|
| Status |
Public on Aug 01, 2024 |
| Title |
4T1 POS rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
4T1
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Breast cancer cells
variant: 4T1 AxR SM POS
treatment: Axitinib
concentration: 0.5µM
cell line: 4T1
|
| Growth protocol |
mouse breast tumor cells (4T1) resistant to axitinib were maintained in RPMI1640 supplemented with 5% FBS and 0.5µM Axitinib. Media was replenished every 3 to 4 days.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA from individual samples was extracted using the RNeasy mini kit (QIAGEN; 74104). Genomic DNA was digested using DNase I (QIAGEN; 79254) as described in the on-column DNase digestion protocol from QIAGEN.
One microgram total RNA was used for library preparation using the TruSeq Stranded mRNA kit (Illumina Inc) following manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
4T1-AxR-SM-POS-1
RS-03036549
|
| Data processing |
Pre-alignment quality control was performed using FASTQC v0.11.5.
Sequenced reads (fastq files) were alinged to the mouse genome GRCm38 M16 (Gencode) using STAR v2.6.0a.
Post-alignment quality control was performed using RSeQC v2.6.5.
Estimated counts at the gene level were quantified using RSEM v1.3.1.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include RSEM estimated counts at the gene level for all samples
|
| |
|
| Submission date |
Feb 27, 2023 |
| Last update date |
Aug 01, 2024 |
| Contact name |
Mark D Long |
| E-mail(s) |
mark.long@roswellpark.org
|
| Organization name |
Roswell Park Comprehensive Cancer Center
|
| Department |
Bioinformatics & Biostatistics
|
| Street address |
Elm & Carlton Streets
|
| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14263 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE226243 |
Gene expression changes in mouse breast cancer cells (4T1) after axitinib resistance and FACS isolation of SA-β-galHi (SM+) and SA-β-galLo (SM-) cells |
|
| Relations |
| BioSample |
SAMN33458764 |
| SRA |
SRX19514704 |
