|
| Status |
Public on Apr 28, 2016 |
| Title |
Ob_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Primary osteoblast
|
| Organism |
Mus musculus |
| Characteristics |
cell type: GFP-sorted osteoblasts
isolated from: calvaria
strain: C57BL/6
age: P1
genotype: Sp7 positive
|
| Treatment protocol |
NA
|
| Growth protocol |
Primary osteoblasts were isolated P1 mouse calvaria and primary chondrocytes were isolated from P1 mouse rib cartilage
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Primary osteoblasts were isolated by 1 unit/ml Liberase TM (05401119001, Roche). Primary chondrocytes were isolated by 2 mg/mL PRONASE Protease (53702, EMD Millipore Corporation) and 0.2% Collagenase D (1088858; Roche Applied Science)
RNA libraries were constructed by Tru-Seq Illumina kit (RS-122-2001, illumina) with some modifications
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Ob_Sp7-GFP2
HH_Osx_2
|
| Data processing |
The raw reads were first subjected to pre-alignment Quality Assurance and Quality Control (QA/QC).
Any base below a Phred value of 20 was trimmed from either side of the read and reads shorter than 25 nt length were removed.
The processed reads were aligned by Tophat2-2.0.8 (Kim et al., 2013) to mm9 reference genome.
The mapping quality and coverage were checked by post-alignment QA/QC.
Aligned reads were quantified by an expectation maximization algorithm (Xing et al., 2006), followed by a normalization of mapped reads per kilo base length of transcript per million reads (RPKM).
Genome_build: mm9
Supplementary_files_format_and_content: .txt file reports abundance measurements
|
| |
|
| Submission date |
Dec 20, 2015 |
| Last update date |
Jun 16, 2021 |
| Contact name |
Hironori Hojo |
| E-mail(s) |
hojo@tetrapod.t.u-tokyo.ac.jp
|
| Phone |
+81-3-5841-1427
|
| Organization name |
The University of Tokyo
|
| Department |
Center for Disease Biology and Integrative Medicine
|
| Lab |
Clinical Biotechnology
|
| Street address |
7-3-1 Hongo
|
| City |
Bunkyo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
113-8655 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE76186 |
Sp7/Osterix is restricted to bone-forming vertebrates where it acts as a Dlx co-factor in osteoblast specification [RNA-Seq] |
| GSE76187 |
Sp7/Osterix is restricted to bone-forming vertebrates where it acts as a Dlx co-factor in osteoblast specification |
|
| Relations |
| Reanalyzed by |
GSE178288 |
| BioSample |
SAMN04357101 |
| SRA |
SRX1492994 |
