|
| Status |
Public on Oct 31, 2024 |
| Title |
MDA-MB-468_SNX631_LT_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
xenograft
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: xenograft
cell line: MDA-MB-468
cell type: triple-negative breast cancer cells
genotype: WT
treatment: MDA-MB-468 xenograft growing in female NSG, treated with SNX631 (350ppm chow) for 96 days
|
| Treatment protocol |
Animals were randomly allocated to study groups when the mean tumor size reached 50-100 mm^3. For everolimus treament, animals were dosed with everolimus (0.4mg/mL solution in the vehicle 70% PEG-400/30% Propylene Glycol, 5 mL/kg, p.o., q.d.). For SNX631 treatment, animals received SNX631-medicated diet (350 ppm, producing 30-45 mg/kg/day dosage on average). For the combination treatment, animals were put on SNX631 mediacated diet (350ppm) four days prior to daily oral gavage with everolimus to accommondate food flavor.
|
| Growth protocol |
MDA-MB-468 were cultured in DMEM high glucose media supplemented with 10% FBS, 1% penicillin/streptomycin, 2 mM glutamine and 1 x non-essential amino acids. Cells were inoculated orthotopically under fat pad (2x10^6 cells in 0.1 mL 50% Matrigel per animal) in female NSG mice to form xenograft tumors.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumor tissues were first submerged in 500 μL RNA-Later stabilization solution (Thermo Fisher Scientific) at room temperature. After stabilization, RNA samples were extracted from tumor tissues using the mRNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol. RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent)
Sequencing libraries were generated using NEBNext Ultra II Directional RNA Library prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
SNX_LT_Rep2
|
| Data processing |
Indexed sequences were checked quality by Fastqc
Indexed sequences were trimmed adaptor sequence by cutadapt (v 2.8) with parameters -m 75 -q 30
Reads were aligned to a hybrid reference genome consisting of both the human GRCh38.p13 primary assembly genome and the mouse GRCm39 primary assembly genome, utilizing STAR (v 2.7.2b) with parameter --outFilterMismatchNoverReadLmax 0.01 --outFilterMultimapNmax 1
Read counts over annotated genes were obtained using featureCount (subreads | version: 2.0.3) with parameters -T 12 -B -O --fraction -s 2 -p --countReadPairs -d 50 -D 800 -g gene_id
Assembly: GRCh38.p13 & GRCm39
Supplementary files format and content: comma-delimited text files include human and mouse gene counts for each sample
|
| |
|
| Submission date |
Jul 02, 2024 |
| Last update date |
Oct 31, 2024 |
| Contact name |
HAO JI |
| E-mail(s) |
[email protected]
|
| Phone |
8037774689
|
| Organization name |
University of South Carolina
|
| Department |
College of Pharmacy
|
| Street address |
715 SUMTER ST CLS RM 109
|
| City |
COLUMBIA |
| State/province |
SC |
| ZIP/Postal code |
29208 |
| Country |
USA |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE271325 |
Transcriptomic analysis of the effects of mTOR inhibitor everolimus, CDK8/19 inhibitor SNX631 and their combination in MDA-MB-468 xenografts |
|
| Relations |
| BioSample |
SAMN42234635 |
| SRA |
SRX25185640 |
