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Sample GSM5244249 Query DataSets for GSM5244249
Status Public on Mar 24, 2024
Title NPcis Tumor 2 Grade III
Sample type SRA
 
Source name Tumor tissue
Organism Mus musculus
Characteristics strain: B6.129
mouse line: NPcis
diagnosis: GEM PNST/Grade III
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the Direct-zol RNA Miniprep kit (Zymo), quantified by Qubit 3.0 Fluorometer, and quality checked by 4200 TapeStation High Sensitivity RNA ScreenTape assay (Agilent).
Libraries were prepared from 350 ng of total RNA using the TruSeq Stranded Total RNA Library Prep Kit (Illumina 20020599)
Libraries were sequenced on Illumina NovaSeq 6000, obtaining 100 million 100-bp paired-end reads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description ET7208T2
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 mouse (GRCm38, mm10) or human (GRCh38, hg38) genome assembly (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotations (vM22 for GRCm38, v31 for GRCh38)
Supplementary_files_format_and_content: gene-level RSEM raw count, TPM, FPKM txt files
 
Submission date Apr 16, 2021
Last update date Mar 24, 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)
GSE172221 A genetic mouse model of malignant peripheral nerve sheath tumor with postnatal Nf1 and p53 loss recapitulates the histology and transcriptome of human tumors
Relations
BioSample SAMN18757405
SRA SRX10615773

Supplementary file Size Download File type/resource
GSM5244249_1331140_SJMMMPNST055711_D1-ET7208T2.RSEM.genes.counts.txt.gz 628.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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