|
| Status |
Public on Jan 01, 2017 |
| Title |
Wildtype 1 |
| Sample type |
SRA |
| |
|
| Source name |
Neonatal mouse calavri
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6J
cell type: Osteoblast
genotype/variation: Wildtype
|
| Treatment protocol |
Cells from wildtype and Cdc73/Hrpt2 cKO mice were isolated and sorted uniformily
|
| Growth protocol |
Calvari were harvested from 5 day-old pups, washed/collagenase digested and strained prior to cell sorting based on transgenic GFP expression controlled by Osteocalcin-Cre. Cells were sorted into Trizol and stored at -80C until RNA isolation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using phenol/chloroform and precipitated over night in isopropanol, pelleted, dried and resuspended in water
Library construction was performed by Hudson Alpha
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
wt_1
|
| Data processing |
Reads were generated on a HiSeq 2500 System and Casava version 1.7 at
Sequenced reads were aligned to the mm10 genome using the subjunc aligner from the Rsubread R package using default parameters
Raw counts for gene-level features were computed using the featureCounts function in the Rsubread package using NCBI RefSeq annotation for mm10 (build 38.1)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including a matrix of raw counts for each sample
|
| |
|
| Submission date |
Dec 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Casey James Droscha |
| Organization name |
Van Andel Institute
|
| Department |
Program for Skeletal Disease and Tumor Microenviroment
|
| Lab |
Cell Signaling & Carcinogenesis
|
| Street address |
333 Bostwick Ave.
|
| City |
Grand Rapids |
| State/province |
Michigan |
| ZIP/Postal code |
49503 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE90890 |
Osteoblast-specific deletion of Hrpt2/Cdc73 results in high bone mass and increased bone turnover |
|
| Relations |
| BioSample |
SAMN06111462 |
| SRA |
SRX2396290 |
