|
| Status |
Public on Mar 02, 2024 |
| Title |
GEMM_CTRL3 |
| Sample type |
SRA |
| |
|
| Source name |
Tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Tumor
genotype: TH-MYCN/ALKF1178L
treatment: Vehicle treatment
|
| Treatment protocol |
The generation of QC6352-resistant BE2C cells was established by exposing the parental BE2C cells to QC6352 in sequential, increasing concentrations of QC6352 (0.1, 0.2, 0.5, 1, 2, and 2.5 µM; each concentration was incubated for 5-7 days). The final concentration of QC6352 was 2.5 µM. GIMEN and SH-SY5Y cells were treated DMSO or QC6352 100 nM for 48 hours. GIMEN cells were overexpressing MYCN or vector. For the tumor samples from TH-MYCN/ALKF1178L mouse model, the tumors were either treated with vehicle or QC6352 25 mg/kg.
|
| Growth protocol |
The cells were cultured in RPMI 1640 supplemented with 10% Fetal Bovine Serum, 1% L-Glutamine, and 1% Penicillin/Streptomycin at 37 °C in an atmosphere of 5% CO2. Transgenic TH-Mycn/AlkF1178L mice were housed with temperature and 12h light /12h dark cycle controlled under specific-pathogen-free conditions (SPF) at the St Jude Children’s Research Hospital mouse facility.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction from cells and tumor tissues was performed using the RNeasy Mini Kit (74106, Qiagen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Total stranded RNA sequencing data were processed by the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60). GEMM mouse samples were mapped to mm10 and other samples were mapped to hg38 (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation ( M22 for GEMM mouse samples; r31, GRCh38.p12 for other samples).
Assembly: GRCh38 (hg38) or GRCm38 (mm10)
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM txt files
|
| |
|
| Submission date |
Aug 09, 2023 |
| Last update date |
Mar 02, 2024 |
| Contact name |
Hongjian Jin |
| E-mail(s) |
hongjian.jin@STJUDE.ORG
|
| Organization name |
St Jude Children's Research Hospital
|
| Department |
Center for Applied Bioinformatics
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38015 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE240505 |
Histone lysine demethylase 4 family proteins maintain the transcriptional program and adrenergic cellular state of MYCN-amplified neuroblastoma [RNA-seq] |
| GSE240506 |
Histone lysine demethylase 4 family proteins maintain the transcriptional program and adrenergic cellular state of MYCN-amplified neuroblastoma |
|
| Relations |
| BioSample |
SAMN36916299 |
| SRA |
SRX21319177 |
