|
| Status |
Public on Apr 06, 2022 |
| Title |
control |
| Sample type |
SRA |
| |
|
| Source name |
mouse 4T1 cell line
|
| Organism |
Mus musculus |
| Characteristics |
strain: Balb c/J
tissue type: breast
cell type: cancer stem cell spheres
treatment: no co-culture
|
| Treatment protocol |
Eight-week-old female Balb/c mice were injected with syngeneic 4T1 tumor cells into the mammary fat pad and housed for 28 days. At day 28, spleens were collected and gently mashed through a cell strainer with 5 mL serum-free RPMI 1640. Red blood cells in this cell suspension were removed using ACK lysis buffer. Cell suspensions were then pelleted as splenocytes. These in vivo tumor-activated splenocytes were then either incubated in Dulbecco's phosphate buffered saline (DPBS) or were reinforcedly activated using anti-CD3/CD28 dynabeads in the presence of IL2. These splenocytes (tumor primed or tumor primed plus reinforced activation) were pipetted to generate an even single cell suspension and then co-cultured with CSC spheroids
|
| Growth protocol |
4T1 cells were cultured using ultralow attachment plates in serum free RPMI1640 supplemented with 2% SM1 supplement, 20 ng/mL EGF, 20 ng/ml FGF and 4 μg/ml heparin for 7 days. At day 7, CSC spheroids, greater than 40 μm, were enriched and collected using a 40 μm cell strainer
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNAseq was analyzed using the Hisat2 (v2.2.0)/Stringtie (v2.1.3) pipeline
Assembly: mm9
Supplementary files format and content: gtf files include FPKM values for each Sample
|
| |
|
| Submission date |
Apr 01, 2022 |
| Last update date |
Apr 07, 2022 |
| Contact name |
Kuan-Hui Ethan Chen |
| E-mail(s) |
kchen@deltastate.edu
|
| Phone |
6628464496
|
| Organization name |
Delta State University
|
| Street address |
1003 W Sunflower Rd
|
| City |
Cleveland |
| State/province |
MS |
| ZIP/Postal code |
38733 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE199983 |
Genetic profiling of breast cancer stem cell spheres exposed to immune surveillence |
|
| Relations |
| BioSample |
SAMN27183164 |
| SRA |
SRX14697820 |
