|
| Status |
Public on Nov 24, 2021 |
| Title |
SKNAS-ISM-001 |
| Sample type |
SRA |
| |
|
| Source name |
Tumor
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: SKNAS xenograft
treatment: indisulam treatment
|
| Treatment protocol |
Cells were treated either with DMSO (vehicle) or with 250 nM of Indisulam (Cayman chemical, catalog number: 22759) for 72 hours. Tumors were let grown to be palpable and then mice were treated with vehicle or Indisulam (25mg/kg). After termination of the treatment, mice were sacfificed and tumor tissues were isolated.
|
| Growth protocol |
BE2C (100,000 per well) and SKNAS cells (150,000) were plated in 6-well plate in RPMI-1640 media (supplemented with 10% FBS and 1% Pen/strep). SIMA (5 million per flank) and SKNAS cells (5 million per flank) were injected into (4-6 weeks old) NSG mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from the cells using RNAeasy mini kit (Qiagen) according to manufacturer’s protocol. Tumor tissues were cut into 1-2mm pieces and sonicated with lysis buffer using RNeasy mini kit (Qiagen) and RNA was isolated according to the manufacturer's protocol.
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), mapped to human genome assembly (GRCh38) (STAR v2.7) and then the gene level values were quantified (RSEM v1.31) based on GENCODE annotation (v31) .
After mapping RNA-seq data, rMATS v4.1.0 was used for RNA alternative splicing analysis by using the mapped BAM files as input.
For stranded RNA-seq data, the argument “--libType fr-firststrand” was applied. To process reads with variable lengths, the argument “--variable-read-length” was also used for rMATS.
To select statistically significantly differential splicing events, the following thresholds were used: FDR <0.05 and the absolute value of IncLevelDifference > 0.1.
Genome_build: hg38
Supplementary_files_format_and_content: rMATS tsv tables, gene-level RSEM raw count, TPM, FPKM txt files
|
| |
|
| Submission date |
Jan 10, 2021 |
| Last update date |
Nov 24, 2021 |
| 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 |
GPL24676 |
| Series (2) |
| GSE164505 |
Exceptional response of high-risk neuroblastoma to RBM39 degrader Indisulam (RNA-Seq) |
| GSE164506 |
Exceptional response of high-risk neuroblastoma to RBM39 degrader Indisulam |
|
| Relations |
| BioSample |
SAMN17274728 |
| SRA |
SRX9816610 |
