|
| Status |
Public on Jun 26, 2024 |
| Title |
2283544_NEJF10-3D-Nor-02 |
| Sample type |
SRA |
| |
|
| Source name |
NEJF10
|
| Organism |
Mus musculus |
| Characteristics |
cell line: NEJF10
cell type: HB
treatment: 3D Culture with 21% O2
|
| Treatment protocol |
NEJF10 cells were cultured in 21% and 1% oxygen in monolayer, or 21% oxygen in 3D spheroid.
|
| Growth protocol |
NEJF10 cells were cultured in DMEM supplemented with 10% Fetal Bovine Serum, 1% L-Glutamine, and 1% Penicillin/Streptomycin at 37 °C in an atmosphere of 5% CO2 with 21% oxygen or 1% oxygen.
|
| 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) and mapped to mouse reference gennome(STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (M22).
Assembly: GRCm38(mm10)
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM txt files
|
| |
|
| Submission date |
Aug 16, 2023 |
| Last update date |
Jun 26, 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 (1) |
| GSE240980 |
Cellular fitness of MYC-driven cancer cells to genetic and pharmacologic perturbations in normoxia, hypoxia and 3D |
|
| Relations |
| BioSample |
SAMN37006695 |
| SRA |
SRX21382760 |
