NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7068796 Query DataSets for GSM7068796
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.
 
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
 
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap