|
| Status |
Public on Mar 20, 2021 |
| Title |
C3H10T1/2 MSCs - OB_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
C3H10T1/2 MSCs
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mesenchymal stem cells
treatment: induced for osteoblast differentiation for 3 days
cell line: C3H10T1/2 MSCs
|
| Treatment protocol |
For OB induction, cells were maintained in complete medium supplemented with 50 μM L-ascorbic acid, 10 mM β-glycerophosphate, 10-3 μM dexamethasone, and 1% penicillin-streptomycin for 3 days.
|
| Growth protocol |
C3H10T1/2 cells were cultured in Modified Eagle’s Medium (MEM) supplemented with 10% FBS, 1% non-essential amino acids, L-glutamine and sodium pyruvate.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Trizol.
Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq RNA Sample Preparation v.2 (cat. no. RS-122-2001, RS-122-2002) (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
OB_NC1sorted
|
| Data processing |
Total RNA quantity and purity were analyzed using a Bioanalyzer 2100 and an RNA 6000 Nano LabChip kit (Agilent), with RNA integrity values of >7.0.
The final cDNA library were created in accordance with the protocol for the TruSeq RNA Sample Preparation v.2
Before assembly, low-quality reads were removed using Trimmomatic software.
Sequencing reads were aligned to the reference genome using the HISAT2 package.
The mapped reads of each sample were assembled and counted using the featureCounts package and a matrix of read counts was generated.
Genome_build: mm10
Supplementary_files_format_and_content: read counts matrix
|
| |
|
| Submission date |
Mar 19, 2021 |
| Last update date |
Mar 20, 2021 |
| Contact name |
zhipeng zou |
| E-mail(s) |
zzp@smu.edu.cn
|
| Organization name |
southern medical university
|
| Department |
Cell Biology
|
| Street address |
tonghe road
|
| City |
guangzhou |
| State/province |
guangdong |
| ZIP/Postal code |
510515 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE169224 |
Genes differentially expressed during early osteoblast (OB) differentiation |
|
| Relations |
| BioSample |
SAMN18373983 |
| SRA |
SRX10386185 |
