given normal diet throughout the study.
|
| Growth protocol |
In vivo animal model
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated from each fracture callus using procedures developed for murine bones (Wang et al., Matrix Biology, 2006; 25(5):271-81). In order to both achieve an optimal balance in biological replicate variability and repeatability RNA from every two of the six fracture calluses were randomly pooled to generate three assay samples.
|
| Label |
biotin
|
| Label protocol |
Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.
|
| Scan protocol |
After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.
|
| Description |
Gene expression data from right femur of AJ Pi[-] animal at day 5 following experimental fracture.
|
| Data processing |
Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene10stmmentrezg R package (version 16.0.0).
|
| |
|
| Submission date |
Jun 01, 2017 |
| Last update date |
Jun 25, 2019 |
| Contact name |
Boston University Microarray and Sequencing Resource |
| E-mail(s) |
msrdata@bu.edu
|
| Organization name |
Boston University
|
| Department |
Microarray and Sequencing Resource
|
| Street address |
72 East Concord Street, E631
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL19485 |
| Series (1) |
| GSE99580 |
A Systems Genetics Approach to Fracture Healing |
|
