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Sample GSM5012399 Query DataSets for GSM5012399
Status Public on Nov 24, 2021
Title BE2C-WT-Ctrl-001
Sample type SRA
 
Source name cell line
Organism Homo sapiens
Characteristics cell type: BE2C
treatment: 0.1% DMSO
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 SAMN17274714
SRA SRX9816591

Supplementary file Size Download File type/resource
GSM5012399_1932330_BE2C-WT-Ctr-001.RSEM.genes.counts.txt.gz 693.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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