|
| Status |
Public on Apr 29, 2024 |
| Title |
dsn_doxo_1 |
| Sample type |
SRA |
| |
|
| Source name |
Primary mouse mammary fibroblasts line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Primary mouse mammary fibroblasts line
strain: B6
time: Day7
|
| Treatment protocol |
Mouse mammary fibroblasts line was derived from the mammary fat pad of a healthy B6 mouse.
For DNA damage-induced senescence (dsn) samples, MMFs at 50-60% confluence were treated with vehicle (H2O) or doxorubicine (100 nM) for 24 hours. Media was refreshed every 3 days. Vehicle group was split routinely to maintain healthy cell density. Cells were lysed for RNA collection on day 7.
For oxidative stres damage-induced senescence (osn) samples, MMFs at 50-60% confluence were treated with vehicle (H2O) or hydrogen peroxide (750 uM) for 2 hours and were allowed to recover for 48 hours. The drug treatment was repeated for two more times. Vehicle group was split routinely to maintain healthy cell density. Cells were lysed for RNA collection on day 6.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Qiagen Rneasy Mini kit.
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq 6000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq2 software. RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
Assembly: mm10
Supplementary files format and content: tab-delimited text files of gene and counts per million matrix including all samples
|
| |
|
| Submission date |
Apr 10, 2023 |
| Last update date |
Apr 29, 2024 |
| Contact name |
Sheila Stewart |
| E-mail(s) |
sheila.stewart@wustl.edu
|
| Organization name |
Washington University School of Medicine
|
| Street address |
660 South Euclid Avenue
|
| City |
Saint Louis |
| ZIP/Postal code |
314-362-7449 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE229352 |
Senescent stroma mediates immunosuppression and drives breast cancer progression [MMF] |
| GSE229356 |
Senescent stroma mediates immunosuppression and drives breast cancer progression |
|
| Relations |
| SRA |
SRX19920744 |
| BioSample |
SAMN34132952 |
