|
| Status |
Public on Nov 15, 2024 |
| Title |
26wk_Cancellous_Contralateral Control Limb_5d2_Animal5dAC |
| Sample type |
SRA |
| |
|
| Source name |
Cancellous
|
| Organism |
Mus musculus |
| Characteristics |
sample number: A06
tissue: Cancellous
loaded: R
animal number: 5dAC
timepoint: 5d2
age: Adult
genotype: C57Bl6J
treatment: Contralateral Control Limb_5d2
|
| Treatment protocol |
10- and 26-week-old female C57Bl/6J were subjected to in vivo mechanical loading of the left tibia (9N peak load at 4 Hz for 1200 cycles per day). Mice were euthanized by cervical dislocation at 1-hour, 3-hours, or 24-hours following the completion of one bout of loading. To evaluate long term time points, a final group received 5 consecutive days of loading with euthanasia on the eighth day following the first loading session
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cancellous bone was separated from the cortical shell. The cortical bone was segmented into three sections: metaphyseal cortex, proximal diaphysis, and mid-diaphysis,and the metaphyseal cortex and mid-diaphysis were then analyzed. All tissues were flash frozen in liquid nitrogen. Samples were pulverized and RNA isolated using a phenol-chloroform extraction followed by the RNeasy kit (Qiagen).
RNA libraries were prepared for 3' mRNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequence reads were trimmed for adaptor sequence. 12bp were trimmed from the 5' end for quality assurance.
Trimmed sequence reads were mapped to mm10 using STAR (parameters- outFilterMismatchNmax: 2 - outFilterMultimapNmax: 1)
Fastqc was run for all files and only samples with high quality from both fastqc & RQN were included for analysis
Each sample contained over 1 million reads. Genes with less than 3 counts per million were not included for analysis.
Normalized gene counts were calculated in DESeq2 with Trimmed Mean of M-values correction
Assembly: mm10
Supplementary files format and content: .xlsx file with normalized gene counts and experimental conditions for each samle
|
| |
|
| Submission date |
Nov 14, 2024 |
| Last update date |
Nov 15, 2024 |
| Contact name |
Carolyn Chlebek |
| E-mail(s) |
[email protected]
|
| Organization name |
Cornell University
|
| Department |
Biomedical Engineering
|
| Lab |
van der Meulen
|
| Street address |
110 Hoy Road
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14850 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE281942 |
Bioenergetic programs of cancellous and cortical bone are distinct and differ with age and mechanical loading |
|
| Relations |
| BioSample |
SAMN44750724 |
| SRA |
SRX26730065 |
