|
| Status |
Public on Feb 02, 2023 |
| Title |
BMSC-shLuci+OGD Sample D3 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow mesenchymal stem cells
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague dawley rat
tissue: Femoral bone marrow
passages: 3-5
|
| Treatment protocol |
group BMSC: normal BMSC without treatment; group BMSC-shLuci: BMSC received shLuci lentivirus only; group BMSC-shRac1: BMSC received shRac1 lentivirus only; group BMSC-shLuci+OGD: BMSC received shLuci lentivirus and OGD 12 h/R 24 h treatment; group BMSC-shRac1: BMSC received shRac1 lentivirus and OGD 12 h/R 24 h treatment;
|
| Growth protocol |
BMSC cells without OGD were maintained in high glucose DMEM supplemented with 10% fetal bovine serum in a normal incubator with 5% CO2 at 37 ℃ and BMSC cells with OGD were maintained in sugar-free DMEM in a humidified atmosphere with 5% CO2, 1% O2, at 37 ℃.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The whole RNA of BMSC cell lines was harvested using Trizol reagent.Total RNA of the sample was subjected to test the RNA integrity using agarose gel electrophoresis, then quantified and examined by Agilent 2100 Bioanalyzer.1-2 ug of total RNA was selected for each sample for sequencing library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
BMSC-shLuci+OGD
With shLuci lentivirus infection and OGD treatment
Sample D3
|
| Data processing |
Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8) used for basecalling
We used the StringTie software (v1.2.3) to estimate the abundance of the gene level and transcript level, referring to the official database information, then to calculate FPKM the gene or transcript level separately and to find the difference using Ballgown software.
Sequenced reads was filtered through Solexa CHASTITY, and to match to the corresponding reference genome Rnor6, by Hisat2 software（v2.0.4）
Genome_build: Rnor6
Supplementary_files_format_and_content: Xlsx include FPKM values for all samples
|
| |
|
| Submission date |
Mar 03, 2020 |
| Last update date |
Feb 02, 2023 |
| Contact name |
huang dong dong |
| E-mail(s) |
hdd368@yeah.net
|
| Phone |
15088555102
|
| Organization name |
wenzhou medical university
|
| Street address |
juyi street 105
|
| City |
wenzhou |
| ZIP/Postal code |
325000 |
| Country |
China |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE146261 |
RNA Seq Analysis of BMSC cell line Transcriptomes under the different conditions. |
|
| Relations |
| BioSample |
SAMN14266185 |
| SRA |
SRX7830409 |
