|
| Status |
Public on Jun 09, 2023 |
| Title |
BMAd cells, GC+GW96621 [D1] |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Bone marrow
cell line: BMAd
cell type: Adipocyte
genotype: WT
treatment: adipogenic differentiation, GC+GW9662
|
| Treatment protocol |
Adipogenic differentiation was induced by StemPro Adipogenesis Differentiation kit (Gibco) for 14 days
Cells were treated with 10−6M DEX or 10−6M DEX plus GW9662 for 24 hours.
|
| Growth protocol |
Bone marrow stem cells were maintained in αMEM supplemented with 15% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini kit (Qiagen). At least 100 ug of total RNA was sent for further process.
Libraries were prepared using the Smart-Seq 2 protocol with a template switching oligonucleotide, followed by PCR amplification and purification.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
D1
|
| Data processing |
Raw data (raw reads) of fastq format were processed with fastp, an ultra-fast FASTQ preprocessor with useful quality
Total reads were aligned to the reference genome using HISAT2 v2.1.0
Featurecount was used to count the reads numbers mapped to each gene. And then TPM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
|
| |
|
| Submission date |
Jun 08, 2022 |
| Last update date |
Jun 09, 2023 |
| Contact name |
Mei Wan |
| E-mail(s) |
mwan4@jhmi.edu
|
| Phone |
2054470577
|
| Organization name |
Johns Hopkins Hospital
|
| Department |
Department of Orthopedics
|
| Lab |
Mei Wan
|
| Street address |
720 Rutland Ave,Ross research buil
|
| City |
baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE205732 |
Glucocorticoid-stimulated senescence phenotype in differentiated bone marrow adipocytes treated with PPARgamma inhibitor |
|
| Relations |
| BioSample |
SAMN28925644 |
| SRA |
SRX15640755 |
