|
Status |
Public on Aug 01, 2024 |
Title |
4T1 POS rep 2 |
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.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
4T1-AxR-SM-POS-2 RS-03036551
|
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
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|
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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 |
SAMN33458762 |
SRA |
SRX19514706 |