|
| Status |
Public on Nov 30, 2022 |
| Title |
Control 1 |
| Sample type |
SRA |
| |
|
| Source name |
E0771
|
| Organism |
Mus musculus |
| Characteristics |
cell line: E0771
cell type: triple-negative malignant mouse breast cancer cell line
genotype: Tie2CreER;ERKi C57BL/6J mice
treatment: Control
time: Day 22
|
| Treatment protocol |
Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS
|
| Growth protocol |
C3H 10T1/2 mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RVI-6
|
| Data processing |
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Jul 25, 2022 |
| Last update date |
Nov 30, 2022 |
| Contact name |
Renato V. Iozzo |
| E-mail(s) |
[email protected]
|
| Organization name |
Thomas Jefferson University
|
| Street address |
1020 Locust Street
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19107 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE209743 |
Effect of endothelial-specific endorepellin expression on gene expression of breast cancer allografts in Tie2CreER;ERKi mice |
|
| Relations |
| BioSample |
SAMN29953761 |
| SRA |
SRX16660607 |
