|
| Status |
Public on Mar 02, 2024 |
| Title |
RNA-seq_SIMA923 |
| Sample type |
SRA |
| |
|
| Source name |
Tumor
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SIMA xenograft
treatment: Vehicle treatment
|
| Treatment protocol |
Cells were treated with 0.1% DMSO or QC6352 100nM for 48h. For SIMA xenografts, tumor were treated either QC6352 50mg/kg body weight once per day or vehicle for 6 day and harvested for RNA extraction.
|
| Growth protocol |
BE2C, KELLY, SIMA, SKNAS, SKNSH and SKNFI cells were cultured with RPMI 1640 media supplemented with 100 U/mlpenicillin/streptomycin and 10% fetal bovine serum. Cells were maintained at 37 °C in an atmosphere of 5% CO2. For xenograft model, SIMA 5x106cells were mixed with matrigel and injected in to CB17SCID mice through subcutaneous method.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
100 to 200 x 10e3 cells were seeded in a 6-well plate. Next day, cells were treated with DMSO and 100 nM of QC6352 for 48 hours. Total RNA from cells and tumor tissues were performed using the RNeasy Mini Kit (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 HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA
raw paired-end reads were mapped by STAR_2.5.3a(parameters "--outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --alignIntronMax 500000 --chimSegmentMin 20 --chimJunctionOverhangMin 20")
gene level quantification and differential gene expression analysis were done by St Jude Cloud RNAseq pipeline (WARDEN, https://platform.stjude.cloud/workflows/warden)
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: gene-based raw counts txt file
|
| |
|
| Submission date |
Jan 08, 2021 |
| 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 |
GPL16791 |
| Series (2) |
| GSE164455 |
KDM4 inhibition disrupts the core regulatory transcriptional circuitry in MYCN-driven neuroblastoma [RNA-seq] |
| GSE164456 |
Histone lysine demethylase 4 family proteins maintain the transcriptional program and adrenergic cellular state of MYCN-amplified neuroblastoma |
|
| Relations |
| BioSample |
SAMN17260053 |
| SRA |
SRX9806768 |
