|
| Status |
Public on Sep 23, 2024 |
| Title |
BMSCs，PCL-O，Day3 |
| Sample type |
SRA |
| |
|
| Source name |
BMSCs cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: BMSCs cell line
cell type: bone marrow mesenchymal stem cells
genotype: WT
treatment: osteogenic differentiation
|
| Treatment protocol |
The complete DMEM medium containing 10% FBS was used as the medium of extraction, and the PCL scaffolds were added to it at an area/volume ratio of 1.25 cm2/ml and immersed for 72 h at 37 °C to prepare the solution for material extraction.
|
| Growth protocol |
5% CO2 medium was added at 37 °C, incubated for complete DMEM medium containing 10% FBS was used as the medium of extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cells were lysed with 1ml TRIzol to extract the RNA samples (n=3), and the specimens were subsequently analyzed
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
NanoDrop 2000 spectrophotometer: Detects RNA purity and concentration；Agient2100/LabChip GX detection: Accurate detection of RNA integrity.
The Qubit 3.0 fluorometric quantifier was used for preliminary quantification, and the concentration should reach more than 1ng/ul. Then, the Qsep400 high-throughput analysis system was used to detect the inserted fragments of the library. After the inserted fragments met the expectations, the effective concentration of the library (the effective concentration of the library was > 2nM) was accurately quantified by Q-PCR method
After the library was qualified, PE150 mode sequencing was performed using Illumina NovaSeq6000 sequencing platform.
After the sequencing data was unloaded, the bioinformatics analysis process provided by BMKCloud(www.biocloud.net) was used for data analysis.
FPKM=cDNAFragments/MappedFragments(Millions)∗TranscriptLength(kb).In the formula, cDNA Fragments represent the number of fragments that are compared to a transcript, that is, the number of double-ended Reads. Mapped Fragments (Millions) indicates the total number of fragments aligned to the transcript, in 10^6; Transcript Length(kb) : Length of the transcript, in units of 10^3 bases.
Assembly: mm10
Supplementary files format and content: tab-delimited file includes raw counts for each Sample
Supplementary files format and content: tab-delimited file includes FPKM values for each Sample
|
| |
|
| Submission date |
Oct 31, 2023 |
| Last update date |
Sep 23, 2024 |
| Contact name |
Cai-Ping Yan |
| E-mail(s) |
ycp19941025@sina.com
|
| Phone |
18408271016
|
| Organization name |
North sichuan medical college
|
| Department |
orthopedics
|
| Street address |
No. 1 The South of Maoyuan Road
|
| City |
南充市 |
| State/province |
sichuan |
| ZIP/Postal code |
637000 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE246630 |
S7, E7 peptide action on BMSCs |
| GSE246631 |
3D-printed Scaffolds to Regulate the Translational Balance between Vascularization and Bone Metabolism |
|
| Relations |
| BioSample |
SAMN38050548 |
| SRA |
SRX22304455 |
